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Sample records for dna cleavage mechanism

  1. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked...

  2. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Wednesday, 26 January 2011 00:00 Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked

  3. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  4. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  5. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  6. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  7. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  8. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  9. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Citation Details In-Document Search Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical

  10. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of

  11. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere

  12. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere

  13. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print Tuesday, 24 January 2012 11:30 DNA replication is a critical...

  14. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2010-11-09

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  15. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2000-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  16. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2007-12-11

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  17. Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint...

    Office of Scientific and Technical Information (OSTI)

    Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Citation Details In-Document Search Title: Structure and Activation Mechanism of the CHK2 DNA Damage ...

  18. A 1.9 Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

    SciTech Connect (OSTI)

    Chen, Jui-Hui; Yajima, Rieko; Chadalavada, Durga M.; Chase, Elaine; Bevilacqua, Philip C.; Golden, Barbara L.

    2010-11-01

    The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot structure and cleave RNA, yielding 2{prime},3{prime}-cyclic phosphate and 5{prime}-hydroxyl termini. The active site nucleotide C75 has a pK{sub a} shifted >2 pH units toward neutrality and has been implicated as a general acid/base in the cleavage reaction. An active site Mg{sup 2+} ion that helps activate the 2{prime}-hydroxyl for nucleophilic attack has been characterized biochemically; however, this ion has not been visualized in any previous structures. To create a snapshot of the ribozyme in a state poised for catalysis, we have crystallized and determined the structure of the HDV ribozyme bound to an inhibitor RNA containing a deoxynucleotide at the cleavage site. This structure includes the wild-type C75 nucleotide and Mg{sup 2+} ions, both of which are required for maximal ribozyme activity. This structure suggests that the position of C75 does not change during the cleavage reaction. A partially hydrated Mg{sup 2+} ion is also found within the active site where it interacts with a newly resolved G {center_dot} U reverse wobble. Although the inhibitor exhibits crystallographic disorder, we modeled the ribozyme-substrate complex using the conformation of the inhibitor strand observed in the hammerhead ribozyme. This model suggests that the pro-RP oxygen of the scissile phosphate and the 2{prime}-hydroxyl nucleophile are inner-sphere ligands to the active site Mg{sup 2+} ion. Thus, the HDV ribozyme may use a combination of metal ion Lewis acid and nucleobase general acid strategies to effect RNA cleavage.

  19. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of...

  20. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print Tuesday, 24 January 2012 11:30 DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose

  1. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA...

    Office of Scientific and Technical Information (OSTI)

    The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The ...

  2. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by

  3. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by

  4. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by

  5. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by

  6. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    threads through the arch. Solving FEN1's structure and mechanism required the presence of DNA with a 5' flap. Just as FEN1 moves the template into position so the 5' flap will be...

  7. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1 Citation Details In-Document Search Title: Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1 Authors: Wang, Renjing ; Persky, Nicole S. ; Yoo, Barney ; Ouerfelli, Ouathek ; Smogorzewska, Agata ; Elledge, Stephen J. ; Pavletich, Nikola P. [1] ; MSKCC) [2] ; Rockefeller) [2] + Show Author Affiliations

  8. Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Citation Details In-Document Search Title: Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase Authors: Cai, Zhenjian ; Chehab, Nabil H. ; Pavletich, Nikola P. ; MSKCC) [1] + Show Author Affiliations ( Publication Date: 2010-01-28 OSTI Identifier: 1006023 Resource Type: Journal Article Resource Relation: Journal Name: Mol. Cell; Journal Volume: 35; Journal

  9. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  10. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  11. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; Van Houten, Bennett; He, Chuan; Ansari, Anjum; et al

    2015-01-06

    The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformations similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump pertubation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

  12. Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions

    SciTech Connect (OSTI)

    Walmacq, Celine; Wang, Lanfeng; Chong, Jenny; Scibelli, Kathleen; Lubkowska, Lucyna; Gnatt, Averell; Brooks, Philip J.; Wang, Dong; Kashlev, Mikhail

    2015-01-20

    In human cells, the oxidative DNA lesion 8,5'-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion. Here, we present biochemical and crystallographic evidence for the mechanism of CydA recognition. Pol II stalling results from impaired loading of the template base (5') next to CydA into the active site, leading to preferential AMP misincorporation. Such predominant AMP insertion, which also occurs at an abasic site, is unaffected by the identity of the 5-templating base, indicating that it derives from nontemplated synthesis according to an A rule known for DNA polymerases and recently identified for Pol II bypass of pyrimidine dimers. Subsequent to AMP misincorporation, Pol II encounters a major translocation block that is slowly overcome. The translocation block combined with the poor extension of the dA.rA mispair reduce transcriptional mutagenesis. Moreover, increasing the active-site flexibility by mutation in the trigger loop, which increases the ability of Pol II to accommodate the bulky lesion, and addition of transacting factor TFIIF facilitate CydA bypass. Thus, blocking lesion entry to the active site, trans-lesion A rule synthesis, and translocation block are common features of transcription across different bulky DNA lesions.

  13. Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Walmacq, Celine; Wang, Lanfeng; Chong, Jenny; Scibelli, Kathleen; Lubkowska, Lucyna; Gnatt, Averell; Brooks, Philip J.; Wang, Dong; Kashlev, Mikhail

    2015-01-20

    In human cells, the oxidative DNA lesion 8,5'-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion. Here, we present biochemical and crystallographic evidence for the mechanism of CydA recognition. Pol II stalling results from impaired loading of the template base (5') next to CydA into the active site, leading to preferential AMP misincorporation. Such predominant AMP insertion, which also occurs at an abasic site, is unaffected by the identity of the 5´-templating base, indicating that it derives from nontemplated synthesismore » according to an A rule known for DNA polymerases and recently identified for Pol II bypass of pyrimidine dimers. Subsequent to AMP misincorporation, Pol II encounters a major translocation block that is slowly overcome. The translocation block combined with the poor extension of the dA.rA mispair reduce transcriptional mutagenesis. Moreover, increasing the active-site flexibility by mutation in the trigger loop, which increases the ability of Pol II to accommodate the bulky lesion, and addition of transacting factor TFIIF facilitate CydA bypass. Thus, blocking lesion entry to the active site, trans-lesion A rule synthesis, and translocation block are common features of transcription across different bulky DNA lesions.« less

  14. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    drives achievement in protein structure research September 15, 2014 Computational analysis key to structural understanding of molecular machine that targets viral DNA LOS ALAMOS, N.M., Sept. 15, 2014-When this week's print issue of the journal Science comes out, a collective cheer will go up from New Mexico, Montana and even the Netherlands, thanks to the type of collaborative effort that is more and more the norm in these connected times. Yes, the research was brilliant, and if we're lucky, it

  15. An unusual carbon-carbon bond cleavage reaction during phosphinothrici...

    Office of Scientific and Technical Information (OSTI)

    An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis Citation Details In-Document Search Title: An unusual carbon-carbon bond cleavage reaction ...

  16. Observation of Cleavage Fracture after Substantial Dimple Rupture in ASTM A710 Steel

    SciTech Connect (OSTI)

    Reuter, Walter Graham; Lloyd, Wilson Randolph

    2000-07-01

    A major concern often arising in structural integrity predictions is the possibility that low-energy brittle fracture could result as a consequence of cleavage either under normal operating or design accident conditions. This can be especially troublesome when the leak-before-break (LBB) approach shows an additional safety margin of the design. For LBB to be applicable, the fracture process must remain ductile (dimple rupture), and not change to cleavage. The American Society for Mechanical Engineers Boiler and Pressure Vessel Code (Code) provides guidelines for avoiding cleavage fracture for Code-accepted materials. Experimental results for a non-Code steel are provided, and show that cleavage may occur for a thickness under16 mm (where the code suggests it will not) after stable crack growth (?a) of up to 20 mm. This work is still in progress; test results are provided along with possible reasons for the mode transition, but complete explanations are still being developed.

  17. Nuclear substructure reorganization during late stageerythropoiesis is selective and does not involve caspase cleavage ofmajor nuclear substructural proteins

    SciTech Connect (OSTI)

    Krauss, Sharon Wald; Lo, Annie J.; Short, Sarah A.; Koury, MarkJ.; Mohandas, Narla; Chasis, Joel Anne

    2005-04-06

    Enucleation, a rare feature of mammalian differentiation, occurs in three cell types: erythroblasts, lens epithelium and keratinocytes. Previous investigations suggest that caspase activation functions in lens epithelial and keratinocyte enucleation, as well as in early erythropoiesis encompassing BFU-E differentiation to proerythroblast. To determine whether caspase activation contributes to later erythropoiesis and whether nuclear substructures other than chromatin reorganize, we analyzed distributions of nuclear subcompartment proteins and assayed for caspase-induced cleavage of subcompartmental target proteins in mouse erythroblasts. We found that patterns of lamin B in the filamentous network interacting with both the nuclear envelope and DNA, nuclear matrix protein NuMA, and splicing factors Sm and SC35 persisted during nuclear condensation, consistent with effective transcription of genes expressed late in differentiation. Thus nuclear reorganization prior to enucleation is selective, allowing maintenance of critical transcriptional processes independent of extensive chromosomal reorganization. Consistent with these data, we found no evidence for caspase-induced cleavage of major nuclear subcompartment proteins during late erythropoiesis, in contrast to what has been observed in early erythropoiesis and in lens epithelial and keratinocyte differentiation. These findings imply that nuclear condensation and extrusion during terminal erythroid differentiation involve novel mechanisms that do not entail major activation of apoptotic machinery.

  18. Mechanism of somatic hypermutation at the WA motif by human DNA...

    Office of Scientific and Technical Information (OSTI)

    at the WA motif by human DNA polymerase eta Authors: Zhao, Ye ; Gregory, Mark T. ; Biertmpfel, Christian ; Hua, Yue-Jin ; Hanaoka, Fumio ; Yang, Wei 1 ; Gakushuin)...

  19. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    50 million times without introducing any errors. But FEN1 is also important in DNA repair, targeting specific repair pathways, which presents different challenges than...

  20. Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

    2015-10-09

    SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis . Here, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism thatmore » is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.« less

  1. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the template's nucleotides. But before polymerase builds the duplicate strand, an RNA primer must bind to the template acting as a short length of "pseudo-DNA" to whose...

  2. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  3. DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01

    DUPLEX produces energy minimized structures of DNA and RNA of any base sequence for single and double strands. The smallest subunits are deoxydinucleoside monophosphates, and up to 12 residues, single or double stranded can be treated. In addition, it can incorporate NMR derived interproton distances an constraints in the minimizations. Both upper and lower bounds for these distances can be specified. The program has been designed to run on a UNICOS Cray supercomputer, but should run, albeit slowly, on a laboratory computer such as a VAX or a workstation.

  4. Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008

    SciTech Connect (OSTI)

    Morgan, William F.; Kovalchuk, Olga; Dolinoy, Dana C.; Dubrova, Yuri E.; Coleman, Matthew A.; Schr, Primo; Pogribny, Igor; Hendzel, Michael

    2010-02-19

    The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.

  5. Detection of nucleic acid sequences by invader-directed cleavage

    DOE Patents [OSTI]

    Brow, Mary Ann D. (Madison, WI); Hall, Jeff Steven Grotelueschen (Madison, WI); Lyamichev, Victor (Madison, WI); Olive, David Michael (Madison, WI); Prudent, James Robert (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  6. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

    Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

    2012-10-16

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  7. Detection of nucleic acids by multiple sequential invasive cleavages 02

    DOE Patents [OSTI]

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  8. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  9. Microbial cleavage of organic C-S bonds

    DOE Patents [OSTI]

    Kilbane, II, John J.

    1994-01-01

    A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

  10. Microbial cleavage of organic C-S bonds

    DOE Patents [OSTI]

    Kilbane, J.J. II.

    1994-10-25

    A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

  11. An unusual carbon-carbon bond cleavage reaction during phosphinothricin

    Office of Scientific and Technical Information (OSTI)

    biosynthesis (Journal Article) | SciTech Connect An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis Citation Details In-Document Search Title: An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine

  12. An unusual carbon-carbon bond cleavage reaction during phosphinothricin

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    biosynthesis (Journal Article) | SciTech Connect An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis Citation Details In-Document Search Title: An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine

  13. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA

    SciTech Connect (OSTI)

    Horton, John R.; Borgaro, Janine G.; Griggs, Rose M.; Quimby, Aine; Guan, Shengxi; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Zhu, Zhenyu; Cheng, Xiaodong

    2014-07-03

    AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves DNA containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ~ 70 , consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ~ 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

  14. Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kowalski, Karol; Valiev, Marat

    2007-01-01

    High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

  15. X-ray Crystallographic Observation of 'In-line' and 'Adjacent' Conformations in a Bulged Self-Cleaving RNA/DNA Hybrid

    SciTech Connect (OSTI)

    Tereshko, V.; Wallace, S.T.; Usman, N.; Wincott, F.; Egli, M.

    2010-03-08

    The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Husken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line ) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.

  16. Structure of the cleavage-activated prefusion form of the parainfluenz...

    Office of Scientific and Technical Information (OSTI)

    the parainfluenza virus 5 fusion protein Citation Details In-Document Search Title: Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein ...

  17. Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization

    SciTech Connect (OSTI)

    Sturgeon, M. R.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2013-01-01

    Carbon-oxygen bonds are the primary inter-monomer linkages lignin polymers in plant cell walls, and as such, catalyst development to cleave these linkages is of paramount importance to deconstruct biomass to its constituent monomers for the production of renewable fuels and chemicals. For many decades, acid catalysis has been used to depolymerize lignin. Lignin is a primary component of plant cell walls, which is connected primarily by aryl-ether linkages, and the mechanism of its deconstruction by acid is not well understood, likely due to its heterogeneous and complex nature compared to cellulose. For effective biomass conversion strategies, utilization of lignin is of significant relevance and as such understanding the mechanisms of catalytic lignin deconstruction to constituent monomers and oligomers is of keen interest. Here, we present a comprehensive experimental and theoretical study of the acid catalysis of a range of dimeric species exhibiting the b-O-4 linkage, the most common inter-monomer linkage in lignin. We demonstrate that the presence of a phenolic species dramatically increases the rate of cleavage in acid at 150 degrees C. Quantum mechanical calculations on dimers with the para-hydroxyl group demonstrate that this acid-catalyzed pathway differs from the nonphenolic dimmers. Importantly, this result implies that depolymerization of native lignin in the plant cell wall will proceed via an unzipping mechanism wherein b-O-4 linkages will be cleaved from the ends of the branched, polymer chains inwards toward the center of the polymer. To test this hypothesis further, we synthesized a homopolymer of b-O-4 with a phenolic hydroxyl group, and demonstrate that it is cleaved in acid from the end containing the phenolic hydroxyl group. This result suggests that genetic modifications to lignin biosynthesis pathways in plants that will enable lower severity processes to fractionate lignin for upgrading and for easier access to the carbohydrate fraction of the plant cell wall.

  18. Useful for cleavage of organic C-S bonds Bacillus sphaericus microorganism

    DOE Patents [OSTI]

    Kilbane II, John J.

    1993-01-01

    A mutant Bacillus sphaericus strain ATCC No. 53969 which has the property of sulfur removal and sulfur metabolism by selective cleavage of C-S bonds in organic carbonaceous materials.

  19. Mutant microorganisms useful for cleavage of organic C-S bonds

    DOE Patents [OSTI]

    Kilbane, II, John J.

    1992-01-01

    A mutant Rhodococcus rhodochrous strain ATCC No. 53968 which has the property of sulfur removal and sulfur metabolism by selective cleavage of C-S bonds in organic carbonaceous materials.

  20. Useful for cleavage of organic C-S bonds Bacillus sphaericus microorganism

    DOE Patents [OSTI]

    Kilbane, J.J. II.

    1993-03-30

    A mutant Bacillus sphaericus strain ATCC No. 53969 which has the property of sulfur removal and sulfur metabolism by selective cleavage of C-S bonds in organic carbonaceous materials.

  1. Mutant microorganisms useful for cleavage of organic C-S bonds

    DOE Patents [OSTI]

    Kilbane, II, John J.

    1991-01-01

    A mutant Bacillus sphaericus strain ATC No. 53969 which has the property of sulfur removal and sulfur metabolism by selective cleavage of C-S bonds in organic carbonaceous materials.

  2. Structure of the cleavage-activated prefusion form of the parainfluenza

    Office of Scientific and Technical Information (OSTI)

    virus 5 fusion protein (Journal Article) | SciTech Connect of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein Citation Details In-Document Search Title: Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein Authors: Welch, Brett D. ; Liu, Yuanyuan ; Kors, Christopher A. ; Leser, George P. ; Jardetzky, Theodore S. ; Lamb, Robert A. [1] ; Stanford-MED) [2] + Show Author Affiliations NWU ( Publication Date: 2014-08-26

  3. Dna Sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  4. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01

    This volume contains the proceedings of the conference entitled Cellular Responses to Environmental DNA Damage held in Banff,Alberta December 1--6, 1991. The conference addresses various aspects of DNA repair in sessions titled DNA repair; Basic Mechanisms; Lesions; Systems; Inducible Responses; Mutagenesis; Human Population Response Heterogeneity; Intragenomic DNA Repair Heterogeneity; DNA Repair Gene Cloning; Aging; Human Genetic Disease; and Carcinogenesis. Individual papers are represented as abstracts of about one page in length.

  5. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

    SciTech Connect (OSTI)

    Horton, J. R.; Wang, H.; Mabuchi, M. Y.; Zhang, X.; Roberts, R. J.; Zheng, Y.; Wilson, G. G.; Cheng, X.

    2014-09-27

    MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.

  6. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

    1995-01-01

    Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

  7. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

    1995-04-11

    A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

  8. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Horton, J. R.; Wang, H.; Mabuchi, M. Y.; Zhang, X.; Roberts, R. J.; Zheng, Y.; Wilson, G. G.; Cheng, X.

    2014-09-27

    MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNAmore » molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.« less

  9. Oxidative cleavage of erucic acid for the synthesis of brassylic acid

    SciTech Connect (OSTI)

    Mohammed J. Nasrullah; Pooja Thapliyal; Erica N. Pfarr; Nicholas S. Dusek; Kristofer L. Schiele; James A. Bahr

    2010-10-29

    The main focus of this work is to synthesize Brassylic Acid (BA) using oxidative cleavage of Erucic Acid (EA). Crambe (Crambe abyssinica) is an industrial oilseed grown in North Dakota. Crambe has potential as an industrial fatty acid feedstock as a source of Erucic acid (EA). It has approximately 50-60 % of EA, a C{sub 22} monounsaturated fatty acid. Oxidative cleavage of unsaturated fatty acids derived from oilseeds produces long chain (9, 11, and 13 carbon atoms) dibasic and monobasic acids. These acids are known commercial feedstocks for the preparation of nylons, polyesters, waxes, surfactants, and perfumes. Other sources of EA are Rapeseed seed oil which 50-60 % of EA. Rapeseed is grown outside USA. The oxidative cleavage of EA was done using a high throughput parallel pressure reactor system. Kinetics of the reaction shows that BA yields reach a saturation at 12 hours. H{sub 2}WO{sub 4} was found to be the best catalyst for the oxidative cleavage of EA. High yields of BA were obtained at 80 C with bubbling of O{sub 2} or 10 bar of O{sub 2} for 12 hours.

  10. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine

    Office of Scientific and Technical Information (OSTI)

    lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition (Journal Article) | SciTech Connect Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search Title: Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition DNA arranges into rectangular columnar superlattices between

  11. DNA polymerase with modified processivity

    DOE Patents [OSTI]

    Bedford, Ella; Tabor, Stanley; Richardson, Charles C.

    1999-01-01

    Chimeric DNA polymerase having a DNA polymerase domain and processivity factor binding domain not naturally associated with DNA polymerase domain.

  12. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine...

    Office of Scientific and Technical Information (OSTI)

    Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search ...

  13. Synthesis of DNA

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P. (Danville, CA)

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  14. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  15. DNA repair of a single UV photoproduct in a designed nucleosome

    SciTech Connect (OSTI)

    Kosmoskil, Joseph V.; Ackerman, Eric J. ); Smerdon, Michael J.

    2001-08-28

    Eukaryotic DNA repair enzymes must interact with the architectural hierarchy of chromatin. The challenge of finding damaged DNA complexed with histone proteins in nucleosomes is complicated by the need to maintain local chromatin structures involved in regulating other DNA processing events. The heterogeneity of lesions induced by DNA-damaging agents has led us to design homogeneously damaged substrates to directly compare repair of naked DNA with that of nucleosomes. Here we report that nucleotide excision repair in Xenopus nuclear extracts can effectively repair a single UV radiation photoproduct located 5 bases from the dyad center of a positioned nucleosome, although the nucleosome is repaired at about half the rate at which the naked DNA fragment is. Extract repair within the nucleosome is > 50-fold more rapid than either enzymatic photoreversal or endonuclease cleavage of the lesion in vitro. Furthermore, nucleosome formation occurs (after repair) only on damaged naked DNA ( 165-bp fragments) during a 1-h incubation in these extracts, even in the presence of a large excess of undamaged DNA. This is an example of selective nucleosome assembly by Xenopus nuclear extracts on a short linear DNA fragment containing a DNA lesion.

  16. Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme

    DOE Patents [OSTI]

    Marrone, Babetta L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Whaley, Thomas W. (Santa Fe, NM)

    1992-01-01

    An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.

  17. Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme

    DOE Patents [OSTI]

    Marrone, Babetta L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Whaley, Thomas W. (Santa Fe, NM)

    1993-01-01

    An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.

  18. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

    Gray, Joe W. (San Francisco, CA); Weier, Heinz-Ulrich G. (Oakland, CA)

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  19. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

    SciTech Connect (OSTI)

    Stella, Stefano; Cascio, Duilio; Johnson, Reid C.

    2010-06-21

    The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of {approx}65{sup o}, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.

  20. An improved DNA force field for ssDNA interactions with gold nanoparticles

    SciTech Connect (OSTI)

    Jiang, Xiankai; Huai, Ping; Fan, Chunhai; Song, Bo E-mail: bosong@sinap.ac.cn; Gao, Jun; Huynh, Tien; Zhou, Ruhong E-mail: bosong@sinap.ac.cn

    2014-06-21

    The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones protecting hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the protection by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

  1. DNA tagged microparticles

    DOE Patents [OSTI]

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  2. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  3. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has

  4. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  5. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  6. Controlling DNA Methylation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Controlling DNA Methylation Though life on earth is composed of a diverse range of organisms, some with many different types of tissues and cells, all these are encoded by a molecule we call DNA. The information required to build a protein is stored in DNA within the cells. Not all the message in the DNA is used in each cell and not all the message is used all the time. During cell differentiation, the cells become dedicated for their specific function which involves selectively activating some

  7. Mechanisms of cellular transformation by carcinogenic agents

    SciTech Connect (OSTI)

    Grunberger, D.; Goff, S.P.

    1987-01-01

    This book contains 14 chapters. Some of the chapter titles are: DNA Modification by Chemical Carcinogens; Role of DNA Lesions and Repair in the Transformation of Human Cells; The Induction and Regulation of Radiogenic Transformation In Vitro: Cellular and Molecular Mechanisms; Cellular Transformation by Adenoviruses; and The fos Gene.

  8. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = —N(C2H5)2(1), —N(C3H4NH2)2(2), or —N(C2H4NH2)2(3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with the apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1; 3.5 and 0.083 s-1 for 2; andmore » 3.8 and 0.0033 s-1 for 3. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~ 10-7, for 1) undergoes the N—N heterolytic bond cleavage (kd ~ 107 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. Thus, the bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.« less

  9. Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms

    SciTech Connect (OSTI)

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to slowly release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a qualitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = -N(C2H5)2 (1), -N(C3H4NH2)2 (2), or -N(C2H4NH2)2 (3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1-H, 3.5 and 83 x 10-3 s-1 for 2-H, and 3.8 and 3.3 x 10-3 s-1 for 3-H. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~0.01%, for 1) undergoes the N-N heterolytic bond cleavage (k ~102 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all these NONOates are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.

  10. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  11. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  12. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

    This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

  13. DNA | Open Energy Information

    Open Energy Info (EERE)

    Lead Agency District Office Development Phase(s) Techniques DNA-NV-030-09-03 Dusty Miller LLC BLM BLM Carson City District Office BLM Stillwater Field Office BLM...

  14. Strength of semiconductors, metals, and ceramics evaluated by a microscopic cleavage model with Morse-type and Lennard-Jones-type interaction

    SciTech Connect (OSTI)

    Hess, Peter

    2014-08-07

    An improved microscopic cleavage model, based on a Morse-type and Lennard-Jones-type interaction instead of the previously employed half-sine function, is used to determine the maximum cleavage strength for the brittle materials diamond, tungsten, molybdenum, silicon, GaAs, silica, and graphite. The results of both interaction potentials are in much better agreement with the theoretical strength values obtained by ab initio calculations for diamond, tungsten, molybdenum, and silicon than the previous model. Reasonable estimates of the intrinsic strength are presented for GaAs, silica, and graphite, where first principles values are not available.

  15. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  16. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  17. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  18. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  19. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  20. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps

  1. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  2. Identification of Human Repetitive DNA Elements

    Energy Science and Technology Software Center (OSTI)

    1995-11-01

    PYTHIA identifies the subfamily membership of Alu sequences, occurrences of repetitive human DNA elements, and simple DNA sequences.

  3. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center (OSTI)

    1995-07-27

    The program controls the operation of various hardware components of an automatic 12-channel parrallel oligosynthesizer. This involves accepting information regarding the DNA sequence to be generated and converting this into a series of instructions to I/O ports to actuate the appropriate hardware components. The design and function of the software is specific to a particular hardware platform and has no utility for controlling other configurations.

  4. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    other invaders from outside our bodies can be deadly foes that bring disease and death. In either case, understanding how bacteria multiply and grow not only increases our...

  5. Structure and mechanism of human DNA polymerase [eta] (Journal...

    Office of Scientific and Technical Information (OSTI)

    ion catalysis. Two residues conserved among Poleta orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On...

  6. Mechanism of DNA interstrand cross-link processing by repair...

    Office of Scientific and Technical Information (OSTI)

    APA Chicago Bibtex Export Metadata Endnote Excel CSV XML Save to My Library Send to Email Send to Email Email address: Content: Close Send Cite: MLA Format Close Cite: APA ...

  7. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

    SciTech Connect (OSTI)

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-12-01

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = N(C2H5)2(1), N(C3H4NH2)2(2), or N(C2H4NH2)2(3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with the apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1; 3.5 and 0.083 s-1 for 2; and 3.8 and 0.0033 s-1 for 3. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~ 10-7, for 1) undergoes the NN heterolytic bond cleavage (kd ~ 107 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.

  8. Mechanical memory

    DOE Patents [OSTI]

    Gilkey, Jeffrey C.; Duesterhaus, Michelle A.; Peter, Frank J.; Renn, Rosemarie A.; Baker, Michael S.

    2006-08-15

    A first-in-first-out (FIFO) microelectromechanical memory apparatus (also termed a mechanical memory) is disclosed. The mechanical memory utilizes a plurality of memory cells, with each memory cell having a beam which can be bowed in either of two directions of curvature to indicate two different logic states for that memory cell. The memory cells can be arranged around a wheel which operates as a clocking actuator to serially shift data from one memory cell to the next. The mechanical memory can be formed using conventional surface micromachining, and can be formed as either a nonvolatile memory or as a volatile memory.

  9. Mechanical memory

    DOE Patents [OSTI]

    Gilkey, Jeffrey C.; Duesterhaus, Michelle A.; Peter, Frank J.; Renn, Rosemarie A.; Baker, Michael S.

    2006-05-16

    A first-in-first-out (FIFO) microelectromechanical memory apparatus (also termed a mechanical memory) is disclosed. The mechanical memory utilizes a plurality of memory cells, with each memory cell having a beam which can be bowed in either of two directions of curvature to indicate two different logic states for that memory cell. The memory cells can be arranged around a wheel which operates as a clocking actuator to serially shift data from one memory cell to the next. The mechanical memory can be formed using conventional surface micromachining, and can be formed as either a nonvolatile memory or as a volatile memory.

  10. Sequential addition of short DNA oligos in DNA-polymerase-based...

    Office of Scientific and Technical Information (OSTI)

    and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of...

  11. DNA attachment to support structures

    DOE Patents [OSTI]

    Balhorn, Rodney L. (Livermore, CA); Barry, Christopher H. (Fresno, CA)

    2002-01-01

    Microscopic beads or other structures are attached to nucleic acids (DNA) using a terminal transferase. The transferase adds labeled dideoxy nucleotide bases to the ends of linear strands of DNA. The labels, such as the antigens digoxigenin and biotin, bind to the antibody compounds or other appropriate complementary ligands, which are bound to the microscopic beads or other support structures. The method does not require the synthesis of a synthetic oligonucleotide probe. The method can be used to tag or label DNA even when the DNA has an unknown sequence, has blunt ends, or is a very large fragment (e.g., >500 kilobase pairs).

  12. Agreement Mechanisms

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Agreement Mechanisms Agreement Mechanisms World-class experts and capabilities countering all aspects of explosive threats, and aiming predominantly at enhanced detection capabilities. CRADA: Cooperative Research and Development Agreement What is it? Work performed in collaboration with a sponsor. What does it do? Enables Los Alamos staff to participate with industry, academia, and nonprofit entities on collaborative R&D activities of mutual benefit. When is it used? An organization's

  13. Computational mechanics

    SciTech Connect (OSTI)

    Goudreau, G.L.

    1993-03-01

    The Computational Mechanics thrust area sponsors research into the underlying solid, structural and fluid mechanics and heat transfer necessary for the development of state-of-the-art general purpose computational software. The scale of computational capability spans office workstations, departmental computer servers, and Cray-class supercomputers. The DYNA, NIKE, and TOPAZ codes have achieved world fame through our broad collaborators program, in addition to their strong support of on-going Lawrence Livermore National Laboratory (LLNL) programs. Several technology transfer initiatives have been based on these established codes, teaming LLNL analysts and researchers with counterparts in industry, extending code capability to specific industrial interests of casting, metalforming, and automobile crash dynamics. The next-generation solid/structural mechanics code, ParaDyn, is targeted toward massively parallel computers, which will extend performance from gigaflop to teraflop power. Our work for FY-92 is described in the following eight articles: (1) Solution Strategies: New Approaches for Strongly Nonlinear Quasistatic Problems Using DYNA3D; (2) Enhanced Enforcement of Mechanical Contact: The Method of Augmented Lagrangians; (3) ParaDyn: New Generation Solid/Structural Mechanics Codes for Massively Parallel Processors; (4) Composite Damage Modeling; (5) HYDRA: A Parallel/Vector Flow Solver for Three-Dimensional, Transient, Incompressible Viscous How; (6) Development and Testing of the TRIM3D Radiation Heat Transfer Code; (7) A Methodology for Calculating the Seismic Response of Critical Structures; and (8) Reinforced Concrete Damage Modeling.

  14. Computational mechanics

    SciTech Connect (OSTI)

    Raboin, P J

    1998-01-01

    The Computational Mechanics thrust area is a vital and growing facet of the Mechanical Engineering Department at Lawrence Livermore National Laboratory (LLNL). This work supports the development of computational analysis tools in the areas of structural mechanics and heat transfer. Over 75 analysts depend on thrust area-supported software running on a variety of computing platforms to meet the demands of LLNL programs. Interactions with the Department of Defense (DOD) High Performance Computing and Modernization Program and the Defense Special Weapons Agency are of special importance as they support our ParaDyn project in its development of new parallel capabilities for DYNA3D. Working with DOD customers has been invaluable to driving this technology in directions mutually beneficial to the Department of Energy. Other projects associated with the Computational Mechanics thrust area include work with the Partnership for a New Generation Vehicle (PNGV) for ''Springback Predictability'' and with the Federal Aviation Administration (FAA) for the ''Development of Methodologies for Evaluating Containment and Mitigation of Uncontained Engine Debris.'' In this report for FY-97, there are five articles detailing three code development activities and two projects that synthesized new code capabilities with new analytic research in damage/failure and biomechanics. The article this year are: (1) Energy- and Momentum-Conserving Rigid-Body Contact for NIKE3D and DYNA3D; (2) Computational Modeling of Prosthetics: A New Approach to Implant Design; (3) Characterization of Laser-Induced Mechanical Failure Damage of Optical Components; (4) Parallel Algorithm Research for Solid Mechanics Applications Using Finite Element Analysis; and (5) An Accurate One-Step Elasto-Plasticity Algorithm for Shell Elements in DYNA3D.

  15. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known...

  16. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the...

  17. Challenges and opportunities for structural DNA nanotechnology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Challenges and opportunities for structural DNA nanotechnology Authors: Pinheiro, A. V., Han, D., Shih, W. M., and Yan, H. Title: Challenges and opportunities for structural DNA...

  18. Fractofusion mechanism

    SciTech Connect (OSTI)

    Yasui, K. . Dept. of Physics)

    1992-11-01

    In this paper, the fractofusion mechanism of cold fusion is investigated theoretically. The conditions necessary for fractofusion during the absorption of deuterium atoms by palladium specimens (the condition of so-called cold fusion experiments) is clarified, including crack generation at grain boundaries, the high orientation angle of grains, rapid crack formation, the increase of electrical resistance around a crack, the large width of cracks, and the generation of many cracks. The origin and quantity of the electrical field inside cracks in the conductor are also clarified. By the fractofusion mechanism, the experimental facts that neutron emissions are observed in bursts, that sometimes they coincide with the deformation of a palladium specimen, and that in many experiments excess neutrons were not observed are qualitatively explained. The upper limit of the total fractofusion yields during the absorption of deuterium atoms by palladium specimens are estimated.

  19. Structure of an aprataxin?DNA complex with insights into AOA1 neurodegenerative disease

    SciTech Connect (OSTI)

    Tumbale, Percy; Appel, C. Denise; Kraehenbuehl, Rolf; Robertson, Patrick D.; Williams, Jessica S.; Krahn, Joe; Ahel, Ivan; Williams, R. Scott (NIEHS); (Manchester)

    2012-09-17

    DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn{sup 2+} complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C{sub 2}HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).

  20. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

  1. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K.

    1998-01-01

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

  2. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1997-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  3. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  4. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments [OSTI]

    Walsh, Karen McNulty

    2011-05-09

    Scientists use complementary strands of synthetic DNA to build functional materials from the bottom up. Future applications include biosensors, optical nano-devices, and new kinds of solar cells.

  5. Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

    SciTech Connect (OSTI)

    Peng, Jamy C.

    2007-05-05

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in euchromatin. Remarkably, human euchromatin and fly heterochromatin share similar features; such as repeated DNA content, intron lengths and open reading frame sizes. Human cells likely stabilize their DNA content via mechanisms and factors similar to those in Drosophila heterochromatin. Furthermore, my thesis work raises implications for H3K9me and chromatin functions in complex-DNA genome stability, repeated DNA homogenization by molecular drive, and in genome reorganization through evolution.

  6. DNA analysis conference in Santa Fe

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA analysis conference in Santa Fe DNA analysis conference in Santa Fe Los Alamos National Laboratory is hosting a DNA sequence analysis and bioinformatics event, the 10th annual Sequencing, Finishing and Analysis in the Future (SFAF) workshop. May 27, 2015 DNA extracted from a soil sample is stored in a small vial of clear liquid. In general, living cells function by using the sequences of bases in their DNA as a blueprint for assembling proteins. A particularly important type of protein is

  7. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

    Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM); Cai, Hong (Los Alamos, NM)

    2001-01-01

    DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.

  8. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1996-05-07

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

  9. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  10. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

    Moyzis, Robert K. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  11. Interconnecting gold islands with DNA origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Interconnecting gold islands with DNA origami Authors: Ding, B., Wu, H., Xu, W., Zhao, Z., Liu, Y., Yu, H., and Yan, H. Title: Interconnecting gold islands with DNA origami Source:...

  12. A DNA tweezer-actuated enzyme nanoreactor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A DNA tweezer-actuated enzyme nanoreactor Authors: Liu, M., Fu, J., Hejesen, C., Yang, Y., Woodbury, N.W., Gothelf, K., Liu, Y., and Yan, H. Title: A DNA tweezer-actuated enzyme...

  13. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect (OSTI)

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; ulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  14. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

    Christian, Allen T.; Coleman, Matthew A.; Tucker, James D.

    2002-01-01

    Amplification of chromosomal DNA in situ to increase the amount of DNA associated with a chromosome or chromosome region is described. The amplification of chromosomal DNA in situ provides for the synthesis of Fluorescence in situ Hybridization (FISH) painting probes from single dissected chromosome fragments, the production of cDNA libraries from low copy mRNAs and improved in Comparative Genomic Hybridization (CGH) procedures.

  15. DNA Origami: A History and Current Perspective

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Origami: A History and Current Perspective Authors: Nangreave, J., Han, D., Liu, Y., and Yan, H. Title: DNA Origami: A History and Current Perspective Source: Current Opinion in Chemical Biology Year: 2010 Volume: 14 Pages: 608-615 ABSTRACT: Researchers have been using DNA for the rational design and construction of nanoscale objects for nearly 30 years. Recently, [`]scaffolded DNA origami' has emerged as one of the most promising assembly techniques in DNA nanotechnology with a broad range of

  16. Structural basis for inhibition of DNA replication by aphidicolin

    SciTech Connect (OSTI)

    Baranovskiy, A. G.; Babayeva, N. D.; Suwa, Y.; Gu, J.; Pavlov, Y. I.; Tahirov, T. H.

    2014-11-27

    Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase ? (Pol ?) in the ternary complex with an RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol ? active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol ?. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.

  17. Structural basis for inhibition of DNA replication by aphidicolin

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Baranovskiy, A. G.; Babayeva, N. D.; Suwa, Y.; Gu, J.; Pavlov, Y. I.; Tahirov, T. H.

    2014-11-27

    Natural tetracyclic diterpenoid aphidicolin is a potent and specific inhibitor of B-family DNA polymerases, haltering replication and possessing a strong antimitotic activity in human cancer cell lines. Clinical trials revealed limitations of aphidicolin as an antitumor drug because of its low solubility and fast clearance from human plasma. The absence of structural information hampered the improvement of aphidicolin-like inhibitors: more than 50 modifications have been generated so far, but all have lost the inhibitory and antitumor properties. Here we report the crystal structure of the catalytic core of human DNA polymerase α (Pol α) in the ternary complex with anmore » RNA-primed DNA template and aphidicolin. The inhibitor blocks binding of dCTP by docking at the Pol α active site and by rotating the template guanine. The structure provides a plausible mechanism for the selectivity of aphidicolin incorporation opposite template guanine and explains why previous modifications of aphidicolin failed to improve its affinity for Pol α. With new structural information, aphidicolin becomes an attractive lead compound for the design of novel derivatives with enhanced inhibitory properties for B-family DNA polymerases.« less

  18. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-07-11

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  19. Probe and method for DNA detection

    DOE Patents [OSTI]

    Yeh, Hsin-Chih; Werner, James Henry; Sharma, Jaswinder Kumar; Martinez, Jennifer Suzanne

    2013-07-02

    A hybridization probe containing two linear strands of DNA lights up upon hybridization to a target DNA using silver nanoclusters that have been templated onto one of the DNA strands. Hybridization induces proximity between the nanoclusters on one strand and an overhang on the other strand, which results in enhanced fluorescence emission from the nanoclusters.

  20. NV-020-08-DNA-52 | Open Energy Information

    Open Energy Info (EERE)

    DNA-52 Jump to: navigation, search NEPA Document Collection for: NV-020-08-DNA-52 DNA for GeothermalExploration, DNA for Thermal Gradient Hole at Gavvs Valley for Geothermal...

  1. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01

    The Fleet DNA Project - designed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) in partnership with Oak Ridge National Laboratory - aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. At the heart of the Fleet DNA Project is a clearinghouse of medium- and heavy-duty commercial fleet transportation data for optimizing the design of advanced vehicle technologies or for selecting a given technology to invest in. An easy-to-access online database will help vehicle manufacturers and fleets understand the broad operational range for many of today's commercial vehicle vocations.

  2. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13

    An electrophoretic device separates and detects particles such as DNA fragments, proteins, and the like. The device has a capillary which is coated with a coating with a low refractive index such as Teflon.RTM. AF. A sample of particles is fluorescently labeled and injected into the capillary. The capillary is filled with an electrolyte buffer solution. An electrical field is applied across the capillary causing the particles to migrate from a first end of the capillary to a second end of the capillary. A detector light beam is then scanned along the length of the capillary to detect the location of the separated particles. The device is amenable to a high throughput system by providing additional capillaries. The device can also be used to determine the actual size of the particles and for DNA sequencing.

  3. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  4. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA

  5. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, Andrew M. (Oakland, CA); Dawson, John (Pacific Palisades, CA)

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  6. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1998-01-13

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

  7. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  8. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

    Krulevitch, Peter A. (Pleasanton, CA); Miles, Robin R. (Danville, CA); Wang, Xiao-Bo (San Diego, CA); Mariella, Raymond P. (Danville, CA); Gascoyne, Peter R. C. (Bellaire, TX); Balch, Joseph W. (Livermore, CA)

    2002-01-01

    Manipulation of DNA molecules in solution has become an essential aspect of genetic analyses used for biomedical assays, the identification of hazardous bacterial agents, and in decoding the human genome. Currently, most of the steps involved in preparing a DNA sample for analysis are performed manually and are time, labor, and equipment intensive. These steps include extraction of the DNA from spores or cells, separation of the DNA from other particles and molecules in the solution (e.g. dust, smoke, cell/spore debris, and proteins), and separation of the DNA itself into strands of specific lengths. Dielectrophoresis (DEP), a phenomenon whereby polarizable particles move in response to a gradient in electric field, can be used to manipulate and separate DNA in an automated fashion, considerably reducing the time and expense involved in DNA analyses, as well as allowing for the miniaturization of DNA analysis instruments. These applications include direct transport of DNA, trapping of DNA to allow for its separation from other particles or molecules in the solution, and the separation of DNA into strands of varying lengths.

  9. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    C. Terwilliger, Randy J. Read, Blake Wiedenheft. Crystal structure of the CRISPR RNA- guided surveillance complex from Escherichia coli. Science, 2014 DOI: 10.1126 science.1256328...

  10. CDK1 enhances mitochondrial bioenergetics for radiation-induced DNA repair

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qin, Lili; Fan, Ming; Candas, Demet; Jiang, Guochun; Papadopoulos, Stelios; Tian, Lin; Woloschak, Gayle; Grdina, David J.; Li, Jian  Jian

    2015-12-06

    Nuclear DNA repair capacity is a critical determinant of cell fate under genotoxic stress conditions. DNA repair is a well-defined energy-consuming process. However, it is unclear how DNA repair is fueled and whether mitochondrial energy production contributes to nuclear DNA repair. Here, we report a dynamic enhancement of oxygen consumption and mitochondrial ATP generation in irradiated normal cells, paralleled with increased mitochondrial relocation of the cell-cycle kinase CDK1 and nuclear DNA repair. The basal and radiation-induced mitochondrial ATP generation is reduced significantly in cells harboring CDK1 phosphorylation-deficient mutant complex I subunits. Similarly, mitochondrial ATP generation and nuclear DNA repair aremore »also compromised severely in cells harboring mitochondrially targeted, kinase-deficient CDK1. These findings demonstrate a mechanism governing the communication between mitochondria and the nucleus by which CDK1 boosts mitochondrial bioenergetics to meet the increased cellular fuel demand for DNA repair and cell survival under genotoxic stress conditions.« less

  11. Construction of highly extensive polymorphic DNA libraries by in-gel competitive reassociation procedure

    SciTech Connect (OSTI)

    Inoue, Shinichi; Kiyama, Ryoiti; Oishi, Michio

    1996-02-01

    Differential genomic DNA libraries between two mouse strains and from two human individuals were constructed by means of the in-gel competitive reassociation (IGCR) procedure, a procedure developed for cloning altered anonymous restriction fragments. The libraries were highly enriched fragments, approximately 60 and 40% for the mouse and human libraries, respectively, and, more importantly, maintained most of the original complexities of the RFLP fragments. Therefore, differential genomic DNA libraries constructed by the IGCR procedure, particularly for human genomic DNA, should offer highly extensive sources for polymorphic DNA sequences necessary for a variety of genome analyses, including studies on the origin and mechanism of biological diversity among the same species. 19 refs., 4 figs.

  12. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect (OSTI)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other application papers of sequencing up to this level were also published in the mid 1990's. A major interest of the sequencing community has always been read length. The longer the sequence read per run the more efficient the process as well as the ability to read repeat sequences. We therefore devoted a great deal of time to studying the factors influencing read length in capillary electrophoresis, including polymer type and molecule weight, capillary column temperature, applied electric field, etc. In our initial optimization, we were able to demonstrate, for the first time, the sequencing of over 1000 bases with 90% accuracy. The run required 80 minutes for separation. Sequencing of 1000 bases per column was next demonstrated on a multiple capillary instrument. Our studies revealed that linear polyacrylamide produced the longest read lengths because the hydrophilic single strand DNA had minimal interaction with the very hydrophilic linear polyacrylamide. Any interaction of the DNA with the polymer would lead to broader peaks and lower read length. Another important parameter was the molecular weight of the linear chains. High molecular weight (> 1 MDA) was important to allow the long single strand DNA to reptate through the entangled polymer matrix. In an important paper, we showed an inverse emulsion method to prepare reproducibility linear polyacrylamide polymer with an average MWT of 9MDa. This approach was used in the polymer for sequencing the human genome. Another critical factor in the successful use of capillary electrophoresis for sequencing was the sample preparation method. In the Sanger sequencing reaction, high concentration of salts and dideoxynucleotide remained. Since the sample was introduced to the capillary column by electrokinetic injection, these salt ions would be favorably injected into the column over the sequencing fragments, thus reducing the signal for longer fragments and hence reading read length. In two papers, we examined the role of individual components from the sequencing reaction and then developed a protocol to reduce the deleterio

  13. A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Source: Angewandte Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding staples. Atomic force microscopy images (see picture) demonstrate the two-dimensional structures formed by using this strategy.

  14. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey. Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  15. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    SciTech Connect (OSTI)

    Shi, Yun-bo

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs.

  16. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

    Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

    2013-07-16

    In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

  17. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  18. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  19. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  20. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

    Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David

    2005-11-01

    Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year project.

  1. Catalytic Hydrolytic Cleavage and Oxy-Cleavage of Lignin Linkages

    SciTech Connect (OSTI)

    Xia, Guanguang; Chen, Baowei; Zhang, Rui; Zhang, Z. Conrad

    2014-07-26

    In this work, new strategies involving organic bases were evaluated to depolymerize lignin to reduced molecular fragments in aqueous medium. NaOH as an inorganic base was also investigated as a reference. Full nature lignin samples are used for the study. As research tools to unravel the complexity of the macro lignin structure and bulky molecular size under this study, size exclusion chromatography and high resolution mass spectrometric analysis, typically used for protein characterizations, were used to follow the progress of lignin depolymerisation by measuring the molecular weight distribution of the products and determining the key molecular fingerprints, respectively. The results show that sodium phenoxide and guanidine carbonate are effective catalysts for lignin depolymerization. It is observed that there exists a synergism between H2O2 and the organic base, which is strongest with guanidine carbonate.

  2. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  3. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  4. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  5. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, Karin D. (Salt Lake City, UT); Chu, Tun-Jen (Salt Lake City, UT); Pitt, William G. (Orem, UT)

    1992-01-01

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

  6. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

    1992-05-12

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

  7. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, J.; Piddington, C.S.; Kovacevich, B.R.; Young, K.D.; Denome, S.A.

    1994-10-18

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous. 13 figs.

  8. Allostery through protein-induced DNA bubbles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Traverso, Joseph J.; Manoranjan, Valipuram S.; Bishop, A. R.; Rasmussen, Kim Ø.; Voulgarakis, Nikolaos K.

    2015-03-12

    Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resultingmore » melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.« less

  9. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, John (Seattle, WA); Piddington, Chris S. (Seattle, WA); Kovacevich, Brian R. (Seattle, WA); Young, Kevin D. (Grand Forks, ND); Denome, Sylvia A. (Thompson, ND)

    1994-01-01

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous.

  10. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)

    2011-07-05

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

  11. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

    Wong; Pak C. (Richland, WA), Wong; Kwong K. (Sugar Land, TX), Foote; Harlan P. (Richland, WA)

    2006-06-06

    Current technologies allow the generation of artificial DNA molecules and/or the ability to alter the DNA sequences of existing DNA molecules. With a careful coding scheme and arrangement, it is possible to encode important information as an artificial DNA strand and store it in a living host safely and permanently. This inventive technology can be used to identify origins and protect R&D investments. It can also be used in environmental research to track generations of organisms and observe the ecological impact of pollutants. Today, there are microorganisms that can survive under extreme conditions. As well, it is advantageous to consider multicellular organisms as hosts for stored information. These living organisms can provide as memory housing and protection for stored data or information. The present invention provides well for data storage in a living organism wherein at least one DNA sequence is encoded to represent data and incorporated into a living organism.

  12. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  13. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Livermore, CA)

    2006-08-01

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

  14. Mechanics | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Mechanics Mechanics A deeper look at the mechanics and gameplay A deeper look at the mechanics and gameplay Mechanics Breakdown In Brief Players must connect buildings together by allocating resources in a resource chain across the map. They must reach and resolve their Objective within a given number of turns to succeed. To accomplish this, they have the following tools at their disposal: Linking Connect buildings together by allocating resources from buildings that produce them to buildings

  15. 2013 INORGANIC REACTION MECHANISMS GORDON RESEARCH CONFERENCE (MARCH 3-8, 2013 - HOTEL GALVEZ, GALVESTON TX)

    SciTech Connect (OSTI)

    Abu-Omar, Mahdi M.

    2012-12-08

    The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.

  16. Rapid Detection and Identification of a Pathogen's DNA Using Phi29 DNA Polymerase

    SciTech Connect (OSTI)

    Xu, Y.; Dunn, J.; Gao, S.; Bruno, J. F.; Luft, B. J.

    2008-10-31

    Zoonotic pathogens including those transmitted by insect vectors are some of the most deadly of all infectious diseases known to mankind. A number of these agents have been further weaponized and are widely recognized as being potentially significant biothreat agents. We describe a novel method based on multiply-primed rolling circle in vitro amplification for profiling genomic DNAs to permit rapid, cultivation-free differential detection and identification of circular plasmids in infectious agents. Using Phi29 DNA polymerase and a two-step priming reaction we could reproducibly detect and characterize by DNA sequencing circular DNA from Borrelia burgdorferi B31 in DNA samples containing as little as 25 pg of Borrelia DNA amongst a vast excess of human DNA. This simple technology can ultimately be adapted as a sensitive method to detect specific DNA from both known and unknown pathogens in a wide variety of complex environments.

  17. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Wyrobek, Andrew J.

    2009-01-18

    Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.

  18. Property:NEPA DNA Worksheet | Open Energy Information

    Open Energy Info (EERE)

    DNA Worksheet Jump to: navigation, search Property Name NEPA DNA Worksheet Property Type Page Description DNA Worksheet files for NEPA Docs. This is a property of type Page. It...

  19. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined...

  20. Internal pipe attachment mechanism

    DOE Patents [OSTI]

    Bast, Richard M. (Livermore, CA); Chesnut, Dwayne A. (Pleasanton, CA); Henning, Carl D. (Livermore, CA); Lennon, Joseph P. (Livermore, CA); Pastrnak, John W. (Livermore, CA); Smith, Joseph A. (Livermore, CA)

    1994-01-01

    An attachment mechanism for repairing or extending fluid carrying pipes, casings, conduits, etc. utilizing one-way motion of spring tempered fingers to provide a mechanical connection between the attachment mechanism and the pipe. The spring tempered fingers flex to permit insertion into a pipe to a desired insertion depth. The mechanical connection is accomplished by reversing the insertion motion and the mechanical leverage in the fingers forces them outwardly against the inner wall of the pipe. A seal is generated by crushing a sealing assembly by the action of setting the mechanical connection.

  1. Internal pipe attachment mechanism

    DOE Patents [OSTI]

    Bast, R.M.; Chesnut, D.A.; Henning, C.D.; Lennon, J.P.; Pastrnak, J.W.; Smith, J.A.

    1994-12-13

    An attachment mechanism is described for repairing or extending fluid carrying pipes, casings, conduits, etc. utilizing one-way motion of spring tempered fingers to provide a mechanical connection between the attachment mechanism and the pipe. The spring tempered fingers flex to permit insertion into a pipe to a desired insertion depth. The mechanical connection is accomplished by reversing the insertion motion and the mechanical leverage in the fingers forces them outwardly against the inner wall of the pipe. A seal is generated by crushing a sealing assembly by the action of setting the mechanical connection. 6 figures.

  2. Gel Electrophoresis of Gold-DNA Nanoconjugates

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pellegrino, T.; Sperling, R. A.; Alivisatos, A. P.; Parak, W. J.

    2007-01-01

    Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effectivemore » diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.« less

  3. Screening Tool for Providers of Double-Stranded DNA - Energy...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Technology Marketing SummaryThe invention screens purchase orders submitted to DNA synthesis companies.DescriptionOrders are screened to find indicators that the ordered DNA...

  4. Unidirectional Scaffold-Strand Arrangement in DNA Origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unidirectional Scaffold-Strand Arrangement in DNA Origami Authors: Han, D., Jiang, S., Samanta, A., Liu, Y., and Yan, H. Title: Unidirectional Scaffold-Strand Arrangement in DNA...

  5. 6.7 Engineered Enzyme Accelerates DNA Sequencing

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Richardson, C. C. (1995) "A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and...

  6. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    scientists. Schematic of DNA structures in various conformations on a gold surface. Differences in overall structure and orientation are emphasized by color-coding of DNA...

  7. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of genomic integrity and responses to DNA damage relevant to pathogens and cancer development. DNA Repair Switch A process similar in spirit to that of a railroad...

  8. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

    2002-01-01

    A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

  9. DNA fragment sizing and sorting by laser-induced fluorescence

    DOE Patents [OSTI]

    Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

    1996-01-01

    A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

  10. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

    2013-06-25

    A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

  11. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08

    Building on the idea of using DNA to link up nanoparticles scientists at Brookhaven National Lab have designed a molecular assembly line for high-precision nano-construction. Nanofabrication is essential for exploiting the unique properties of nanoparticl

  12. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9...

  13. Extracting biological knowledge from DNA sequences

    SciTech Connect (OSTI)

    De La Vega, F.M.; Thieffry, D.; Collado-Vides, J.

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  14. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, Richard A. (Contra Costa County, CA); Huang, Xiaohua C. (Mt. View, CA); Quesada, Mark A. (San Francisco, CA)

    1995-01-01

    A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

  15. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  16. Mechanical seal assembly

    DOE Patents [OSTI]

    Kotlyar, Oleg M. (Salt Lake City, UT)

    2002-01-01

    An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transfering it to the mechanical diode.

  17. Mechanical seal assembly

    DOE Patents [OSTI]

    Kotlyar, Oleg M. (Salt Lake City, UT)

    2001-01-01

    An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transferring it to the mechanical diode.

  18. Oligonucleotide and Long Polymeric DNA Encoding

    SciTech Connect (OSTI)

    Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

    2003-11-24

    This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

  19. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for

  20. Computational Structural Mechanics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    load-2 TRACC RESEARCH Computational Fluid Dynamics Computational Structural Mechanics Transportation Systems Modeling Computational Structural Mechanics Overview of CSM Computational structural mechanics is a well-established methodology for the design and analysis of many components and structures found in the transportation field. Modern finite-element models (FEMs) play a major role in these evaluations, and sophisticated software, such as the commercially available LS-DYNA® code, is

  1. Monroe Thomas, Mechanical Technician

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and endstation moves. Though he's training another mechanical technician to operate the crane, it's Monroe who is called upon for critical moves. He plays a key role in...

  2. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

    Roslaniec, Mary C. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Jett, James H. (Los Alamos, NM); Cram, L. Scott (Los Alamos, NM)

    1998-01-01

    Optical selection and collection of DNA fragments. The present invention includes the optical selection and collection of large (>.mu.g) quantities of clonable, chromosome-specific DNA from a sample of chromosomes. Chromosome selection is based on selective, irreversible photoinactivation of unwanted chromosomal DNA. Although more general procedures may be envisioned, the invention is demonstrated by processing chromosomes in a conventional flow cytometry apparatus, but where no droplets are generated. All chromosomes in the sample are first stained with at least one fluorescent analytic dye and bonded to a photochemically active species which can render chromosomal DNA unclonable if activated. After passing through analyzing light beam(s), unwanted chromosomes are irradiated using light which is absorbed by the photochemically active species, thereby causing photoinactivation. As desired chromosomes pass this photoinactivation point, the inactivating light source is deflected by an optical modulator; hence, desired chromosomes are not photoinactivated and remain clonable. The selection and photoinactivation processes take place on a microsecond timescale. By eliminating droplet formation, chromosome selection rates 50 times greater than those possible with conventional chromosome sorters may be obtained. Thus, usable quantities of clonable DNA from any source thereof may be collected.

  3. Plasma induced DNA damage: Comparison with the effects of ionizing radiation

    SciTech Connect (OSTI)

    Lazovi?, S.; Maleti?, D.; Pua?, N.; Malovi?, G.; Petrovi?, Z. Lj.; Leskovac, A.; Filipovi?, J.; Joksi?, G.

    2014-09-22

    We use human primary fibroblasts for comparing plasma and gamma rays induced DNA damage. In both cases, DNA strand breaks occur, but of fundamentally different nature. Unlike gamma exposure, contact with plasma predominantly leads to single strand breaks and base-damages, while double strand breaks are mainly consequence of the cell repair mechanisms. Different cell signaling mechanisms are detected confirming this (ataxia telangiectasia mutated - ATM and ataxia telangiectasia and Rad3 related - ATR, respectively). The effective plasma doses can be tuned to match the typical therapeutic doses of 2?Gy. Tailoring the effective dose through plasma power and duration of the treatment enables safety precautions mainly by inducing apoptosis and consequently reduced frequency of micronuclei.

  4. Mechanical code comparator

    DOE Patents [OSTI]

    Peter, Frank J.; Dalton, Larry J.; Plummer, David W.

    2002-01-01

    A new class of mechanical code comparators is described which have broad potential for application in safety, surety, and security applications. These devices can be implemented as micro-scale electromechanical systems that isolate a secure or otherwise controlled device until an access code is entered. This access code is converted into a series of mechanical inputs to the mechanical code comparator, which compares the access code to a pre-input combination, entered previously into the mechanical code comparator by an operator at the system security control point. These devices provide extremely high levels of robust security. Being totally mechanical in operation, an access control system properly based on such devices cannot be circumvented by software attack alone.

  5. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Intriguing DNA Editor Has a Structural Trigger Print Wednesday, 30 July 2014 00:00 A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9

  6. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N. (San Leandro, CA); Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Young, Jennifer A. (Berkeley, CA); Clague, David S. (Livermore, CA)

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  7. Rotary mechanical latch

    DOE Patents [OSTI]

    Spletzer, Barry L.; Martinez, Michael A.; Marron, Lisa C.

    2012-11-13

    A rotary mechanical latch for positive latching and unlatching of a rotary device with a latchable rotating assembly having a latching gear that can be driven to latched and unlatched states by a drive mechanism such as an electric motor. A cam arm affixed to the latching gear interfaces with leading and trailing latch cams affixed to a flange within the drive mechanism. The interaction of the cam arm with leading and trailing latch cams prevents rotation of the rotating assembly by external forces such as those due to vibration or tampering.

  8. Electronic door locking mechanism

    DOE Patents [OSTI]

    Williams, G.L.; Kirby, P.G.

    1997-10-21

    The invention is a motorized linkage for engaging a thumb piece in a door mechanism. The device has an exterior lock assembly with a small battery cell and combination lock. Proper entry by a user of a security code allows the battery to operate a small motor within the exterior lock assembly. The small motor manipulates a cam-plunger which moves an actuator pin into a thumb piece. The user applies a force on to the thumb piece. This force is transmitted by the thumb piece to a latch engagement mechanism by the actuator pin. The latch engagement mechanism operates the door latch. 6 figs.

  9. Electronic door locking mechanism

    DOE Patents [OSTI]

    Williams, Gary Lin; Kirby, Patrick Gerald

    1997-01-01

    The invention is a motorized linkage for engaging a thumb piece in a door mechanism. The device has an exterior lock assembly with a small battery cell and combination lock. Proper entry by a user of a security code allows the battery to operate a small motor within the exterior lock assembly. The small motor manipulates a cam-plunger which moves an actuator pin into a thumb piece. The user applies a force on to the thumb piece. This force is transmitted by the thumb piece to a latch engagement mechanism by the actuator pin. The latch engagement mechanism operates the door latch.

  10. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  11. Protection of cisplatin-induced spermatotoxicity, DNA damage and chromatin abnormality by selenium nano-particles

    SciTech Connect (OSTI)

    Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali; Shahverdi, Ahmad Reza; Ahmadi, Abbas; Baeeri, Maryam; Mohammadirad, Azadeh; Abdollahi, Mohammad

    2013-02-01

    Cisplatin (CIS), an anticancer alkylating agent, induces DNA adducts and effectively cross links the DNA strands and so affects spermatozoa as a male reproductive toxicant. The present study investigated the cellular/biochemical mechanisms underlying possible protective effect of selenium nano-particles (Nano-Se) as an established strong antioxidant with more bioavailability and less toxicity, on reproductive toxicity of CIS by assessment of sperm characteristics, sperm DNA integrity, chromatin quality and spermatogenic disorders. To determine the role of oxidative stress (OS) in the pathogenesis of CIS gonadotoxicity, the level of lipid peroxidation (LPO), antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and peroxynitrite (ONOO) as a marker of nitrosative stress (NS) and testosterone (T) concentration as a biomarker of testicular function were measured in the blood and testes. Thirty-two male Wistar rats were equally divided into four groups. A single IP dose of CIS (7 mg/kg) and protective dose of Nano-Se (2 mg/kg/day) were administered alone or in combination. The CIS-exposed rats showed a significant increase in testicular and serum LPO and ONOO level, along with a significant decrease in enzymatic antioxidants levels, diminished serum T concentration and abnormal histologic findings with impaired sperm quality associated with increased DNA damage and decreased chromatin quality. Coadministration of Nano-Se significantly improved the serum T, sperm quality, and spermatogenesis and reduced CIS-induced free radical toxic stress and spermatic DNA damage. In conclusion, the current study demonstrated that Nano-Se may be useful to prevent CIS-induced gonadotoxicity through its antioxidant potential. Highlights: ? Cisplatin (CIS) affects spermatozoa as a male reproductive toxicant. ? Effect of Nano-Se on CIS-induced spermatotoxicity was investigated. ? CIS-exposure induces oxidative sperm DNA damage and impairs steroidogenesis. ? Nano-Se retained sperm quality against CIS-induced free radicals toxic stress.

  12. Phase Field Fracture Mechanics.

    SciTech Connect (OSTI)

    Robertson, Brett Anthony

    2015-11-01

    For this assignment, a newer technique of fracture mechanics using a phase field approach, will be examined and compared with experimental data for a bend test and a tension test. The software being used is Sierra Solid Mechanics, an implicit/explicit finite element code developed at Sandia National Labs in Albuquerque, New Mexico. The bend test experimental data was also obtained at Sandia Labs while the tension test data was found in a report online from Purdue University.

  13. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    are also crucial components of various other cellular pathways, such as DNA repair, cell cycle control, and chromatin structure. Sliding DNA clamps are loaded onto DNA by...

  14. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    2000-10-03

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

  15. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a...

  16. Encapsulation of Gold Nanoparticles in a DNA Origami Cage

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Encapsulation of Gold Nanoparticles in a DNA Origami Cage Authors: Zhao, Z., Jacovetty, E. L., Liu, Y., and Yan, H. Title: Encapsulation of Gold Nanoparticles in a DNA Origami Cage...

  17. DNA Gridiron Nanostructures Based on Four-Arm Junctions

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Gridiron Nanostructures Based on Four-Arm Junctions Authors: Han, D., Pal, S., Yang, Y., Jiang, S., Nangreave, J., Liu, Y., and Yan, H. Title: DNA Gridiron Nanostructures Based...

  18. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  19. Foreign DNA Capture during CRISPR-CAS Adaptive Immunity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Print Thursday, 21 January 2016 16:45 While we humans view bacteria as the enemy, bacteria have enemies too, for example, viruses. To protect themselves, bacteria have developed an adaptive-type immune system that revolves around a unit of DNA known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. A CRISPR unit of DNA is made up of

  20. DNA origami with Complex Curvatures in 3D

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    with Complex Curvatures in 3D 15 Apr 2011 Center researchers have developed a new DNA origami design strategy for engineering complex, arbitrarily shaped 3D DNA nanostructures that have substantial intrinsic curvatures. This strategy has been presented in a paper by Professors Hao Yan, Yan Liu and coworkers that was featured on the cover of Science for April 15, 2011. Use of DNA as a structural material is in the basis of the DNA nanotechnology searching for ways to assemble nanoscale structures

  1. Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase

    SciTech Connect (OSTI)

    Adhikary, Suraj; Eichman, Brandt F.

    2014-10-02

    DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N{sup 6}-ethenoadenine ({var_epsilon}A) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their {var_epsilon}A activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.

  2. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-10-17

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  3. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect (OSTI)

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  4. DOI-BLM-NM-L000-2012-0200-DNA | Open Energy Information

    Open Energy Info (EERE)

    00-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0200-DNA DNA at Lightning Dock Geothermal Area for GeothermalWell Field, DNA for Injection...

  5. DOI-BLM-NV-C010-2012--044-DNA | Open Energy Information

    Open Energy Info (EERE)

    DOI-BLM-NV-C010-2012--044-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012--044-DNA DNA for GeothermalPower Plant, DNA for Ormatt Nevada Sundry...

  6. DOI-BLM-NV-C010-2013-0037-DNA | Open Energy Information

    Open Energy Info (EERE)

    37-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0037-DNA DNA at Gabbs Valley Geothermal Area for GeothermalWell Field, DNA for Wild Rose Unit...

  7. DOI-BLM-NV-C010-2010-0006-DNA | Open Energy Information

    Open Energy Info (EERE)

    DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2010-0006-DNA DNA at Gabbs Valley Geothermal Area for GeothermalExploration, DNA for Thermal Gradient...

  8. DOI-BLM-NM-L000-2012-0111-DNA | Open Energy Information

    Open Energy Info (EERE)

    111-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0111-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration, DNA for Three...

  9. DOI-BLM-NV-C010-2012-0005-DNA | Open Energy Information

    Open Energy Info (EERE)

    05-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012-0005-DNA DNA at McCoy Geothermal Area for GeothermalWell Field DNA for Observation Wells 62-8...

  10. DOI-BLM-NV-C010-2011-0517-DNA | Open Energy Information

    Open Energy Info (EERE)

    7-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2011-0517-DNA DNA at Dead Horse Wells Geothermal Area for GeothermalExploration DNA at Dead Horse...

  11. DOI-BLM-NM-L000-2012-0042-DNA | Open Energy Information

    Open Energy Info (EERE)

    2-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0042-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration DNA for Well 55-7 at...

  12. DOI-BLM-NV-B020-2008-0071-DNA | Open Energy Information

    Open Energy Info (EERE)

    0071-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-B020-2008-0071-DNA DNA at Reese River Geothermal Area for GeothermalExploration DNA at Reese River...

  13. DOI-BLM-NV-C010-2013-0026-DNA | Open Energy Information

    Open Energy Info (EERE)

    6-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0026-DNA DNA at Dixie Valley Geothermal Area for GeothermalWell Field, DNA for Production...

  14. Residential Mechanical Precooling

    SciTech Connect (OSTI)

    German, a.; Hoeschele, M.

    2014-12-01

    This research conducted by the Alliance for Residential Building Innovation team evaluated mechanical air conditioner pre-cooling strategies in homes throughout the United States. EnergyPlus modeling evaluated two homes with different performance characteristics in seven climates. Results are applicable to new construction homes and most existing homes built in the last 10 years, as well as fairly efficient retrofitted homes.

  15. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 510 minutes.

  16. A Golden Ruler Used to Measure DNA Structure in Solution

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    8 A Golden Ruler Used to Measure DNA Structure in Solution The first crystal structures of DNA double helices appeared in 1979 and directly confirmed the atomic model of Watson-Crick from 25 years earlier. Since then, DNA has been modeled as a relatively rigid polymer. An isotropic elastic rod model of the polymer has proven to be exceptionally good at integrating classical biochemical measurements on DNA with recent single-molecule results for DNA on length scales of 100 nm or longer.

  17. DNA Origami with Complex Curvatures in Three-Dimensional Space

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Origami with Complex Curvatures in Three-Dimensional Space Authors: Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. Title: DNA Origami with Complex Curvatures in Three-Dimensional Space Source: Science Year: 2011 Volume: 332 Pages: 342-346 ABSTRACT: We present a strategy to design and construct self-assembling DNA nanostructures that define intricate curved surfaces in three-dimensional (3D) space using the DNA origami folding technique. Double-helical DNA is bent to follow

  18. Stepped electrophoresis for movement and concentration of DNA

    DOE Patents [OSTI]

    Miles, Robin R.; Wang, Amy Wei-Yun; Mariella, Jr., Raymond P.

    2005-03-15

    A fluidic channel patterned with a series of thin-film electrodes makes it possible to move and concentrate DNA in a fluid passing through the fluidic channel. The DNA has an inherent negative charge and by applying a voltage between adjacent electrodes the DNA is caused to move. By using a series of electrodes, when one electrode voltage or charge is made negative with respect to adjacent electrodes, the DNA is repelled away from this electrode and attached to a positive charged electrode of the series. By sequentially making the next electrode of the series negative, the DNA can be moved to and concentrated over the remaining positive electrodes.

  19. DNA-Guided Crystallization of Colloidal Nanoparticles

    SciTech Connect (OSTI)

    Nykypanchuk,D.; Maye, M.; van der Lelie, D.; Gang, O.

    2008-01-01

    Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks--to realize novel magnetic, plasmonic and photonic metamaterials for example. A conceptually simple idea for overcoming this problem is the use of 'encodable' interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules6, 7, 8, 9, 10. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited14, 15, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles' surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only {approx}4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.

  20. Allosteric Modulation of DNA by Small Molecules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell

  1. Determining orientation and direction of DNA sequences

    DOE Patents [OSTI]

    Goodwin, Edwin H. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    2000-01-01

    Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.

  2. MCM ring hexamerization is a prerequisite for DNA-binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

  3. Preparation of water soluble L-arginine capped CdSe/ZnS QDs and their interaction with synthetic DNA: Picosecond-resolved FRET study

    SciTech Connect (OSTI)

    Giri, Anupam; Goswami, Nirmal; Lemmens, Peter; Pal, Samir Kumar

    2012-08-15

    Graphical abstract: Frster resonance energy transfer (FRET) studies on the interaction of water soluble arginine-capped CdSe/ZnS QDs with ethidium bromide (EB) labeled synthetic dodecamer DNA. Highlights: ? We have solubilized CdSe/ZnS QD in water replacing their TOPO ligand by L-arginine. ? We have studied arginine@QDDNA interaction using FRET technique. ? Arginine@QDs act as energy donor and ethidium bromide-DNA acts as energy acceptor. ? We have applied a kinetic model to understand the kinetics of energy transfer. ? Circular dichroism studies revealed negligible perturbation in the DNA B-form in the arg@QD-DNA complex. -- Abstract: We have exchanged TOPO (trioctylphosphine oxide) ligand of CdSe/ZnS core/shell quantum dots (QDs) with an amino acid L-arginine (Arg) at the toluene/water interface and eventually rendered the QDs from toluene to aqueous phase. We have studied the interaction of the water soluble Arg-capped QDs (energy donor) with ethidium (EB) labeled synthetic dodecamer DNA (energy acceptor) using picoseconds resolved Frster resonance energy transfer (FRET) technique. Furthermore, we have applied a model developed by M. Tachiya to understand the kinetics of energy transfer and the distribution of acceptor (EB-DNA) molecules around the donor QDs. Circular dichroism (CD) studies revealed a negligible perturbation in the native B-form structure of the DNA upon interaction with Arg-capped QDs. The melting and the rehybridization pathways of the DNA attached to the QDs have been monitored by the CD which reveals hydrogen bonding is the associative mechanism for interaction between Arg-capped QDs and DNA.

  4. Sierra Mechanics suite

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanics suite - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs Advanced Nuclear

  5. DNA repair decline during mouse spermiogenesis results in the accumulation of heritable DNA damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wryobek, Andrew J

    2008-02-21

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7- 1 dbf). Analysis of chromosomalaberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  6. DNA Repair Decline During Mouse Spermiogenesis Results in the Accumulation of Heritable DNA Damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wyrobek, Andrew J.

    2007-12-01

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7-1 dbf). Analysis of chromosomal aberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  7. Cadmium sulfate and CdTe-quantum dots alter DNA repair in zebrafish (Danio rerio) liver cells

    SciTech Connect (OSTI)

    Tang, Song; Cai, Qingsong; Chibli, Hicham; Allagadda, Vinay; Nadeau, Jay L.; Mayer, Gregory D.

    2013-10-15

    Increasing use of quantum dots (QDs) makes it necessary to evaluate their toxicological impacts on aquatic organisms, since their contamination of surface water is inevitable. This study compares the genotoxic effects of ionic Cd versus CdTe nanocrystals in zebrafish hepatocytes. After 24 h of CdSO{sub 4} or CdTe QD exposure, zebrafish liver (ZFL) cells showed a decreased number of viable cells, an accumulation of Cd, an increased formation of reactive oxygen species (ROS), and an induction of DNA strand breaks. Measured levels of stress defense and DNA repair genes were elevated in both cases. However, removal of bulky DNA adducts by nucleotide excision repair (NER) was inhibited with CdSO{sub 4} but not with CdTe QDs. The adverse effects caused by acute exposure of CdTe QDs might be mediated through differing mechanisms than those resulting from ionic cadmium toxicity, and studying the effects of metallic components may be not enough to explain QD toxicities in aquatic organisms. - Highlights: Both CdSO{sub 4} and CdTe QDs lead to cell death and Cd accumulation. Both CdSO{sub 4} and CdTe QDs induce cellular ROS generation and DNA strand breaks. Both CdSO{sub 4} and CdTe QDs induce the expressions of stress defense and DNA repair genes. NER repair capacity was inhibited with CdSO{sub 4} but not with CdTe QDs.

  8. Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4

    SciTech Connect (OSTI)

    Wong, Jimson H.Y.; Brown, Jessica A.; Suo, Zucai; Blum, Paul; Nohmi, Takehiko; Ling, Hong

    2010-08-23

    Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3{prime}G (first insertion) and 5{prime}G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.

  9. Fracture mechanics: 26. volume

    SciTech Connect (OSTI)

    Reuter, W.G.; Underwood, J.H.; Newman, J.C. Jr.

    1995-12-31

    The original objective of these symposia was to promote technical interchange between researchers from the US and worldwide in the field of fracture. This objective was recently expanded to promote technical interchange between researchers in the field of fatigue and fracture. The symposium began with the Swedlow Memorial Lecture entitled ``Patterns and Perspectives in Applied Fracture Mechanics.`` The remaining 42 papers are divided into the following topical sections: Constraint crack initiation; Constraint crack growth; Weldments; Engineered materials; Subcritical crack growth; Dynamic loading; and Applications. Papers within the scope of the Energy Data Base have been processed separately.

  10. Mechanical Systems Qualification Standard

    Office of Environmental Management (EM)

    61-2008 June 2008 DOE STANDARD MECHANICAL SYSTEMS QUALIFICATION STANDARD DOE Defense Nuclear Facilities Technical Personnel U.S. Department of Energy AREA TRNG Washington, D.C. 20585 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. DOE-STD-1161-2008 ii This document is available on the Department of Energy Technical Standards Program Web Site at http://www.hss.energy.gov/nuclearsafety/techstds/ DOE-STD-1161-2008 iv INTENTIONALLY BLANK DOE-STD-1161-2008 v TABLE OF

  11. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  12. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  13. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  14. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  15. Mechanism for Clastogenic Activity of Naphthalene

    SciTech Connect (OSTI)

    Buchholz, Bruce A.

    2015-09-29

    Naphthalene incubations form DNA adducts in vitro in a dose dependent manner in both mouse and rat tissues. Rodent tissue incubations with naphthalene indicate that naphthalene forms as many DNA adducts as Benzo(a)pyrene, a known DNA binding carcinogen. The mouse airway has the greatest number of DNA adducts, corresponding to the higher metabolic activation of naphthalene in this location. Both rat tissues, the rat olfactory (tumor target) and the airways (non-tumor target), have similar levels of NA-DNA adducts, indicating that short term measures of initial adduct formation do not directly correlate with sites of tumor formation in the NTP bioassays.

  16. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1988-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide or Hoechst 33258 is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as halodeoxy-uridine (HdU), more specifically bromodeoxyuridine (BrdU) is used as a probe for the measurement of HdU or BrdU uptake by the cells as a measure of DNA synthesis.

  17. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of thismore » support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.« less

  18. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO? catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    SciTech Connect (OSTI)

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO?(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO?(111) compared with pyramidal Ni? particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni? species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO? has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.

  19. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect (OSTI)

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  20. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect (OSTI)

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  1. Photocatalytic probing of DNA sequence by using TiO{sub 2}/dopamine-DNA triads.

    SciTech Connect (OSTI)

    Liu, J.; de la Garza, L.; Zhang, L.; Dimitrijevic, N. M.; Zuo, X.; Tiede, D. M.; Rajh, T.

    2007-10-15

    A method to control charge transfer reaction in DNA using hybrid nanometer-sized TiO{sub 2} nanoparticles was developed. In this system extended charge separation reflects the sequence of DNA and was measured using metallic silver deposition or by photocurrent response. Light-induced extended charge separation in these systems was found to be dependent on the DNA-bridge length and sequence. The yield of photocatalytic deposition of silver was studied in systems having GG accepting sites imbedded in AT runs at varying distances from the TiO{sub 2} nanoparticle surface. Weak distance dependence of charge separation indicative of a hole hopping through mediating adenine (A) sites was found. The quantum yield of silver deposition in the system having a GG accepting site placed 8.5 {angstrom} from the nanoparticle surface was found to be {Phi} = 0.70 (70%) and {Phi} = 0.56 (56%) for (A){sub n} and (AT){sub n/2} bridge, respectively. Hole injection to GG trapping sites as far as 70 {angstrom} from a nanoparticle surface in the absence of G hopping sites was measured. Introduction of G hopping sites increased the efficiency of hole injection. The efficiency of photocatalytic deposition of metallic silver was found to be sensitive to the presence of a single nucleobase mismatch in the DNA sequence.

  2. DNA release from lipoplexes by anionic lipids: correlation with lipid

    Office of Scientific and Technical Information (OSTI)

    mesomorphism, interfacial curvature, and membrane fusion (Journal Article) | SciTech Connect DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion Citation Details In-Document Search Title: DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge

  3. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, C.M.; Berg, D.E.; Wang, G.

    1997-07-08

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed. 4 figs.

  4. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, Claire M. (W. Willington, CT); Berg, Douglas E. (St. Louis, MO); Wang, Gan (Storrs, CT)

    1997-01-01

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed.

  5. DNA-Based Optomechanical Molecular Motor

    SciTech Connect (OSTI)

    McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.

    2011-03-16

    An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol-1 of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.

  6. Oxidative DNA damage and repair in children exposed to low levels of arsenic in utero and during early childhood: Application of salivary and urinary biomarkers

    SciTech Connect (OSTI)

    Hinhumpatch, Pantip; Navasumrit, Panida; Chaisatra, Krittinee; Promvijit, Jeerawan; Mahidol, Chulabhorn; Ruchirawat, Mathuros

    2013-12-15

    The present study aimed to assess arsenic exposure and its effect on oxidative DNA damage and repair in young children exposed in utero and continued to live in arsenic-contaminated areas. To address the need for biological specimens that can be acquired with minimal discomfort to children, we used non-invasive urinary and salivary-based assays for assessing arsenic exposure and early biological effects that have potentially serious health implications. Levels of arsenic in nails showed the greatest magnitude of difference between exposed and control groups, followed by arsenic concentrations in saliva and urine. Arsenic levels in saliva showed significant positive correlations with other biomarkers of arsenic exposure, including arsenic accumulation in nails (r = 0.56, P < 0.001) and arsenic concentration in urine (r = 0.50, P < 0.05). Exposed children had a significant reduction in arsenic methylation capacity indicated by decreased primary methylation index and secondary methylation index in both urine and saliva samples. Levels of salivary 8-OHdG in exposed children were significantly higher (? 4-fold, P < 0.01), whereas levels of urinary 8-OHdG excretion and salivary hOGG1 expression were significantly lower in exposed children (? 3-fold, P < 0.05), suggesting a defect in hOGG1 that resulted in ineffective cleavage of 8-OHdG. Multiple regression analysis results showed that levels of inorganic arsenic (iAs) in saliva and urine had a significant positive association with salivary 8-OHdG and a significant negative association with salivary hOGG1 expression. - Highlights: The effects of arsenic exposure in utero and through early childhood were studied. Arsenic-exposed children had a reduction in arsenic methylation capacity. Exposed children had more DNA damage, observed as elevated salivary 8-OHdG. Lower salivary hOGG1 in exposed children indicated impairment of 8-OHdG repair. Salivary and urinary 8-OHdG levels were discordant.

  7. Three-Dimensional Modeling and Simulation of DNA Hybridization...

    Office of Scientific and Technical Information (OSTI)

    Three-Dimensional Modeling and Simulation of DNA Hybridization Kinetics and Mass Transport as Functions of Temperature in a Microfluidic Channel. Citation Details In-Document...

  8. Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures

    SciTech Connect (OSTI)

    Moon, Y.; Seo, S.; Park, J.; Park, T.; Ahn, J. R., E-mail: jrahn@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Shin, J.; Dugasani, S. R. [Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Woo, S. H. [College of Pharmacy, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Park, S. H., E-mail: sunghapark@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-06-09

    Despite many studies on how geometry can be used to control the electronic properties of graphene, certain limitations to fabrication of designed graphene nanostructures exist. Here, we demonstrate controlled topographical replication of graphene by artificial deoxyribonucleic acid (DNA) nanostructures. Owing to the high degree of geometrical freedom of DNA nanostructures, we controlled the nanoscale topography of graphene. The topography of graphene replicated from DNA nanostructures showed enhanced thermal stability and revealed an interesting negative temperature coefficient of sheet resistivity when underlying DNA nanostructures were denatured at high temperatures.

  9. DNA-NV-030-09-03 | Open Energy Information

    Open Energy Info (EERE)

    Info Energy Sector Geothermal energy Environmental Analysis Type DNA Applicant Dusty Miller LLC Geothermal Area Gabbs Valley Geothermal Area Project Location Nevada Project Phase...

  10. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment...

  11. Ionic switch controls the DNA state in phage λ

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Li, Dong; Liu, Ting; Zuo, Xiaobing; Li, Tao; Qiu, Xiangyun; Evilevitch, Alex

    2015-06-19

    We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid bymore » changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.« less

  12. Evolutionary theory, web-search technology combine for DNA analysis

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sequedex: bioinformatics breakthrough Evolutionary theory, web-search technology combine ... Evolutionary theory, web-search technology combine for DNA analysis Bioinformatics ...

  13. Fleet DNA Project - Data Dictionary for Public Download Files

    SciTech Connect (OSTI)

    Duran, A.; Burton, E.; Kelly, K.; Walkowicz, K.

    2014-09-01

    Reference document for the Fleet DNA results data shared on the NREL public website. The document includes variable definitions and descriptions to assist users in understanding data.

  14. DNA release from lipoplexes by anionic lipids: correlation with...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL ... Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; CAPACITY; DNA; ENERGY ...

  15. PEBBLES Mechanics Simulation Speedup

    SciTech Connect (OSTI)

    Joshua J. Cogliati; Abderrafi M. Ougouag

    2010-05-01

    Pebble bed reactors contain large numbers of spherical fuel elements arranged randomly. Determining the motion and location of these fuel elements is required for calculating certain parameters of pebble bed reactor operation. These simulations involve hundreds of thousands of pebbles and involve determining the entire core motion as pebbles are recirculated. Single processor algorithms for this are insufficient since they would take decades to centuries of wall-clock time. This paper describes the process of parallelizing and speeding up the PEBBLES pebble mechanics simulation code. Both shared memory programming with the Open Multi-Processing API and distributed memory programming with the Message Passing Interface API are used in simultaneously in this process. A new shared memory lock-less linear time collision detection algorithm is described. This method allows faster detection of pebbles in contact than generic methods. These combine to make full recirculations on AVR sized reactors possible in months of wall clock time.

  16. Rotary drive mechanism

    SciTech Connect (OSTI)

    Kenderdine, E.W.

    1991-10-08

    This patent describes a rotary drive mechanism which includes a rotary solenoid having a stator and multi-poled rotor. A moving member rotates with the rotor and is biased by a biasing device. The biasing device causes a further rotational movement after rotation by the rotary solenoid. Thus, energization of the rotary solenoid moves the member in one direction to one position and biases the biasing device against the member. Subsequently, de- energization of the rotary solenoid causes the biasing device to move the member in the same direction to another position from where the moving member is again movable by energization and de-energization of the rotary solenoid. Preferably, the moving member is a multi-lobed cam having the same number of lobes as the rotor has poles. An anti- overdrive device is also preferably provided for preventing overdrive in the forward direction or a reverse rotation of the moving member and for precisely aligning the moving member.

  17. Mechanically expandable annular seal

    DOE Patents [OSTI]

    Gilmore, R.F.

    1983-07-19

    A mechanically expandable annular reusable seal assembly to form an annular hermetic barrier between two stationary, parallel, and planar containment surfaces is described. A rotatable ring, attached to the first surface, has ring wedges resembling the saw-tooth array of a hole saw. Matching seal wedges are slidably attached to the ring wedges and have their motion restricted to be perpendicular to the second surface. Each seal wedge has a face parallel to the second surface. An annular elastomer seal has a central annular region attached to the seal wedges' parallel faces and has its inner and outer circumferences attached to the first surface. A rotation of the ring extends the elastomer seal's central region perpendicularly towards the second surface to create the fluid tight barrier. A counter rotation removes the barrier. 6 figs.

  18. Mechanically expandable annular seal

    DOE Patents [OSTI]

    Gilmore, Richard F. (Kennewick, WA)

    1983-01-01

    A mechanically expandable annular reusable seal assembly to form an annular hermetic barrier between two stationary, parallel, and planar containment surfaces. A rotatable ring, attached to the first surface, has ring wedges resembling the saw-tooth array of a hole saw. Matching seal wedges are slidably attached to the ring wedges and have their motion restricted to be perpendicular to the second surface. Each seal wedge has a face parallel to the second surface. An annular elastomer seal has a central annular region attached to the seal wedges' parallel faces and has its inner and outer circumferences attached to the first surface. A rotation of the ring extends the elastomer seal's central region perpendicularly towards the second surface to create the fluidtight barrier. A counterrotation removes the barrier.

  19. Rotary drive mechanism

    DOE Patents [OSTI]

    Kenderdine, Eugene W. (Albuquerque, NM)

    1991-01-01

    A rotary drive mechanism includes a rotary solenoid having a stator and multi-poled rotor. A moving member rotates with the rotor and is biased by a biasing device. The biasing device causes a further rotational movement after rotation by the rotary solenoid. Thus, energization of the rotary solenoid moves the member in one direction to one position and biases the biasing device against the member. Subsequently, de-energization of the rotary solenoid causes the biasing device to move the member in the same direction to another position from where the moving member is again movable by energization and de-energization of the rotary solenoid. Preferably, the moving member is a multi-lobed cam having the same number of lobes as the rotor has poles. An anti-overdrive device is also preferably provided for preventing overdrive in the forward direction or a reverse rotation of the moving member and for precisely aligning the moving member.

  20. Microfabricated therapeutic actuator mechanisms

    DOE Patents [OSTI]

    Northrup, M.A.; Ciarlo, D.R.; Lee, A.P.; Krulevitch, P.A.

    1997-07-08

    Electromechanical microstructures (microgrippers), either integrated circuit (IC) silicon-based or precision machined, to extend and improve the application of catheter-based interventional therapies for the repair of aneurysms in the brain or other interventional clinical therapies. These micromechanisms can be specifically applied to release platinum coils or other materials into bulging portions of the blood vessels also known as aneurysms. The ``micro`` size of the release mechanism is necessary since the brain vessels are the smallest in the body. Through a catheter more than one meter long, the micromechanism located at one end of the catheter can be manipulated from the other end thereof. The microgripper (micromechanism) of the invention will also find applications in non-medical areas where a remotely actuated microgripper or similar actuator would be useful or where micro-assembling is needed. 22 figs.

  1. Microfabricated therapeutic actuator mechanisms

    DOE Patents [OSTI]

    Northrup, Milton A.; Ciarlo, Dino R.; Lee, Abraham P.; Krulevitch, Peter A.

    1997-01-01

    Electromechanical microstructures (microgrippers), either integrated circuit (IC) silicon-based or precision machined, to extend and improve the application of catheter-based interventional therapies for the repair of aneurysms in the brain or other interventional clinical therapies. These micromechanisms can be specifically applied to release platinum coils or other materials into bulging portions of the blood vessels also known as aneurysms. The "micro" size of the release mechanism is necessary since the brain vessels are the smallest in the body. Through a catheter more than one meter long, the micromechanism located at one end of the catheter can be manipulated from the other end thereof. The microgripper (micromechanism) of the invention will also find applications in non-medical areas where a remotely actuated microgripper or similar actuator would be useful or where micro-assembling is needed.

  2. Quantitative Analysis of Clustered DNA Damages Induced by Silicon Beams of Different Kinetic Energy

    SciTech Connect (OSTI)

    Keszenman D. J.; Keszenman, D.J.; Bennett, P.V.; Sutherland, B.M.; Wilson, P.F.

    2013-05-14

    Humans may b exposed to highly energetic charged particle radiation as a result of medical treatments, occupational activitie or accidental events. In recent years, our increasing presence and burgeoning interest in space exploration beyond low Earth orbit has led to a large increase in the research of the biological effects ofcharged particle radiation typical of that encountered in the space radiation environment. The study of the effects of these types of radiation qualities in terms ofDNA damage induction and repair is fundamental to understand mechanisms both underlying their greater biological effectiveness as we)) as the short and long term risks of health effects such as carcinogenesis, degen rative diseases and premature aging. Charged particle radiation induces a variety of DNA alterations, notably bistranded clustered damages, defined as two or more closely-opposed strand break , oxidized bases or abasic sites within a few helical turns. The induction of such highly complex DNA damage enhances the probability of incorrect or incomplete repair and thus constitutes greater potential for genomic instability, cell death and transformation.

  3. Phase transformation and mechanical behavior in annealed 2205 duplex stainless steel welds

    SciTech Connect (OSTI)

    Badji, Riad Bouabdallah, Mabrouk; Bacroix, Brigitte; Kahloun, Charlie; Belkessa, Brahim; Maza, Halim

    2008-04-15

    The phase transformations and mechanical behaviour during welding and subsequent annealing treatment of 2205 duplex stainless steel have been investigated. Detailed microstructural examination showed the presence of higher ferrite amounts in the heat affected zone (HAZ), while higher amounts of austenite were recorded in the centre region of the weld metal. Annealing treatments in the temperature range of 800-1000 deg. C resulted in a precipitation of {sigma} phase and M{sub 23}C{sub 6} chromium carbides at the {gamma}/{delta} interfaces that were found to be preferential precipitation sites. Above 1050 deg. C, the volume fraction of {delta} ferrite increases with annealing temperature. The increase of {delta} ferrite occurs at a faster rate in the HAZ than in the base metal and fusion zone. Optimal mechanical properties and an acceptable ferrite/austenite ratio throughout the weld regions corresponds to annealing at 1050 deg. C. Fractographic examinations showed that the mode of failure changed from quasi-cleavage fracture to dimple rupture with an increase in the annealing temperature from 850 to 1050 deg. C.

  4. Diffusion-controlled reactions modeling in Geant4-DNA

    SciTech Connect (OSTI)

    Karamitros, M.; Luan, S.; Bernal, M.A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H.N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a kd tree data structure for quickly locating, for a given molecule, its closest reactants. The performance advantage is presented in terms of complexity, and the accuracy of the new algorithm is demonstrated by simulating radiation chemistry in the context of the Geant4-DNA project. Application The time-dependent radiolytic yields of the main chemical species formed after irradiation are computed for incident protons at different energies (from 50 MeV to 500 keV). Both the time-evolution and energy dependency of the yields are discussed. The evolution, at one microsecond, of the yields of hydroxyls and solvated electrons with respect to the linear energy transfer is compared to theoretical and experimental data. According to our results, at high linear energy transfer, modeling radiation chemistry in the trading compartment representation might be adopted.

  5. Fluid Dynamics and Solid Mechanics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Solid Mechanics Basic and applied research in theoretical continuum dynamics, modern hydrodynamic theory, materials modeling, global climate modeling, numerical...

  6. Automated DNA Base Pair Calling Algorithm

    Energy Science and Technology Software Center (OSTI)

    1999-07-07

    The procedure solves the problem of calling the DNA base pair sequence from two channel electropherogram separations in an automated fashion. The core of the program involves a peak picking algorithm based upon first, second, and third derivative spectra for each electropherogram channel, signal levels as a function of time, peak spacing, base pair signal to noise sequence patterns, frequency vs ratio of the two channel histograms, and confidence levels generated during the run. Themore »ratios of the two channels at peak centers can be used to accurately and reproducibly determine the base pair sequence. A further enhancement is a novel Gaussian deconvolution used to determine the peak heights used in generating the ratio.« less

  7. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect (OSTI)

    Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

    2011-11-29

    DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.

  8. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

  9. DNA damage in cells exhibiting radiation-induced genomic instability

    SciTech Connect (OSTI)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesis that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.

  10. Energy and Technology Review: Unlocking the mysteries of DNA repair

    SciTech Connect (OSTI)

    Quirk, W.A.

    1993-04-01

    DNA, the genetic blueprint, has the remarkable property of encoding its own repair following diverse types of structural damage induced by external agents or normal metabolism. We are studying the interplay of DNA damaging agents, repair genes, and their protein products to decipher the complex biochemical pathways that mediate such repair. Our research focuses on repair processes that correct DNA damage produced by chemical mutagens and radiation, both ionizing and ultraviolet. The most important type of DNA repair in human cells is called excision repair. This multistep process removes damaged or inappropriate pieces of DNA -- often as a string of 29 nucleotides containing the damage -- and replaces them with intact ones. We have isolated, cloned, and mapped several human repair genes associated with the nucleotide excision repair pathway and involved in the repair of DNA damage after exposure to ultraviolet light or mutagens in cooked food. We have shown that a defect in one of these repair genes, ERCC2, is responsible for the repair deficiency in one of the groups of patients with the recessive genetic disorder xeroderma pigmentosum (XP group D). We are exploring ways to purify sufficient quantities (milligrams) of the protein products of these and other repair genes so that we can understand their functions. Our long-term goals are to link defective repair proteins to human DNA repair disorders that predispose to cancer, and to produce DNA-repair-deficient mice that can serve as models for the human disorders.

  11. DNA damage in cells exhibiting radiation-induced genomic instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesismore » that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.« less

  12. DOI-BLM-NV-W030-2012-0011-DNA | Open Energy Information

    Open Energy Info (EERE)

    Notes GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DNA R&C Doc FINAL DOI-BLM-NV-W030-2012-0011-DNA.pdf...

  13. DOI-BLM-NV-C010-2013-0007-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 942013: DNA file uploaded Documents DNA Worksheet: DOI-BLM-NV-C010-2013-0007-DNA....

  14. DOI-BLM-NV-C010-2012-0020-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 8292013: DNA uploaded Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0020-DNA.pdf...

  15. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Structures of Clamp-Loader Complexes Are Key to DNA Replication Print Wednesday, 30 May 2012 00:00 DNA Replication:...

  16. An intercalation-locked parallel-stranded DNA tetraplex

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs betweenmore » adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  17. Sensitive method for measurement of telomeric DNA content in human tissues

    DOE Patents [OSTI]

    Bryant, Jennifer E.; Hutchings, Kent G.; Moyzis, Robert K.; Griffith, Jeffrey K.

    1999-02-16

    A sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue.

  18. DOI-BLM-NV-C010-2012-0073-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. 8292013- uploaded DNA and corrected lease number, incorrect on DNA form should be...

  19. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended...

  20. INL '@work' heavy equipment mechanic

    SciTech Connect (OSTI)

    Christensen, Cad

    2008-01-01

    INL's Cad Christensen is a heavy equipment mechanic. For more information about INL careers, visit http://www.facebook.com/idahonationallaboratory.

  1. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    12.3.2 to investigate the small-scale mechanics of indium nanostructures. Scanning x-ray microdiffraction (SXRD) studies revealed that the indium microstructure is typical...

  2. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Print The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit...

  3. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Auxin Regulation Mechanism Discovered Print Wednesday, 29 August 2007 00:00 The plant hormone auxin regulates many plant growth and development processes, including shoot growth,...

  4. INL '@work' heavy equipment mechanic

    ScienceCinema (OSTI)

    Christensen, Cad

    2013-05-28

    INL's Cad Christensen is a heavy equipment mechanic. For more information about INL careers, visit http://www.facebook.com/idahonationallaboratory.

  5. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1996-01-09

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form. The method comprises: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  6. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1996-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  7. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7{beta}, 8{alpha}-dihydoxy-9{alpha}, l0{alpha}-epoxy-7,8,9, 10-tetrahydrobenzo[{alpha}]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, ({minus})-trans-, (+)-cis- and ({minus})-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( {approximately} 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant {pi}-{pi} stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G{sub 2} or G{sub 3} (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N{sup 2}-dG in DNA isolated from the skin of mice treated topically with benzo[{alpha}]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N{sup 2}-dG.

  8. QUANTUM MECHANICS WITHOUT STATISTICAL POSTULATES

    SciTech Connect (OSTI)

    G. GEIGER; ET AL

    2000-11-01

    The Bohmian formulation of quantum mechanics describes the measurement process in an intuitive way without a reduction postulate. Due to the chaotic motion of the hidden classical particle all statistical features of quantum mechanics during a sequence of repeated measurements can be derived in the framework of a deterministic single system theory.

  9. Mechanical Solutions Inc | Open Energy Information

    Open Energy Info (EERE)

    Mechanical Solutions Inc Jump to: navigation, search Name: Mechanical Solutions Inc Place: New York Product: New York-based contractor. References: Mechanical Solutions Inc1 This...

  10. Vehicle Technologies Office Merit Review 2014: Fleet DNA

    Broader source: Energy.gov [DOE]

    Presentation given by National Renewable Energy Laboratory at 2014 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Office Annual Merit Review and Peer Evaluation Meeting about fleet DNA.

  11. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs...

    Office of Scientific and Technical Information (OSTI)

    tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of...

  12. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1998-11-03

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.

  13. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an...

  14. Charge Transport within a Three-Dimensional DNA Nanostructure...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Charge Transport within a Three-Dimensional DNA Nanostructure Framework Authors: Lu, N., Pei, H., Ge, Z., Simmons, C.R., Yan, H., and Fan, C. Title: Charge Transport within a...

  15. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1987-10-07

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

  16. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1990-10-09

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

  17. Method for rapid base sequencing in DNA and RNA

    DOE Patents [OSTI]

    Jett, James H.; Keller, Richard A.; Martin, John C.; Moyzis, Robert K.; Ratliff, Robert L.; Shera, E. Brooks; Stewart, Carleton C.

    1990-01-01

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed.

  18. Flow cytomeric measurement of DNA and incorporated nucleoside analogs

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1989-01-01

    A method is provided for simultaneously measuring total cellular DNA and incorporated nucleoside analog. The method entails altering the cellular DNA of cells grown in the presence of a nucleoside analog so that single stranded and double stranded portions are present. Separate stains are used against the two portions. An immunochemical stain is used against the single stranded portion to provide a measure of incorporated nucleoside analog, and a double strand DNA-specific stain is used against the double stranded portion to simultaneously provide a measure of total cellular DNA. The method permits rapid flow cytometric analysis of cell populations, rapid identification of cycling and noncycling subpopulations, and determination of the efficacy of S phase cytotoxic anticancer agents.

  19. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1998-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

  20. Statistical mechanics based on fractional classical and quantum mechanics

    SciTech Connect (OSTI)

    Korichi, Z.; Meftah, M. T.

    2014-03-15

    The purpose of this work is to study some problems in statistical mechanics based on the fractional classical and quantum mechanics. At first stage we have presented the thermodynamical properties of the classical ideal gas and the system of N classical oscillators. In both cases, the Hamiltonian contains fractional exponents of the phase space (position and momentum). At the second stage, in the context of the fractional quantum mechanics, we have calculated the thermodynamical properties for the black body radiation, studied the Bose-Einstein statistics with the related problem of the condensation and the Fermi-Dirac statistics.

  1. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, N.V.

    1994-01-04

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon. .

  2. Forensic DNA data banking by state crime labortaories

    SciTech Connect (OSTI)

    McEwen, J.E.

    1995-06-01

    This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs` policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI`s evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security. 9 refs., 3 tabs.

  3. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    1994-01-04

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  4. Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations.

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Abstract not provided. Authors: Sparks, Elizabeth Schares ; Manginell, Ronald Paul Publication Date: 2011-10-01 OSTI Identifier: 1106575 Report Number(s): SAND2011-7607C 464923 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: MSEC 105

  5. Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Jefferson Lab Upcoming Science Lectures on DNA and Chocolate NEWPORT NEWS, Va., Feb. 24, 2011 - Jefferson Lab will host a public lecture on March 29 titled DNA: The Strand That Connects Us All presented by Matt Kaplan from the Human Origins Genotyping Laboratory, Phoenix, Ariz. Kaplan will discuss how the methods and discoveries of human population genetics studies are applied for personal genealogical reconstruction and anthropological testing. Kaplan will start with a short general review

  6. DNA-Directed Artificial Light-Harvesting Antenna

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Directed Artificial Light-Harvesting Antenna Authors: Dutta, P. K., Varghese, R., Nangreave, J., Lin, S., Yan, H., and Liu, Y. Title: DNA-Directed Artificial Light-Harvesting Antenna Source: Journal of the American Chemical Society Year: 2011 Volume: 133 Pages: 11985-11993 ABSTRACT: Designing and constructing multichromophoric, artificial light-harvesting antennas with controlled interchromophore distances, orientations, and defined donor?acceptor ratios to facilitate efficient

  7. WRNIP1 functions upstream of DNA polymerase ? in the UV-induced DNA damage response

    SciTech Connect (OSTI)

    Yoshimura, Akari; Kobayashi, Yume; Tada, Shusuke; Seki, Masayuki; Enomoto, Takemi

    2014-09-12

    Highlights: The UV sensitivity of POLH{sup ?/?} cells was suppressed by disruption of WRNIP1. In WRNIP1{sup ?/?/?}/POLH{sup ?/?} cells, mutation frequencies and SCE after irradiation reduced. WRNIP1 defect recovered rate of fork progression after irradiation in POLH{sup ?/?} cells. WRNIP1 functions upstream of Pol? in the translesion DNA synthesis pathway. - Abstract: WRNIP1 (WRN-interacting protein 1) was first identified as a factor that interacts with WRN, the protein that is defective in Werner syndrome (WS). WRNIP1 associates with DNA polymerase ? (Pol?), but the biological significance of this interaction remains unknown. In this study, we analyzed the functional interaction between WRNIP1 and Pol? by generating knockouts of both genes in DT40 chicken cells. Disruption of WRNIP1 in Pol?-disrupted (POLH{sup ?/?}) cells suppressed the phenotypes associated with the loss of Pol?: sensitivity to ultraviolet light (UV), delayed repair of cyclobutane pyrimidine dimers (CPD), elevated frequency of mutation, elevated levels of UV-induced sister chromatid exchange (SCE), and reduced rate of fork progression after UV irradiation. These results suggest that WRNIP1 functions upstream of Pol? in the response to UV irradiation.

  8. Probing the Conformational Distributions of Sub-Persistence Length DNA

    SciTech Connect (OSTI)

    Mastroianni, Alexander; Sivak, David; Geissler, Phillip; Alivisatos, Paul

    2009-06-08

    We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.

  9. Phase space quantum mechanics - Direct

    SciTech Connect (OSTI)

    Nasiri, S.; Sobouti, Y.; Taati, F.

    2006-09-15

    Conventional approach to quantum mechanics in phase space (q,p), is to take the operator based quantum mechanics of Schroedinger, or an equivalent, and assign a c-number function in phase space to it. We propose to begin with a higher level of abstraction, in which the independence and the symmetric role of q and p is maintained throughout, and at once arrive at phase space state functions. Upon reduction to the q- or p-space the proposed formalism gives the conventional quantum mechanics, however, with a definite rule for ordering of factors of noncommuting observables. Further conceptual and practical merits of the formalism are demonstrated throughout the text.

  10. The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Otani, Hiroshi; Stogios, Peter J.; Xu, Xiaohui; Nocek, Boguslaw; Li, Shu -Nan; Savchenko, Alexei; Eltis, Lindsay D.

    2015-09-22

    CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl–CoA (Kd = 11 ± 1 μM). The presence of p-coumaroyl–CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA in vitro. The crystal structures of ligand-free CouR and its p-coumaroyl–CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR–p-coumaroyl–CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer and their CoAmore » moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl–CoA (Kd = 89 ± 6 μM). Altogether, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.« less

  11. Durability Improvements Through Degradation Mechanism Studies...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Degradation Mechanism Studies Durability Improvements Through Degradation Mechanism Studies Presented at the Department of Energy Fuel Cell Projects Kickoff Meeting,...

  12. Sandia Energy - Statistical Mechanics with Density Functional...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Statistical Mechanics with Density Functional Theory Accuracy Home Highlights - HPC Statistical Mechanics with Density Functional Theory Accuracy Previous Next Statistical...

  13. Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid

    SciTech Connect (OSTI)

    Hata, Kuniki; Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 ; Urushibara, Ayumi; Yamashita, Shinichi; Shikazono, Naoya; Yokoya, Akinari; Katsumura, Yosuke; Nuclear Professional School, School of Engineering, The University of Tokyo, 2-22 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1188

    2013-05-03

    Highlights: We report a novel mechanism of radiation protection of DNA by chemical activity of ascorbic acid. The chemical repair of DNA damage was revealed using biochemical assay and chemical kinetics analysis. We found that ascorbic acid significantly repairs precursors of nucleobase lesions and abasic sites. However, ascorbic acid seldom repairs precursors of DNA-strand breaks. -- Abstract: We quantified the damage yields produced in plasmid DNA by ?-irradiation in the presence of low concentrations (10100 ?M) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield of DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins. By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 5060% of base lesions and AP-sites were repaired by 10 ?M ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.

  14. Mechanically balanced tapered plug valve

    DOE Patents [OSTI]

    Anaya, Jose R. (Coacalco, MX)

    1985-01-01

    The invention is a novel hermetic tapered plug valve having a spring-like resilient mechanism for providing axial balance to the plug and thereby prevent valve lock up.

  15. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Publication about this research: G. Lee, J.Y. Kim, A.S. Budiman, N. Tamura, M. Kunz, K. Chen, M.J. Burek, J.R. Greer, and T.Y. Tsui, "Fabrication, structure and mechanical...

  16. An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996

    SciTech Connect (OSTI)

    Netzel, T.L.

    1997-03-01

    The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.

  17. Cytogenetic status and oxidative DNA-damage induced by atorvastatin in human peripheral blood lymphocytes: Standard and Fpg-modified comet assay

    SciTech Connect (OSTI)

    Gajski, Goran Garaj-Vrhovac, Vera; Orescanin, Visnja

    2008-08-15

    To investigate the genotoxic potential of atorvastatin on human lymphocytes in vitro standard comet assay was used in the evaluation of basal DNA damage and to investigate possible oxidative DNA damage produced by reactive oxygen species (ROS) Fpg-modified version of comet assay was also conducted. In addition to these techniques the new criteria for scoring micronucleus test were applied for more complete detection of baseline damage in binuclear lymphocytes exposed to atorvastatin 80 mg/day in different time periods by virtue of measuring the frequency of micronuclei, nucleoplasmic bridges and nuclear buds. All parameters obtained with the standard comet assay and Fpg-modified comet assay were significantly higher in the treated than in control lymphocytes. The Fpg-modified comet assay showed a significantly greater tail length, tail intensity, and tail moment in all treated lymphocytes than did the standard comet assay, which suggests that oxidative stress is likely to be responsible for DNA damage. DNA damage detected by the standard comet assay indicates that some other mechanism is also involved. In addition to the comet assay, a total number of micronuclei, nucleoplasmic bridges and nuclear buds were significantly higher in the exposed than in controlled lymphocytes. Regression analyses showed a positive correlation between the results obtained by the comet (Fpg-modified and standard) and micronucleus assay. Overall, the study demonstrated that atorvastatin in its highest dose is capable of producing damage on the level of DNA molecule and cell.

  18. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Unique Auxin Regulation Mechanism Discovered Print Wednesday, 29 August 2007 00:00 The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit ripening, tropisms, and flowering. But how such a simple molecule elicits such a variety of cellular responses has been a mystery. An important breakthrough came in 2005, wh en a conserved plant protein known as TIR1 (part of a protein destruction

  19. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  20. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  1. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  2. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  3. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  4. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  5. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of

  6. Mechanical Behavior of Indium Nanostructures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Behavior of Indium Nanostructures Mechanical Behavior of Indium Nanostructures Print Wednesday, 26 May 2010 00:00 Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale

  7. Mechanical Response of Thermoelectric Materials

    SciTech Connect (OSTI)

    Wereszczak, Andrew A.; Case, Eldon D.

    2015-05-01

    A sufficient mechanical response of thermoelectric materials (TEMats) to structural loadings is a prerequisite to the exploitation of any candidate TEMat's thermoelectric efficiency. If a TEMat is mechanically damaged or cracks from service-induced stresses, then its thermal and electrical functions can be compromised or even cease. Semiconductor TEMats tend to be quite brittle and have a high coefficient of thermal expansion; therefore, they can be quite susceptible to mechanical failure when subjected to operational thermal gradients. Because of this, sufficient mechanical response (vis-a-vis, mechanical properties) of any candidate TEMat must be achieved and sustained in the context of the service-induced stress state to which it is subjected. This report provides an overview of the mechanical responses of state-of-the-art TEMats; discusses the relevant properties that are associated with those responses and their measurement; and describes important, nonequilibrium phenomena that further complicate their use in thermoelectric devices. For reference purposes, the report also includes several appendixes that list published data on elastic properties and strengths of a variety of TEMats.

  8. Endogenous DNA Damage and Risk of Testicular Germ Cell Tumors

    SciTech Connect (OSTI)

    Cook, M B; Sigurdson, A J; Jones, I M; Thomas, C B; Graubard, B I; Korde, L; Greene, M H; McGlynn, K A

    2008-01-18

    Testicular germ cell tumors (TGCT) are comprised of two histologic groups, seminomas and nonseminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable endogenous DNA damage. To assess our hypothesis, we conducted a case-case analysis of seminomas and nonseminomas using the alkaline comet assay to quantify single-strand DNA breaks and alkali-labile sites. The Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort provided 112 TGCT cases (51 seminomas & 61 nonseminomas). A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95%CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modeled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with nonseminoma compared to seminoma (OR{sub 50th percentile} = 3.31, 95%CI: 1.00, 10.98; OR{sub 75th percentile} = 3.71, 95%CI: 1.04, 13.20; p for trend=0.039). OTM exhibited similar, albeit statistically non-significant, risk estimates (OR{sub 50th percentile} = 2.27, 95%CI: 0.75, 6.87; OR{sub 75th percentile} = 2.40, 95%CI: 0.75, 7.71; p for trend=0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that endogenous DNA damage levels are higher in patients who develop nonseminoma compared with seminoma. This may partly explain the more aggressive biology and younger age-of-onset of this histologic subgroup compared with the relatively less aggressive, later-onset seminoma.

  9. Structural Origins of DNA Target Selection and Nucleobase Extrusion by a

    Office of Scientific and Technical Information (OSTI)

    DNA Cytosine Methyltransferase (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase Citation Details In-Document Search Title: Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase Authors: Didovyk, Andriy ; Verdine, Gregory L. [1] ; DFCI) [2] + Show Author Affiliations (Harvard) ( Publication Date: 2013-03-04

  10. Zinc chromate induces chromosome instability and DNA double strand breaks in human lung cells

    SciTech Connect (OSTI)

    Xie Hong; Holmes, Amie L.; Young, Jamie L.; Qin Qin; Joyce, Kellie; Pelsue, Stephen C.; Peng Cheng; Wise, Sandra S.; Jeevarajan, Antony S.; Wallace, William T.; Hammond, Dianne; Wise, John Pierce E-mail: John.Wise@usm.maine.edu

    2009-02-01

    Hexavalent chromium Cr(VI) is a respiratory toxicant and carcinogen, with solubility playing an important role in its carcinogenic potential. Zinc chromate, a water insoluble or 'particulate' Cr(VI) compound, has been shown to be carcinogenic in epidemiology studies and to induce tumors in experimental animals, but its genotoxicity is poorly understood. Our study shows that zinc chromate induced concentration-dependent increases in cytotoxicity, chromosome damage and DNA double strand breaks in human lung cells. In response to zinc chromate-induced breaks, MRE11 expression was increased and ATM and ATR were phosphorylated, indicating that the DNA double strand break repair system was initiated in the cells. In addition, our data show that zinc chromate-induced double strand breaks were only observed in the G2/M phase population, with no significant amount of double strand breaks observed in G1 and S phase cells. These data will aid in understanding the mechanisms of zinc chromate toxicity and carcinogenesis.

  11. Water versus DNA: New insights into proton track-structure modeling in radiobiology and radiotherapy

    SciTech Connect (OSTI)

    Champion, Christophe; Galassi, Mariel E.; Weck, Philippe F.; Fojon, Omar A.; Hanssen, Jocelyn; Rivarola, Roberto D.

    2015-09-25

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Thus the consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  12. Construction and biological activities of the first infectious cDNA clones of the genus Foveavirus

    SciTech Connect (OSTI)

    Meng, Baozhong; Venkataraman, Srividhya; Li, Caihong; Wang, Weizhou; Dayan-Glick, Cathy; Mawassi, Munir

    2013-01-20

    Grapevine rupestris stem pitting-associated virus (GRSPaV, genus Foveavirus, family Betaflexiviridae) is one of the most prevalent viruses in grapevines and is associated with three distinct diseases: rupestris stem pitting, vein necrosis and Syrah decline. Little is known about the biology and pathological properties of GRSPaV. In this work, we engineered a full-length infectious cDNA clone for GRSPaV and a GFP-tagged variant, both under the transcriptional control of Cauliflower mosaic virus 35 S promoter. We demonstrated that these cDNA clones were infectious in grapevines and Nicotiana benthamiana through fluorescence microscopy, RT-PCR, Western blotting and immuno electron microscopy. Interestingly, GRSPaV does not cause systemic infection in four of the most commonly used herbaceous plants, even in the presence of the movement proteins of two other viruses which are known to complement numerous movement-defective viruses. These infectious clones are the first of members of Foveavirus which would allow further investigations into mechanisms governing different aspects of replication for GRSPaV and perhaps related viruses.

  13. Water versus DNA: New insights into proton track-structure modeling in radiobiology and radiotherapy

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Champion, Christophe; Quinto, Michele A.; Monti, Juan M.; Galassi, Mariel E.; Weck, Philippe F.; Fojon, Omar A.; Hanssen, Jocelyn; Rivarola, Roberto D.

    2015-09-25

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well asmore » their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Thus the consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.« less

  14. A new structural framework for integrating replication protein A into DNA processing machinery

    SciTech Connect (OSTI)

    Brosey, Chris; Yan, Chunli; Tsutakawa, Susan; Heller, William; Rambo, Robert; Tainer, John; Ivanov, Ivaylo; Chazin, Walter

    2013-01-17

    By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

  15. Process of labeling specific chromosomes using recombinant repetitive DNA

    DOE Patents [OSTI]

    Moyzis, R.K.; Meyne, J.

    1988-02-12

    Chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family members and consensus sequences of the repetitive DNA families for the chromosome preferential sequences. The selected low homology regions are then hybridized with chromosomes to determine those low homology regions hybridized with a specific chromosome under normal stringency conditions.

  16. New Catalytic DNA Biosensors for Radionuclides and Metal ion

    SciTech Connect (OSTI)

    Yi Lu

    2008-03-01

    We aim to develop new DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides, such as uranium, technetium, and plutonium, and metal contaminants, such as lead, chromium, and mercury. The sensors will be highly sensitive and selective. They will be applied to on-site, real-time assessment of concentration, speciation, and stability of the individual contaminants before and during bioremediation, and for long-term monitoring of DOE contaminated sites. To achieve this goal, we have employed a combinatorial method called in vitro selection to search from a large DNA library (~ 1015 different molecules) for catalytic DNA molecules that are highly specific for radionuclides or other metal ions through intricate 3-dimensional interactions as in metalloproteins. Comprehensive biochemical and biophysical studies have been performed on the selected DNA molecules. The findings from these studies have helped to elucidate fundamental principles for designing effective sensors for radionuclides and metal ions. Based on the study, the DNA have been converted to fluorescent or colorimetric sensors by attaching to it fluorescent donor/acceptor pairs or gold nanoparticles, with 11 part-per-trillion detection limit (for uranium) and over million fold selectivity (over other radionuclides and metal ions tested). Practical application of the biosensors for samples from the Environmental Remediation Sciences Program (ERSP) Field Research Center (FRC) at Oak Ridge has also been demonstrated.

  17. Majorana Electroformed Copper Mechanical Analysis

    SciTech Connect (OSTI)

    Overman, Nicole R.; Overman, Cory T.; Kafentzis, Tyler A.; Edwards, Danny J.; Hoppe, Eric W.

    2012-04-30

    The MAJORANA DEMONSTRATOR is a large array of ultra-low background high-purity germanium detectors, enriched in 76Ge, designed to search for zero-neutrino double-beta decay. The DEMONSTRATOR will utilize ultra high purity electroformed copper for a variety of detector components and shielding. A preliminary mechanical evaluation was performed on the Majorana prototype electroformed copper material. Several samples were removed from a variety of positions on the mandrel. Tensile testing, optical metallography, scanning electron microscopy, and hardness testing were conducted to evaluate mechanical response. Analyses carried out on the Majorana prototype copper to this point show consistent mechanical response from a variety of test locations. Evaluation shows the copper meets or exceeds the design specifications.

  18. Negative hydrogen ion production mechanisms

    SciTech Connect (OSTI)

    Bacal, M.; Wada, M.

    2015-06-15

    Negative hydrogen/deuterium ions can be formed by processes occurring in the plasma volume and on surfaces facing the plasma. The principal mechanisms leading to the formation of these negative ions are dissociative electron attachment to ro-vibrationally excited hydrogen/deuterium molecules when the reaction takes place in the plasma volume, and the direct electron transfer from the low work function metal surface to the hydrogen/deuterium atoms when formation occurs on the surface. The existing theoretical models and reported experimental results on these two mechanisms are summarized. Performance of the negative hydrogen/deuterium ion sources that emerged from studies of these mechanisms is reviewed. Contemporary negative ion sources do not have negative ion production electrodes of original surface type sources but are operated with caesium with their structures nearly identical to volume production type sources. Reasons for enhanced negative ion current due to caesium addition to these sources are discussed.

  19. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, M.D.; Soares, M.B.

    1997-12-30

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

  20. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, Maria DeFatima (New York, NY); Soares, Marcelo Bento (New York, NY)

    1997-01-01

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

  1. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  2. Battery Vent Mechanism And Method

    DOE Patents [OSTI]

    Ching, Larry K. W. (Littleton, CO)

    2000-02-15

    Disclosed herein is a venting mechanism for a battery. The venting mechanism includes a battery vent structure which is located on the battery cover and may be integrally formed therewith. The venting mechanism includes an opening extending through the battery cover such that the opening communicates with a plurality of battery cells located within the battery case. The venting mechanism also includes a vent manifold which attaches to the battery vent structure. The vent manifold includes a first opening which communicates with the battery vent structure opening and second and third openings which allow the vent manifold to be connected to two separate conduits. In this manner, a plurality of batteries may be interconnected for venting purposes, thus eliminating the need to provide separate vent lines for each battery. The vent manifold may be attached to the battery vent structure by a spin-welding technique. To facilitate this technique, the vent manifold may be provided with a flange portion which fits into a corresponding groove portion on the battery vent structure. The vent manifold includes an internal chamber which is large enough to completely house a conventional battery flame arrester and overpressure safety valve. In this manner, the vent manifold, when installed, lessens the likelihood of tampering with the flame arrester and safety valve.

  3. Mechanical scriber for semiconductor devices

    DOE Patents [OSTI]

    Lin, Peter T. (East Brunswick, NJ)

    1985-01-01

    A mechanical scriber using a scribing tip, such as a diamond, provides controlled scriber forces with a spring-loaded compound lever arrangement. The scribing force and range of scribing depth are adjusted by a pair of adjustable micrometer heads. A semiconductor device, such as a multilayer solar cell, can be formed into scribed strips at each layer.

  4. Mechanical scriber for semiconductor devices

    DOE Patents [OSTI]

    Lin, P.T.

    1985-03-05

    A mechanical scriber using a scribing tip, such as a diamond, provides controlled scriber forces with a spring-loaded compound lever arrangement. The scribing force and range of scribing depth are adjusted by a pair of adjustable micrometer heads. A semiconductor device, such as a multilayer solar cell, can be formed into scribed strips at each layer. 5 figs.

  5. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

    DOE Patents [OSTI]

    Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

    2010-05-04

    A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

  6. Mechanical effects in cookoff modeling

    SciTech Connect (OSTI)

    Gross, R.J.; Baer, M.R.; Hobbs, M.L.

    1994-07-01

    Complete cookoff modeling of energetic material in confined geometries must couple thermal, chemical and mechanical effects. In the past, modeling has focused on the prediction of the onset of combustion behavior based only on thermal-chemistry effects with little or no regard to the mechanical behavior of the energetic material. In this paper, an analysis tool is outlined which couples thermal, chemical, and mechanical behavior for one-dimensional Geometries comprised of multi-materials. A reactive heat flow code, XCHEM, and a quasistatic mechanics code, SANTOS, have been completely coupled using, a reactive, elastic-plastic constitutive model describing pressurization of the energetic material. This new Thermally Reactive Elastic-plastic explosive code, TREX, was developed to assess the coupling, of mechanics with thermal chemistry making multidimensional cookoff analysis possible. In this study, TREX is applied to confined and unconfined systems. The confined systems simulate One-Dimensional Time to explosion (ODTX) experiments in both spherical and cylindrical configurations. The spherical ODTX system is a 1.27 cm diameter sphere of TATB confined by aluminum exposed to a constant external temperature. The cylindrical ODTX system is an aluminum tube filled with HMX, NC, and inert exposed to a constant temperature bath. Finally. an unconfined system consisting of a hollow steel cylinder filled with a propellant composed of Al, RMX, and NC, representative of a rocket motor, is considered. This model system is subjected to transient internal and external radiative/convective boundary conditions representative of 5 minutes exposure to a fire. The confined systems show significant pressure prior to ignition, and the unconfined system shows extrusion of the propellent suggesting that the energetic material becomes more shock sensitive.

  7. Career Map: Mechanical Engineer | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Mechanical Engineer Career Map: Mechanical Engineer A mechanical engineer works with a large yellow robotic arm. Mechanical Engineer Position Title Mechanical Engineer Alternate Title(s) Project Engineer, Quality Engineer, Research Engineer, Design Engineer, Sales Engineer Education & Training Level Advanced, Bachelor's degree required, prefer graduate degree Education & Training Level Description Mechanical engineers need a bachelor's degree. A graduate degree is typically needed for

  8. DNA encoding for plant digalactosyldiacylglycerol galactosyltransferase and methods of use

    DOE Patents [OSTI]

    Benning, Christoph; Doermann, Peter

    2003-11-04

    The cDNA encoding digalactosyldiacylglycerol galactosyltransferase (DGD1) is provided. The deduced amino acid sequence is also provided. Methods of making and using DGD1 to screen for new herbicides and alter a plant's leaf lipid composition are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors.

  9. An overview of DNA fingerprinting with sup 32 P nucleotides

    SciTech Connect (OSTI)

    Pappas, G.G.

    1992-01-01

    The DNA probes radiolabeled with {sup 32}P, a primary tool employed by researchers in the life sciences for > 20 yr, are used by private companies, state-run laboratories, and the FBI to generate autoradiographs displaying the unique banding patterns that constitute the DNA fingerprint. The ability to identify an individual or animal from a biological sample has profound implications. Unidentified bodies, unrecognizable remains, and missing children can be tested and the DNA fingerprint compared to those of family members for positive identification. Paternity can be established before a child's birth. Immigration disputes can easily be resolved. Other uses include pedigree determination and testing for cell-line cross-contamination. Using a DNA fingerprint to determine the guilt or innocence of an individual allegedly involved in a violent crime is very controversial and has great legal and moral implications for society. Forensic laboratories have been challenged to ensure a level of quality control and quality assurance consistent with the weight given to these tests when used as evidence in a court of law.

  10. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    SciTech Connect (OSTI)

    Lu, Yi

    2003-06-01

    The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.

  11. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    SciTech Connect (OSTI)

    Lu, Yi

    2002-06-01

    The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize.

  12. Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McInerney, Peter; Adams, Paul; Hadi, Masood Z.

    2014-01-01

    As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR applications, including 3 polymerases typically used for cloning applications requiring high fidelity. Errormore » rate measurement values reported here were obtained by direct sequencing of cloned PCR products. The strategy employed here allows interrogation of error rate across a very large DNA sequence space, since 94 unique DNA targets were used as templates for PCR cloning. The six enzymes included in the study, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu , Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. Mutation spectra are reported, with the 3 high fidelity enzymes displaying broadly similar types of mutations. For these enzymes, transition mutations predominate, with little bias observed for type of transition.« less

  13. Derivatized versions of ligase enzymes for constructing DNA sequences

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Tucker, James D. (Novi, MN); Dzenitis, John M. (Livermore, CA); Papavasiliou, Alexandros P. (Oakland, CA)

    2006-08-15

    A method of making very long, double-stranded synthetic poly-nucleotides. A multiplicity of short oligonucleotides is provided. The short oligonucleotides are sequentially hybridized to each other. Enzymatic ligation of the oligonucleotides provides a contiguous piece of PCR-ready DNA of predetermined sequence.

  14. NREL: Technology Transfer - Popular Mechanics: Scientists Break...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Popular Mechanics: Scientists Break This Virtual Power Grid to Save the Real One July 27, 2015 Popular Mechanics describes how NREL's Energy Systems Integration Facility (ESIF)...

  15. Shaoxing Jinggong Mechanical and Electrical Research Institute...

    Open Energy Info (EERE)

    Shaoxing Jinggong Mechanical and Electrical Research Institute Company SJMERI Jump to: navigation, search Name: Shaoxing Jinggong Mechanical and Electrical Research Institute...

  16. Multiple Mechanisms of Uranium Immobilization by Cellulomonas...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Multiple Mechanisms of Uranium Immobilization by Cellulomonas sp. Strain ES6 Citation Details In-Document Search Title: Multiple Mechanisms of Uranium ...

  17. Excitation Energy Sorting Mechanisms in Fission (Conference)...

    Office of Scientific and Technical Information (OSTI)

    Excitation Energy Sorting Mechanisms in Fission Citation Details In-Document Search Title: Excitation Energy Sorting Mechanisms in Fission You are accessing a document from the...

  18. CONTROL OF MECHANICALLY ACTIVATED POLYMERSOME FUSION: FACTORS...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Journal Article: CONTROL OF MECHANICALLY ACTIVATED POLYMERSOME FUSION: FACTORS AFFECTING FUSION. Citation Details In-Document Search Title: CONTROL OF MECHANICALLY ACTIVATED...

  19. Mechanism and Substrate Recognition of 2-Hydroxyethylphosphonate...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: Mechanism and Substrate Recognition of 2-Hydroxyethylphosphonate Dioxygenase Citation Details In-Document Search Title: Mechanism ...

  20. Sandia National Laboratories: Careers: Mechanical Engineering

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    at Sandia Applied mechanics Modeling and simulation Conceptual and mechanical design definition Material selection and fabrication oversight Stress, dynamic, and thermal analysis...

  1. Chemically assisted mechanical refrigeration process

    DOE Patents [OSTI]

    Vobach, A.R.

    1987-06-23

    There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator. 5 figs.

  2. Chemically assisted mechanical refrigeration process

    DOE Patents [OSTI]

    Vobach, Arnold R.

    1987-01-01

    There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer (11) at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer (11) to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator (10) to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator.

  3. Chemically assisted mechanical refrigeration process

    DOE Patents [OSTI]

    Vobach, Arnold R.

    1987-01-01

    There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer (11) at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer (11) to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator (10) to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing he evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator.

  4. Chemically assisted mechanical refrigeration process

    DOE Patents [OSTI]

    Vobach, A.R.

    1987-11-24

    There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator. 5 figs.

  5. Locking mechanism for indexing device

    DOE Patents [OSTI]

    Lindemeyer, Carl W. (Aurora, IL)

    1984-01-01

    Disclosed is a locking mechanism for an indexing spindle. A conventional r gear having outwardly extending teeth is affixed to the spindle. Also included is a rotatably mounted camshaft whose axis is arranged in skewed relationship with the axis of the spindle. A disk-like wedge having opposing camming surfaces is eccentrically mounted on the camshaft. As the camshaft is rotated, the camming surfaces of the disc-like member are interposed between adjacent gear teeth with a wiping action that wedges the disc-like member between the gear teeth. A zero backlash engagement between disc-like member and gear results, with the engagement having a high mechanical advantage so as to effectively lock the spindle against bidirectional rotation.

  6. Mechanisms of Low Dose Radio-Suppression of Genomic Instability

    SciTech Connect (OSTI)

    Engelward, Bevin P

    2009-09-16

    The major goal of this project is to contribute toward the elucidation of the impact of long term low dose radiation on genomic stability. We have created and characterized novel technologies for delivering long term low dose radiation to animals, and we have studied genomic stability by applying cutting edge molecular analysis technologies. Remarkably, we have found that a dose rate that is 300X higher than background radiation does not lead to any detectable genomic damage, nor is there any significant change in gene expression for genes pertinent to the DNA damage response. These results point to the critical importance of dose rate, rather than just total dose, when evaluating public health risks and when creating regulatory guidelines. In addition to these studies, we have also further developed a mouse model for quantifying cells that have undergone a large scale DNA sequence rearrangement via homologous recombination, and we have applied these mice in studies of both low dose radiation and space radiation. In addition to more traditional approaches for assessing genomic stability, we have also explored radiation and possible beneficial effects (adaptive response), long term effects (persistent effects) and effects on communication among cells (bystander effects), both in vitro and in vivo. In terms of the adaptive response, we have not observed any significant induction of an adaptive response following long term low dose radiation in vivo, delivered at 300X background. In terms of persistent and bystander effects, we have revealed evidence of a bystander effect in vivo and with researchers at and demonstrated for the first time the molecular mechanism by which cells remember radiation exposure. Understanding the underlying molecular mechanisms by which radiation can induce genomic instability is fundamental to our ability to assess the biological impact of low dose radiation. Finally, in a parallel set of studies we have explored the effects of heavy iron particle radiation on large scale sequence rearrangements and we have discovered tissue specific differences in sensitivity to homologous recombination. DOE support has given rise to critical new knowledge about the biological impact of low dose rate radiation and about the underlying mechanisms that govern genomic stability in response to radiation exposure. This work has spurred interest in radiation among MIT scientists, and has fostered ongoing research projects that will continue to contribute toward our understanding of the biological effects of low dose radiation exposure.

  7. Mechanical Engineering Department Technical Review

    SciTech Connect (OSTI)

    Carr, R.B.; Denney, R.M.

    1981-07-01

    The Mechanical Engineering Department Technical Review is published to inform readers of various technical activities within the Department, promote exchange of ideas, and give credit to personnel who are achieving the results. The report is presented in two parts: technical achievements and publication abstracts. The first is divided into seven sections, each of which reports on an engineering division and its specific activities related to nuclear tests, nuclear explosives, weapons, energy systems, engineering sciences, magnetic fusion, and materials fabrication.

  8. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Print The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit ripening, tropisms, and flowering. But how such a simple molecule elicits such a variety of cellular responses has been a mystery. An important breakthrough came in 2005, wh en a conserved plant protein known as TIR1 (part of a protein destruction machinery system) was identified as a receptor for auxin. Now, an

  9. Particle Suspension Mechanisms - Supplemental Material

    SciTech Connect (OSTI)

    Dillon, M B

    2011-03-03

    This supplemental material provides a brief introduction to particle suspension mechanisms that cause exfoliated skin cells to become and remain airborne. The material presented here provides additional context to the primary manuscript and serves as background for designing possible future studies to assess the impact of skin cells as a source of infectious aerosols. This introduction is not intended to be comprehensive and interested readers are encouraged to consult the references cited.

  10. Mechanical Engineering Department technical abstracts

    SciTech Connect (OSTI)

    Denney, R.M.

    1982-07-01

    The Mechanical Engineering Department publishes listings of technical abstracts twice a year to inform readers of the broad range of technical activities in the Department, and to promote an exchange of ideas. Details of the work covered by an abstract may be obtained by contacting the author(s). Overall information about current activities of each of the Department's seven divisions precedes the technical abstracts.

  11. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Print The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit ripening, tropisms, and flowering. But how such a simple molecule elicits such a variety of cellular responses has been a mystery. An important breakthrough came in 2005, wh en a conserved plant protein known as TIR1 (part of a protein destruction machinery system) was identified as a receptor for auxin. Now, an

  12. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Print The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit ripening, tropisms, and flowering. But how such a simple molecule elicits such a variety of cellular responses has been a mystery. An important breakthrough came in 2005, wh en a conserved plant protein known as TIR1 (part of a protein destruction machinery system) was identified as a receptor for auxin. Now, an

  13. Unique Auxin Regulation Mechanism Discovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unique Auxin Regulation Mechanism Discovered Print The plant hormone auxin regulates many plant growth and development processes, including shoot growth, root branching, fruit ripening, tropisms, and flowering. But how such a simple molecule elicits such a variety of cellular responses has been a mystery. An important breakthrough came in 2005, wh en a conserved plant protein known as TIR1 (part of a protein destruction machinery system) was identified as a receptor for auxin. Now, an

  14. GUI for Structural Mechanics Codes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Development of GUI for Structural Mechanics Codes The TRACC Cluster gives its users a lot of flexibility when it comes to requesting software version of LS-DYNA and computational resources for submitted jobs. To fully utilize that flexibility, users need to get familiar with on-line documentation of all the installed releases of different software and modules on the cluster. As on other LINUX based HPC systems, the submission and controlling of LS-DYNA is done through text commands. Especially

  15. Mechanical engineering department technical review

    SciTech Connect (OSTI)

    Carr, R.B. Denney, R.M.

    1981-01-01

    The Mechanical Engineering Department Technical Review is published to: (1) inform the readers of various technical activities within the department, (2) promote exchange of ideas, and (3) give credit to the personnel who are achieving the results. The report is formatted into two parts: technical acievements and publication abstracts. The first is divided into eight sections, one for each division in the department providing the reader with the names of the personnel and the division accomplishing the work.

  16. Mechanism of instantaneous coal outbursts

    SciTech Connect (OSTI)

    Guan, P.; Wang, H.Y.; Zhang, Y.X.

    2009-10-15

    Thousands of mine workers die every year from mining accidents, and instantaneous coal outbursts in underground coal mines are one of the major killers. Various models for these outbursts have been proposed, but the precise mechanism is still unknown. We hypothesize that the mechanism of coal outbursts is similar to magma fragmentation during explosive volcanic eruptions; i.e., it is caused by high gas pressure inside coal but low ambient pressure on it, breaking coal into pieces and releasing the high-pressure gas in a shock wave. Hence, coal outbursts may be regarded as another type of gas-driven eruption, in addition to explosive volcanic, lake, and possible ocean eruptions. We verify the hypothesis by experiments using a shock-tube apparatus. Knowing the mechanism of coal outbursts is the first step in developing prediction and mitigation measures. The new concept of gas-driven solid eruption is also important to a better understanding of salt-gas outbursts, rock-gas outbursts, and mud volcano eruptions.

  17. Sensitive method for measurement of telomeric DNA content in human tissues

    DOE Patents [OSTI]

    Bryant, J.E.; Hutchings, K.G.; Moyzis, R.K.; Griffith, J.K.

    1999-02-16

    This research discloses a sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue. 5 figs.

  18. DOI-BLM-NV-C010-2012-0028-DNA | Open Energy Information

    Open Energy Info (EERE)

    DNA at Dead Horse Wells Geothermal Area for GeothermalWell Field DNA for Flow Test Well 85-11 and Simultaneously Injection Test Well 68-1 and 24A-6 at Dead Horse Wells...

  19. DOI-BLM-NV-C010-2012-0019-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0019-DNA.pdf Retrieved from "http:...

  20. DOI-BLM-NV-C010-2012-0068-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0068-DNA.pdf Retrieved from "http:...

  1. DOI-BLM-NV-C010-2012-0016-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0016-DNA.pdf Retrieved from "http:...

  2. DOI-BLM-NV-C010-2012-0048-DNA | Open Energy Information

    Open Energy Info (EERE)

    Notes GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0048-DNA.pdf Retrieved from "http:...

  3. DOI-BLM-NV-C010-2012-0058-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0058-DNA.pdf Retrieved from "http:...

  4. DOI-BLM-NV-C010-2012-0046-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2012-0046-DNA.pdf Retrieved from "http:...

  5. DOI-BLM-NV-C010-2013-0023-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2013-0023-DNA.pdf Retrieved from "http:...

  6. DOI-BLM-NV-C010-2013-0020-DNA | Open Energy Information

    Open Energy Info (EERE)

    GDP from BLM's Grass Wells Database, LR2000 SRPs, or State Mineral Commissions Databases. Documents DNA Worksheet: DOI-BLM-NV-C010-2013-0020-DNA.pdf Retrieved from "http:...

  7. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Print DNA Replication: An Open-and-Shut Case Every time a cell divides, whether in humans or in other organisms, its...

  8. Lipid phase control of DNA delivery (Journal Article) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: Lipid phase control of DNA delivery Citation Details In-Document Search Title: Lipid phase control of DNA delivery Cationic lipids ...

  9. Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2...

    Office of Scientific and Technical Information (OSTI)

    Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Citation Details In-Document Search Title: Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 ...

  10. Molecular behavior of DNA origami in higher order self-assembly

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Molecular behavior of DNA origami in higher order self-assembly Authors: Li, Z., Liu, M., Wang, L., Nangreave, J., Yan, H., and Liu, Y. Title: Molecular behavior of DNA origami in...

  11. MOLECULAR MECHANISM OF SUPPRESSION OF NEOPLASTIC TRANSFORMATION BY LOW DOSES OF LOW LET RADIATION

    SciTech Connect (OSTI)

    J.LESIE REDPATH, PH.D.

    2011-03-29

    We are currently funded (9/01-8/04) by the DOE Low Dose Radiation Research Program to examine mechanisms underlying the suppression of neoplastic transformation in vitro by low doses of low LET radiation. For the new studies proposed under Notice 04-21, we intend to follow up on our observation that upregulation of DNA repair may be an important factor and that its importance is dose-dependent. The experimental system will be the human hybrid cell neoplastic transformation assay that we are currently using. We propose to test the following hypothesis: Down-regulation of DNA dsb repair will abrogate the low dose suppression of neoplastic transformation. Using the technique of RNA silencing, it is proposed to test the effect of down-regulation of the two major DNA dsb repair pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ), on the dose response relationship for neoplastic transformation. Based on prior studies, we predict that this will result in abrogation of the suppressive effect at doses in the range 1 to 10 cGy, but not at lower doses. The proposed experiments will also help address the question as to which of the two DNA repair pathways may be the most important in causing suppression of transformation. HR is a pathway that is predominant in S and G2 phase cells and is known to be less error-prone than the NHEJ pathway that is predominant in G1 phase. We hypothesize that down-regulation of HR will result in the most effective abrogation of suppression. An important component of this study will be the determination of the how abrogation of DNA dsb repair impacts the spontaneous transformation frequency, presumably a consequence of endogeneous DNA damage. Experiments will be carried out using partially synchronized populations of cells enriched for G1 and S/G2 respectively. In addition to the endpoint of neoplastic transformation the impact of down-regulation of HR and NHEJ on the formation and disappearance of the DNA dsb marker, gamma-H2AX, will be studied.

  12. Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA

    SciTech Connect (OSTI)

    Chakraborty, R.; Zhong, Y.; Jin, L. ); Budowle, B. )

    1994-08-01

    The authors provide experimental evidence showing that, during the restriction-enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, they show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, they derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci. 47 refs., 2 figs., 4 tabs.

  13. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Print DNA Replication: An Open-and-Shut Case Every time a cell divides, whether in humans or in other organisms, its chromosomes must be copied quickly but without mistakes. When copying errors do occur, the resulting mutations can lead to cancer or other life-threatening diseases, so understanding the copying process is important for improving human health. The protein that copies DNA (DNA polymerase) requires a ring-shaped protein

  14. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Print DNA Replication: An Open-and-Shut Case Every time a cell divides, whether in humans or in other organisms, its chromosomes must be copied quickly but without mistakes. When copying errors do occur, the resulting mutations can lead to cancer or other life-threatening diseases, so understanding the copying process is important for improving human health. The protein that copies DNA (DNA polymerase) requires a ring-shaped protein

  15. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Print DNA Replication: An Open-and-Shut Case Every time a cell divides, whether in humans or in other organisms, its chromosomes must be copied quickly but without mistakes. When copying errors do occur, the resulting mutations can lead to cancer or other life-threatening diseases, so understanding the copying process is important for improving human health. The protein that copies DNA (DNA polymerase) requires a ring-shaped protein

  16. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structures of Clamp-Loader Complexes Are Key to DNA Replication Print DNA Replication: An Open-and-Shut Case Every time a cell divides, whether in humans or in other organisms, its chromosomes must be copied quickly but without mistakes. When copying errors do occur, the resulting mutations can lead to cancer or other life-threatening diseases, so understanding the copying process is important for improving human health. The protein that copies DNA (DNA polymerase) requires a ring-shaped protein

  17. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic

    Office of Scientific and Technical Information (OSTI)

    Thermophile Alvinella pompejana (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Citation Details In-Document Search Title: Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Human DNA polymerase η (HsPol η ) plays an important role in translesion synthesis (TLS), which allows for replication past DNA

  18. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic

    Office of Scientific and Technical Information (OSTI)

    Thermophile Alvinella pompejana (Journal Article) | DOE PAGES Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Title: Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana Human DNA polymerase η (HsPol η ) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-induced cis-syn cyclobutane pyrimidine dimers (CPDs). Here, we

  19. Concentrating Solar Power: Efficiently Leveraging Equilibrium Mechanisms

    Office of Environmental Management (EM)

    for Engineering New Thermochemical Storage | Department of Energy Power: Efficiently Leveraging Equilibrium Mechanisms for Engineering New Thermochemical Storage Concentrating Solar Power: Efficiently Leveraging Equilibrium Mechanisms for Engineering New Thermochemical Storage Concentrating Solar Power: Efficiently Leveraging Equilibrium Mechanisms for Engineering New Thermochemical Storage The Concentrating Solar Power: Efficiently Leveraging Equilibrium Mechanisms for Engineering New

  20. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec; Tretiak, Sergei; Taylor, Antoinette J.; Balatsky, Alexander V.

    2011-01-01

    We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4 ° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides andmore » the tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.« less

  1. Raman-based system for DNA sequencing-mapping and other separations

    DOE Patents [OSTI]

    Vo-Dinh, Tuan (Knoxville, TN)

    1994-01-01

    DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated.

  2. Raman-based system for DNA sequencing-mapping and other separations

    DOE Patents [OSTI]

    Vo-Dinh, T.

    1994-04-26

    DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated. 11 figures.

  3. Probability of double-strand breaks in genome-sized DNA by {gamma}-ray decreases markedly as the DNA concentration increases

    SciTech Connect (OSTI)

    Shimobayashi, Shunsuke F.; Iwaki, Takafumi; Mori, Toshiaki; Yoshikawa, Kenichi

    2013-05-07

    By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by {gamma}-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P{sub 1}, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.

  4. DOE fundamentals handbook: Mechanical science. Volume 2

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    The Mechanical Science Handbook was developed to assist nuclear facility operating contractors in providing operators, maintenance personnel, and the technical staff with the necessary fundamentals training to ensure a basic understanding of mechanical components and mechanical science. The handbook includes information diesel engines, heat exchangers, pumps, valves, and miscellaneous mechanical components. This information will provide personnel with a foundation for understanding the construction and operation of mechanical components that are associated with various DOE nuclear facility operations and maintenance.

  5. Controlled Thermo-Mechanical Processing

    SciTech Connect (OSTI)

    None

    2005-09-01

    The CTMP technology has the potential for widespread application in all major sectors of the domestic tube and pipe industry; two of the largest sectors are seamless mechanical tubing and seamless oil country tubular goods. It has been proven for the spheroidized annealing heat cycle for through-hardened steels and has led to the development of a recipe for automotive gear steels. Potential applications also exist in the smaller sectors of seamless line pipe, pressure tubing, and stainless tubing. The technology could also apply to non-ferrous metal industries, such as titanium.

  6. How reclamation tests mechanical governors

    SciTech Connect (OSTI)

    Agee, J.C.; Girgis, G.K.; Cline, R.

    1996-08-01

    The Bureau of Reclamation has developed its own equipment for testing mechanical-hydraulic governors for hydroelectric generators. The device, called a Permanent Magnet Generator (PMG) Simulator, generates a three-phase voltage that will drive the governor ballhead motor at variable speed. Utilizing this equipment, most traditional governor tests can be completed with the generating unit dewatered. In addition, frequency response testing and other detailed analytical tests can be performed to validate governor models. This article describes the development and design of the equipment, and it also discusses its usage in a case study of events at Glen Canyon Dam.

  7. Mechanical accessories for mobile teleoperators

    SciTech Connect (OSTI)

    Feldman, M.J.; Herndon, J.N.

    1985-01-01

    The choice of optimum mechanical accessories for mobile teleoperators involves matching the criteria for emergency response with the available technology. This paper presents a general background to teleoperations, a potpourri of the manipulator systems available, and an argument for force reflecting manipulation. The theme presented is that the accomplishment of humanlike endeavors in hostile environments will be most successful when man model capabilities are utilized. The application of recent electronic technology to manipulator development has made new tools available to be applied to emergency response activities. The development activities described are products of the Consolidated Fuel Reprocessing Program at the Oak Ridge National Laboratory. 13 refs., 7 figs.

  8. Cell-penetrating DNA-binding protein as a safe and efficient naked DNA delivery carrier in vitro and in vivo

    SciTech Connect (OSTI)

    Kim, Eun-Sung; Yang, Seung-Woo; Hong, Dong-Ki; Kim, Woo-Taek; Kim, Ho-Guen; Lee, Sang-Kyou

    2010-01-29

    Non-viral gene delivery is a safe and suitable alternative to viral vector-mediated delivery to overcome the immunogenicity and tumorigenesis associated with viral vectors. Using the novel, human-origin Hph-1 protein transduction domain that can facilitate the transduction of protein into cells, we developed a new strategy to deliver naked DNA in vitro and in vivo. The new DNA delivery system contains Hph-1-GAL4 DNA-binding domain (DBD) fusion protein and enhanced green fluorescent protein (EGFP) reporter plasmid that includes the five repeats of GAL4 upstream activating sequence (UAS). Hph-1-GAL4-DBD protein formed complex with plasmid DNA through the specific interaction between GAL4-DBD and UAS, and delivered into the cells via the Hph-1-PTD. The pEGFP DNA was successfully delivered by the Hph-1-GAL4 system, and the EGFP was effectively expressed in mammalian cells such as HeLa and Jurkat, as well as in Bright Yellow-2 (BY-2) plant cells. When 10 {mu}g of pEGFP DNA was intranasally administered to mice using Hph-1-GAL4 protein, a high level of EGFP expression was detected throughout the lung tissue for 7 days. These results suggest that an Hph-1-PTD-mediated DNA delivery strategy may be an useful non-viral DNA delivery system for gene therapy and DNA vaccines.

  9. Bellcrank mechanisms for Stirling engines

    SciTech Connect (OSTI)

    Senft, J.R.; Senft, V.J.

    1996-12-31

    This paper describes a family of linkage drive systems for Stirling engines containing several new members. These mechanisms are adaptable to all three configurations of Stirling engine, impose minimal side loads on pistons and displacer rods, and include compact forms suitable for pressurized high performance engines. This group of drive systems is generated by a simple common scheme. Near sinusoidal motion is taken from a crankshaft carrying a single crankpin by two connecting rods each driving a bellcrank. The stationary pivots of the bellcranks are located so that their oscillatory motion has the phase angle separation required between the piston and displacer. The bellcranks are further configured to bring the third pin motion to a location suitable for coupling with the piston or displacer of the engine in a way which minimizes side loading. The paper presents a number of new linkage drives from the dual bellcrank family and indicates how they are embodied in beta and alpha type Stirling engines. The paper includes a design for a small multipurpose engine incorporating one of the subject mechanisms.

  10. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOE Patents [OSTI]

    Ji, H.; Smith, L.M.

    1997-01-07

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support. 3 figs.

  11. Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial

    Office of Scientific and Technical Information (OSTI)

    8-Oxoguanine DNA Glycosylase MutM (Journal Article) | SciTech Connect and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM Citation Details In-Document Search Title: Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM Authors: Sung, Rou-Jia ; Zhang, Michael ; Qi, Yan ; Verdine, Gregory L. [1] ; Harvard) [2] ; DFCI) [2] + Show Author Affiliations (Harvard-Med) ( Publication Date: 2013-07-26

  12. Electrical transport characteristics of DNA wrapped carbon nanotubes contacted to palladium and palladium oxide electrodes.

    SciTech Connect (OSTI)

    Dentinger, Paul M.; Leonard, Francois; Jones, Frank Eugene; Talin, Albert Alec

    2005-03-01

    DNA-wrapped carbon nanotubes (DNA-CNT) have generated attention due the ability to disperse cleanly into solution, and by the possibility of sorting nanotubes according to size and conductivity. In order to learn more about the effects of DNA on the electrical transport characteristics of single wall carbon nanotubes, we fabricate and test a series of devices consisting of DNA-wrapped CNTs placed across gold, palladium, and palladium oxide electrodes. In addition, we look at how DNA functionalized CNTs react to presence of hydrogen, which has previously been shown to affect the conductivity of CNTs when in contact with palladium.

  13. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOE Patents [OSTI]

    Ji, Huamin (4817 Sheboygan Ave., Madison, WI 53705); Smith, Lloyd M. (1115 Amherst Dr., Madison, WI 53705)

    1997-01-01

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support.

  14. Polymorphism of DNA-anionic Liposome Complexes Reveals Hierarchy of

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ion-mediated Interactions Polymorphism of DNA-anionic Liposome Complexes Reveals Hierarchy of Ion-mediated Interactions Hongjun Liang,* Daniel Harries,+ and Gerard C. L. Wong* *Department of Materials Science & Engineering, Department of Physics, Department of Bioengineering, University of Illinois at Urbana-Champaign, IL 61801, USA +Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA Gene therapy using

  15. Extraction of PCR-amplifiable genomic DNA from Bacillus anthracisspores

    SciTech Connect (OSTI)

    Torok, Tamas

    2003-05-19

    Bacterial endospore disruption and nucleic acid extractionresulting in DNA of PCR-amplifiable quality and quantity are not trivial.Responding to the needs of the Hazardous Materials Response Unit (HMRU),Laboratory Division, Federal Bureau of Investigation, protocols weredeveloped to close these gaps. Effectiveness and reproducibility of thetechniques were validated with laboratory grown pure spores of Bacillusanthracis and its close phylogenetic neighbors, and with spiked soils anddamaged samples.

  16. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  17. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 11 figures.

  18. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 12 figs.

  19. DNA Extraction by Isotachophoresis in a Microfluidic Channel

    SciTech Connect (OSTI)

    Stephenson, S J

    2011-08-10

    Biological assays have many applications. For example, forensics personnel and medical professionals use these tests to diagnose diseases and track their progression or identify pathogens and the host response to them. One limitation of these tests, however, is that most of them target only one piece of the sample - such as bacterial DNA - and other components (e.g. host genomic DNA) get in the way, even though they may be useful for different tests. To address this problem, it would be useful to extract several different substances from a complex biological sample - such as blood - in an inexpensive and efficient manner. This summer, I worked with Maxim Shusteff at Lawrence Livermore National Lab on the Rapid Automated Sample Prep project. The goal of the project is to solve the aforementioned problem by creating a system that uses a series of different extraction methods to extract cells, bacteria, and DNA from a complex biological sample. Biological assays can then be run on purified output samples. In this device, an operator could input a complex sample such as blood or saliva, and would receive separate outputs of cells, bacteria, viruses, and DNA. I had the opportunity to work this summer with isotachophoresis (ITP), a technique that can be used to extract nucleic acids from a sample. This technique is intended to be the last stage of the purification device. Isotachophoresis separates particles based on different electrophoretic mobilities. This technique is convenient for out application because free solution DNA mobility is approximately equal for DNA longer than 300 base pairs in length. The sample of interest - in our case DNA - is fed into the chip with streams of leading electrolyte (LE) and trailing electrolyte (TE). When an electric field is applied, the species migrate based on their electrophoretic mobilities. Because the ions in the leading electrolyte have a high electrophoretic mobility, they race ahead of the slower sample and trailing electrolyte ions. Conversely, the trailing electrolyte ions have a slow electrophoretic mobility, so they lag behind the sample, thus trapping the species of interest between the LE and TE streams. In a typical isotachophoresis configuration, the electric field is applied in a direction parallel to the direction of flow. The species then form bands that stretch across the width of the channel. A major limitation of that approach is that only a finite amount of sample can be processed at once, and the sample must be processed in batches. For our purposes, a form of free-flow isotachophoresis is more convenient, where the DNA forms a band parallel to the edges of the channel. To achieve this, in our chip, the electric field is applied transversely. This creates a force perpendicular to the direction of flow, which causes the different ions to migrate across the flow direction. Because the mobility of the DNA is between the mobility of the leading and the trailing electrolyte, the DNA is focused in a tight band near the center of the channel. The stream of DNA can then be directed to a different output to produce a highly concentrated outlet stream without batch processing. One hurdle that must be overcome for successful ITP is isolating the electrochemical reactions that result from the application of high voltage for the actual process of isotachophoresis. The electrochemical reactions that occur around metal electrodes produce bubbles and pH changes that are detrimental to successful ITP. The design of the chips we use incorporates polyacrylamide gels to serve as electrodes along the central channel. For our design, the metal electrodes are located away from the chip, and high conductivity buffer streams carry the potential to the chip, functioning as a 'liquid electrode.' The stream then runs alongside a gel barrier. The gel electrode permits ion transfer while simultaneously isolating the separation chamber from any contaminants in the outer, 'liquid electrode' streams. The difference in potential from one side of the chip to the other creates an electric field. This field traverses the inner, separation channel, containing the leading electrolyte, the trailing electrolyte, and the sample of interest (DNA). To increase the ease of use of the chips, a newer chip design has been fabricated. This design has wire electrodes integrated on the chip, rather than elsewhere. To keep the pH changes and bubbling isolated from the separation channel, the chip contains deeper wells near the electrodes so that the flowing buffer can wash away any gases that form around the electrode. This design is significantly more compact because it eliminates the cumbersome electrode boxes. Eliminating the electrode boxes also decreases the required voltage, making the experiments safer. This happens because when the 'liquid electrode' streams travel through small diameter tubing, they lose much of their voltage due to the electrical resistance of the fluid in the tubing.

  20. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  1. Molecular Behavior of DNA Origami in Higher-Order Self-Assembly

    SciTech Connect (OSTI)

    Li, Zhe; Liu, Minghui; Lei, Wang; Nangreave, Jeanette; Yan, Hao; Liu, Yan

    2010-09-08

    DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ~20 nm) and DNA origami tiles with larger dimensions (up to ~100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.

  2. Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model

    SciTech Connect (OSTI)

    Hud, N.V.

    1995-10-01

    Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent with all available data. Recently, the authors proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here the authors propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

  3. Miniature mechanical transfer optical coupler

    DOE Patents [OSTI]

    Abel, Philip (Overland Park, KS); Watterson, Carl (Kansas City, MO)

    2011-02-15

    A miniature mechanical transfer (MT) optical coupler ("MMTOC") for optically connecting a first plurality of optical fibers with at least one other plurality of optical fibers. The MMTOC may comprise a beam splitting element, a plurality of collimating lenses, and a plurality of alignment elements. The MMTOC may optically couple a first plurality of fibers disposed in a plurality of ferrules of a first MT connector with a second plurality of fibers disposed in a plurality of ferrules of a second MT connector and a third plurality of fibers disposed in a plurality of ferrules of a third MT connector. The beam splitting element may allow a portion of each beam of light from the first plurality of fibers to pass through to the second plurality of fibers and simultaneously reflect another portion of each beam of light from the first plurality of fibers to the third plurality of fibers.

  4. Technical abstracts: Mechanical engineering, 1990

    SciTech Connect (OSTI)

    Broesius, J.Y.

    1991-03-01

    This document is a compilation of the published, unclassified abstracts produced by mechanical engineers at Lawrence Livermore National Laboratory (LLNL) during the calendar year 1990. Many abstracts summarize work completed and published in report form. These are UCRL-JC series documents, which include the full text of articles to be published in journals and of papers to be presented at meetings, and UCID reports, which are informal documents. Not all UCIDs contain abstracts: short summaries were generated when abstracts were not included. Technical Abstracts also provides descriptions of those documents assigned to the UCRL-MI (miscellaneous) category. These are generally viewgraphs or photographs presented at meetings. An author index is provided at the back of this volume for cross referencing.

  5. Fundamental mechanisms of micromachine reliability

    SciTech Connect (OSTI)

    DE BOER,MAARTEN P.; SNIEGOWSKI,JEFFRY J.; KNAPP,JAMES A.; REDMOND,JAMES M.; MICHALSKE,TERRY A.; MAYER,THOMAS K.

    2000-01-01

    Due to extreme surface to volume ratios, adhesion and friction are critical properties for reliability of Microelectromechanical Systems (MEMS), but are not well understood. In this LDRD the authors established test structures, metrology and numerical modeling to conduct studies on adhesion and friction in MEMS. They then concentrated on measuring the effect of environment on MEMS adhesion. Polycrystalline silicon (polysilicon) is the primary material of interest in MEMS because of its integrated circuit process compatibility, low stress, high strength and conformal deposition nature. A plethora of useful micromachined device concepts have been demonstrated using Sandia National Laboratories' sophisticated in-house capabilities. One drawback to polysilicon is that in air the surface oxidizes, is high energy and is hydrophilic (i.e., it wets easily). This can lead to catastrophic failure because surface forces can cause MEMS parts that are brought into contact to adhere rather than perform their intended function. A fundamental concern is how environmental constituents such as water will affect adhesion energies in MEMS. The authors first demonstrated an accurate method to measure adhesion as reported in Chapter 1. In Chapter 2 through 5, they then studied the effect of water on adhesion depending on the surface condition (hydrophilic or hydrophobic). As described in Chapter 2, they find that adhesion energy of hydrophilic MEMS surfaces is high and increases exponentially with relative humidity (RH). Surface roughness is the controlling mechanism for this relationship. Adhesion can be reduced by several orders of magnitude by silane coupling agents applied via solution processing. They decrease the surface energy and render the surface hydrophobic (i.e. does not wet easily). However, only a molecular monolayer coats the surface. In Chapters 3-5 the authors map out the extent to which the monolayer reduces adhesion versus RH. They find that adhesion is independent of RH up to a threshold value, depending on the coating chemistry. The mechanism for the adhesion increase beyond this threshold value is that the coupling agent reconfigures from a surface to a bulk phase (Chapter 3). To investigate the details of how the adhesion increase occurs, the authors developed the mechanics for adhesion hysteresis measurements. These revealed that near-crack tip compression is the underlying cause of the adhesion increase (Chapter 4). A vacuum deposition chamber for silane coupling agent deposition was constructed. Results indicate that vapor deposited coatings are less susceptible to degradation at high RH (Chapter 5). To address issues relating to surfaces in relative motion, a new test structure to measure friction was developed. In contrast to other surface micromachined friction test structures, uniform apparent pressure is applied in the frictional contact zone (Chapter 6). The test structure will enable friction studies over a large pressure and dynamic range. In this LDRD project, the authors established an infrastructure for MEMS adhesion and friction metrology. They then characterized in detail the performance of hydrophilic and hydrophobic films under humid conditions, and determined mechanisms which limit this performance. These studies contribute to a fundamental understanding for MEMS reliability design rules. They also provide valuable data for MEMS packaging requirements.

  6. Creep damage mechanisms in composites

    SciTech Connect (OSTI)

    Nutt, S.R.

    1994-10-17

    During the past year, research has focused on processing and characterization of intermetallic composites synthesized by plasma spray deposition. This versatile process allows rapid synthesis of a variety of different composite systems with potential applications for coatings, functionally gradient materials, rapid proto-typing and 3d printing, as well as near-net-shape processing of complex shapes. We have been pursuing an experimental program of research aimed at a fundamental understanding of the microstructural processes involved in the synthesis of intermetallic composites, including diffusion, heat transfer, grain boundary migration, and the dependence of these phenomena on deposition parameters. The work has been motivated by issues arising from composite materials manufacturing technologies. Recent progress is described in section B on the following topics: (1) Reactive atomization and deposition of intermetallic composites (Ni3Al); (2) Reactive synthesis of MoSi2-SiC composites; (3) Mechanical alloying of nanocrystalline alloys; (4) Tensile creep deformation of BMAS glass-ceramic composites.

  7. Eight plane IPND mechanical testing.

    SciTech Connect (OSTI)

    Zhao, A.; Guarino, V.; Wood, K.; Nephew, T.; Ayres, D.; Lee, A.; High Energy Physics; FNAL

    2008-03-18

    A mechanical test of an 8 plane IPND mechanical prototype, which was constructed using extrusions from the testing/tryout of the 16 cell prototype extrusion die in Argonne National Laboratory, was conducted. There were 4 vertical and 4 horizontal planes in this 8 plane IPND prototype. Each vertical plane had four 16 cell extrusions, while each horizontal plane had six 16 cell extrusions. Each plane was glued together using the formulation of Devcon adhesive, Devcon 60. The vertical extrusions used in the vertical planes shares the same dimensions as the horizontal extrusions in the horizontal planes with the average web thickness of 2.1 mm and the average wall thickness of 3.1 mm. This mechanical prototype was constructed with end-seals on the both ends of the vertical extrusions. The gaps were filled with epoxy between extrusions and end-seals. The overall dimension of IPND is 154.8 by 103.1 by 21.7 inches with the weight of approximately 1200 kg, as shown in a figure. Two similar mechanical tests of 3 layer and 11 layer prototypes have been done in order to evaluate the strength of the adhesive joint between extrusions in the NOvA detector. The test showed that the IPND prototype was able to sustain under the loading of weight of itself and scintillator. Two FEA models were built to verify the measurement data from the test. The prediction from FEA slice model seems correlated reasonably well to the test result, even under a 'rough' estimated condition for the wall thickness (from an untuned die) and an unknown property of 'garage type' extrusion. A full size of FEA 3-D model also agrees very well with the test data from strain gage readings. It is worthy to point out that the stress distribution of the structure is predominantly determined by the internal pressure, while the buckling stability relies more on the loading weight from the extrusions themselves and scintillate. Results of conducted internal pressure tests, including 3- cell, 11-cell and the IPND prototypes, have been correlated to the FEA analysis very well. The authors believe they have quite good understanding of response of the NOvA structures subjected to the internal pressure, while the understanding of buckling stability is far behind. Therefore, more effect should be laid to improve the buckling considering that the FEA analysis usually is not able accurately modeling the stability as good as the stress analysis. The IPND structure was mostly built using 'scrape' piece extrusions (whatever available in shop). Therefore, a future test should be more focus on by using a actual real extrusions, for example like Nova -27 (if a final choice is made) and extrusion from a tuned die (very important). The authors should/will repeat 11 layers test with an actual thicker piece for the vertical to verify the adhesive joint and similar large scale prototype with a symmetry case, either 9 or 11 layers with the dial indicator on the both side.

  8. Plant salt-tolerance mechanisms

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Deinlein, Ulrich; Stephan, Aaron B.; Horie, Tomoaki; Luo, Wei; Xu, Guohua; Schroeder, Julian I.

    2014-06-01

    Crop performance is severely affected by high salt concentrations in soils. To engineer more salt-tolerant plants it is crucial to unravel the key components of the plant salt-tolerance network. Here we review our understanding of the core salt-tolerance mechanisms in plants. Recent studies have shown that stress sensing and signaling components can play important roles in regulating the plant salinity stress response. We also review key Na+ transport and detoxification pathways and the impact of epigenetic chromatin modifications on salinity tolerance. In addition, we discuss the progress that has been made towards engineering salt tolerance in crops, including marker-assisted selectionmore » and gene stacking techniques. We also identify key open questions that remain to be addressed in the future.« less

  9. Plant salt-tolerance mechanisms

    SciTech Connect (OSTI)

    Deinlein, Ulrich; Stephan, Aaron B.; Horie, Tomoaki; Luo, Wei; Xu, Guohua; Schroeder, Julian I.

    2014-06-01

    Crop performance is severely affected by high salt concentrations in soils. To engineer more salt-tolerant plants it is crucial to unravel the key components of the plant salt-tolerance network. Here we review our understanding of the core salt-tolerance mechanisms in plants. Recent studies have shown that stress sensing and signaling components can play important roles in regulating the plant salinity stress response. We also review key Na+ transport and detoxification pathways and the impact of epigenetic chromatin modifications on salinity tolerance. In addition, we discuss the progress that has been made towards engineering salt tolerance in crops, including marker-assisted selection and gene stacking techniques. We also identify key open questions that remain to be addressed in the future.

  10. Apparatus and method for generating mechanical waves

    DOE Patents [OSTI]

    Allensworth, D.L.; Chen, P.J.

    1982-10-25

    Mechanical waves are generated in a medium by subjecting an electromechanical element to an alternating electric field having a frequency which induces mechanical resonance therein and is below any electrical resonance frequency thereof.

  11. Apparatus and method for generating mechanical waves

    DOE Patents [OSTI]

    Allensworth, Dwight L. (Albuquerque, NM); Chen, Peter J. (Albuquerque, NM)

    1985-01-01

    Mechanical waves are generated in a medium by subjecting an electromechanical element to an alternating electric field having a frequency which induces mechanical resonance therein and is below any electrical resonance frequency thereof.

  12. Mechanical properties and tribological behavior of contaminate...

    Office of Scientific and Technical Information (OSTI)

    behavior of contaminate nanoparticles on micromachined surfaces. Citation Details In-Document Search Title: Mechanical properties and tribological behavior of ...

  13. Training: Mechanical Insulation | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Mechanical Insulation Training: Mechanical Insulation April 16, 2014 - 6:34pm Addthis Learn about the diverse training sessions offered. The courses are taught by highly qualified instructors who have met rigorous standards. View additional plant-wide resources. Mechanical Insulation Education and Awareness E-Learning Series Availability: Online self-paced workshop. The Mechanical Insulation Education & Awareness Campaign, or MIC, is an eLearning series offered by the U.S. Department of

  14. Mechanical Engineer | Princeton Plasma Physics Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Mechanical Engineer Department: Engineering Supervisor(s): Bill Blanchard Staff: EM 3 Requisition Number: 1500 The Mechanical Design Engineer will develop, design, manufacture, and test mechanical components and auxiliary systems required for support of the experimental devices. The engineer will also design, specify, fabricate, and erect various mechanical structures to provide support against gravitational and electromagnetic forces. The position requires knowledge of stress analysis, magnetic

  15. Understanding Mechanisms of Radiological Contamination

    SciTech Connect (OSTI)

    Rick Demmer; John Drake; Ryan James, PhD

    2014-03-01

    Over the last 50 years, the study of radiological contamination and decontamination has expanded significantly. This paper addresses the mechanisms of radiological contamination that have been reported and then discusses which methods have recently been used during performance testing of several different decontamination technologies. About twenty years ago the Idaho Nuclear Technology Engineering Center (INTEC) at the INL began a search for decontamination processes which could minimize secondary waste. In order to test the effectiveness of these decontamination technologies, a new simulated contamination, termed SIMCON, was developed. SIMCON was designed to replicate the types of contamination found on stainless steel, spent fuel processing equipment. Ten years later, the INL began research into methods for simulating urban contamination resulting from a radiological dispersal device (RDD). This work was sponsored by the Defense Advanced Research Projects Agency (DARPA) and included the initial development an aqueous application of contaminant to substrate. Since 2007, research sponsored by the US Environmental Protection Agency (EPA) has advanced that effort and led to the development of a contamination method that simulates particulate fallout from an Improvised Nuclear Device (IND). The IND method diverges from previous efforts to create tenacious contamination by simulating a reproducible loose contamination. Examining these different types of contamination (and subsequent decontamination processes), which have included several different radionuclides and substrates, sheds light on contamination processes that occur throughout the nuclear industry and in the urban environment.

  16. Radiation-Induced Upregulation of Gene Expression From Adenoviral Vectors Mediated by DNA Damage Repair and Regulation

    SciTech Connect (OSTI)

    Nokisalmi, Petri; Rajecki, Maria; Pesonen, Sari; Escutenaire, Sophie; Soliymani, Rabah; Tenhunen, Mikko; Ahtiainen, Laura; Hemminki, Akseli

    2012-05-01

    Purpose: In the present study, we evaluated the combination of replication-deficient adenoviruses and radiotherapy in vitro. The purpose of the present study was to analyze the mechanism of radiation-mediated upregulation of adenoviral transgene expression. Methods and Materials: Adenoviral transgene expression (luciferase or green fluorescent protein) was studied with and without radiation in three cell lines: breast cancer M4A4-LM3, prostate cancer PC-3MM2, and lung cancer LNM35/enhanced green fluorescent protein. The effect of the radiation dose, modification of the viral capsid, and five different transgene promoters were studied. The cellular responses were studied using mass spectrometry and immunofluorescence analysis. Double strand break repair was modulated by inhibitors of heat shock protein 90, topoisomerase-I, and DNA protein kinase, and transgene expression was measured. Results: We found that a wide range of radiation doses increased adenoviral transgene expression regardless of the cell line, transgene, promoter, or viral capsid modification. Treatment with adenovirus, radiation, and double strand break repair inhibitors resulted in persistence of double strand breaks and subsequent increases in adenovirus transgene expression. Conclusions: Radiation-induced enhancement of adenoviral transgene expression is linked to DNA damage recognition and repair. Radiation induces a global cellular response that results in increased production of RNA and proteins, including adenoviral transgene products. This study provides a mechanistic rationale for combining radiation with adenoviral gene delivery.

  17. Contributing Data to the Fleet DNA Project (Brochure)

    SciTech Connect (OSTI)

    Not Available

    2014-09-01

    The Fleet DNA clearinghouse of commercial fleet transportation data helps vehicle manufacturers and developers optimize vehicle designs and helps fleet managers choose advanced technologies for their fleets. This online tool - available at www.nrel.gov/fleetdna - provides data summaries and visualizations similar to real-world 'genetics' for medium- and heavy-duty commercial fleet vehicles operating within a variety of vocations. To contribute your fleet data, please contact Adam Duran of the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) at adam.duran@nrel.gov or 303-275-4586.

  18. Fleet DNA Project … Data Dictionary for Public Download Files

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fleet DNA Project - Data Dictionary for Public Download Files A. Duran, E. Burton, K. Kelly, and K. Walkowicz Technical Report NREL/TP-5400-62572 September 2014 NREL is a national laboratory of the U.S. Department of Energy Office of Energy Efficiency & Renewable Energy Operated by the Alliance for Sustainable Energy, LLC This report is available at no cost from the National Renewable Energy Laboratory (NREL) at www.nrel.gov/publications. Contract No. DE-AC36-08GO28308 National Renewable

  19. Low-cost, Rapid DNA Sequencing Technique - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Biomass and Biofuels Biomass and Biofuels Advanced Materials Advanced Materials Find More Like This Return to Search Low-cost, Rapid DNA Sequencing Technique Oak Ridge National Laboratory Contact ORNL About This Technology Publications: PDF Document Publication 11-G00264_ID2098.pdf (476 KB) <p align="left">&nbsp;</p> <p><span style="font-size: x-small;">Schematic model of setup of nano-gap between two electrodes, with (a) and without (b) a molecule

  20. Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting

    DOE Patents [OSTI]

    Chen, Fanqing Frank; Liu, Gang L; Lee, Luke P

    2013-10-29

    This invention provides a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of nucleic acid (e.g., DNA) length changes and perform nucleic acid footprinting. In various embodiments the ruler comprises a nucleic acid attached to a nanoparticle, such that changes in the nucleic acid length are detectable using surface plasmon resonance. The nanoplasmonic ruler provides a fast and convenient platform for mapping nucleic acid-protein interactions, for nuclease activity monitoring, and for other footprinting related methods.

  1. A hybrid DNA-templated gold nanocluster for enhanced enzymatic reduction of oxygen

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Chakraborty, Saumen; Babanova, Sofia; Rocha, Reginaldo C.; Desireddy, Anil; Artyushkova, Kateryna; Boncella, Amy E.; Atanassov, Plamen; Martinez, Jennifer S.

    2015-08-19

    We report the synthesis and characterization of a new DNA-templated gold nanocluster (AuNC) of ~1 nm in diameter and possessing ~7 Au atoms. When integrated with bilirubin oxidase (BOD) and single walled carbon nanotubes (SWNTs), the AuNC acts as an enhancer of electron transfer (ET) and lowers the overpotential of electrocatalytic oxygen reduction reaction (ORR) by ~15 mV as compared to the enzyme alone. In addition, the presence of AuNC causes significant enhancements in the electrocatalytic current densities at the electrode. Control experiments show that such enhancement of ORR by the AuNC is specific to nanoclusters and not to plasmonicmore » gold particles. Rotating ring disk electrode (RRDE) measurements confirm 4e– reduction of O2 to H2O with minimal production of H2O2, suggesting that the presence of AuNC does not perturb the mechanism of ORR catalyzed by the enzyme. This unique role of the AuNC as enhancer of ET at the enzyme-electrode interface makes it a potential candidate for the development of cathodes in enzymatic fuel cells, which often suffer from poor electronic communication between the electrode surface and the enzyme active site. In conclusion, the AuNC displays phosphorescence with large Stokes shift and microsecond lifetime.« less

  2. Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

    SciTech Connect (OSTI)

    Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; Mori, Eiichiro; Bhattacharya, Souparno; Kobayashi, Junya; Yannone, Steven  M.; Chen, David  J.; Asaithamby, Aroumougame

    2014-11-20

    WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRN to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.

  3. The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor

    SciTech Connect (OSTI)

    Hauk, G.; McKnight, J; Nodelman, I; Bowman, G

    2010-01-01

    Chromatin remodelers are ATP-driven machines that assemble, slide, and remove nucleosomes from DNA, but how the ATPase motors of remodelers are regulated is poorly understood. Here we show that the double chromodomain unit of the Chd1 remodeler blocks DNA binding and activation of the ATPase motor in the absence of nucleosome substrates. The Chd1 crystal structure reveals that an acidic helix joining the chromodomains can pack against a DNA-binding surface of the ATPase motor. Disruption of the chromodomain-ATPase interface prevents discrimination between nucleosomes and naked DNA and reduces the reliance on the histone H4 tail for nucleosome sliding. We propose that the chromodomains allow Chd1 to distinguish between nucleosomes and naked DNA by physically gating access to the ATPase motor, and we hypothesize that related ATPase motors may employ a similar strategy to discriminate among DNA-containing substrates.

  4. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, C.R.; Ito, Takashi; Smith, C.L.

    1996-01-09

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel. 6 figs.

  5. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, Charles R.; Ito, Takashi; Smith, Cassandra L.

    1996-01-01

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel.

  6. Methods for producing partially digested restriction DNA fragments and for producing a partially modified PCR product

    DOE Patents [OSTI]

    Wong, Kwong-Kwok (Richland, WA)

    2000-01-01

    The present invention is an improved method of making a partially modified PCR product from a DNA fragment with a polymerase chain reaction (PCR). In a standard PCR process, the DNA fragment is combined with starting deoxynucleoside triphosphates, a primer, a buffer and a DNA polymerase in a PCR mixture. The PCR mixture is then reacted in the PCR producing copies of the DNA fragment. The improvement of the present invention is adding an amount of a modifier at any step prior to completion of the PCR process thereby randomly and partially modifying the copies of the DNA fragment as a partially modified PCR product. The partially modified PCR product may then be digested with an enzyme that cuts the partially modified PCR product at unmodified sites thereby producing an array of DNA restriction fragments.

  7. Sandia Energy - Sandia chemists discover new pathway in mechanism...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    spectra, we could use these spectra as fingerprints of each intermediate, like a forensic scientist would do when investigating DNA evidence on alleged suspects of a crime,"...

  8. High-throughput analysis of T-DNA location and structure using sequence capture

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; Comai, Luca

    2015-10-07

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

  9. Final Report: The DNA Files: Unraveling the mysteries of genetics, January 1, 1998-March 31, 1999

    SciTech Connect (OSTI)

    Scott, Bari

    1999-05-01

    The DNA Files is an award-winning radio documentary series on genetics created by SoundVision Productions. The DNA Files was hosted by John Hockenberry and was presented in documentary and discussion format. The programs covered a range of topics from prenatal and predictive gene testing, gene therapy, and commercialization of genetic information to new evolutionary genetic evidence, transgenic vegetables and use of DNA in forensics.

  10. Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Citation Details In-Document Search Title: Structural Basis of UV DNA-Damage Recognition by the DDB1-DDB2 Complex Ultraviolet (UV) light-induced pyrimidine photodimers are repaired by the nucleotide excision repair pathway. Photolesions have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. The DDB1DDB2 complex serves in

  11. Contributing Data to the Fleet DNA Project (Brochure), NREL (National Renewable Energy Laboratory)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Photo from iStock/9420677 Contributing Data to the Fleet DNA Project Sponsored by the U.S. Department of Energy, the Fleet DNA project aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. The Fleet DNA clearinghouse of commercial fleet transportation data helps vehicle manufacturers and developers optimize vehicle designs and helps fleet managers choose advanced

  12. Volume visualization of multiple alignment of large genomicDNA (Book) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Book: Volume visualization of multiple alignment of large genomicDNA Citation Details In-Document Search Title: Volume visualization of multiple alignment of large genomicDNA Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting

  13. Stoichiometric control of DNA-grafted colloid self-assembly

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vo, Thi; Venkatasubramanian, Venkat; Kumar, Sanat; Srinivasan, Babji; Pal, Suchetan; Zhang, Yugang; Gang, Oleg

    2015-04-06

    In this study, there has been considerable interest in understanding the self-assembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB₂, and Cr₃Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example,more » a stoichiometric ratio of 3:1 typically results in the Cr₃Si structure. However, AlB₂ can form when appropriate building blocks are used so that the AlB₂ standard-state free energy is low enough to overcome the entropic preference for Cr₃Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence.« less

  14. Method and apparatus for synthesis of arrays of DNA probes

    DOE Patents [OSTI]

    Cerrina, Francesco (Madison, WI); Sussman, Michael R. (Madison, WI); Blattner, Frederick R. (Madison, WI); Singh-Gasson, Sangeet (Madison, WI); Green, Roland (Madison, WI)

    2002-04-23

    The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing an image former that includes a light source that provides light to a micromirror device comprising an array of electronically addressable micromirrors, each of which can be selectively tilted between one of at least two positions. Projection optics receives the light reflected from the micromirrors along an optical axis and precisely images the micromirrors onto the active surface of the substrate, which may be used to activate the surface of the substrate. The first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different pattern of micromirrors, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto. The micromirror array can be controlled in conjunction with a DNA synthesizer supplying appropriate reagents to a flow cell containing the active substrate to control the sequencing of images presented by the micromirror array in coordination of the reagents provided to the substrate.

  15. Stoichiometric control of DNA-grafted colloid self-assembly

    SciTech Connect (OSTI)

    Vo, Thi; Venkatasubramanian, Venkat; Kumar, Sanat; Srinivasan, Babji; Pal, Suchetan; Zhang, Yugang; Gang, Oleg

    2015-04-06

    In this study, there has been considerable interest in understanding the self-assembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB?, and Cr?Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example, a stoichiometric ratio of 3:1 typically results in the Cr?Si structure. However, AlB? can form when appropriate building blocks are used so that the AlB? standard-state free energy is low enough to overcome the entropic preference for Cr?Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence.

  16. DNA extraction protocols cause differences in 16S rRNA amplicon...

    Office of Scientific and Technical Information (OSTI)

    microorganisms that relies on obtaining microbial DNA from intact body segments. ... Sponsoring Org: USDOE Country of Publication: United States Language: English Subject: 60 ...

  17. adaptation of DNA repair Byrne, Rose T; Klingele, Audrey J; Cabot...

    Office of Scientific and Technical Information (OSTI)

    Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair Byrne, Rose T; Klingele, Audrey J; Cabot, Eric L; Schackwitz, Wendy S; Martin, Jeffrey A;...

  18. DNA origami using "tiles" not "staples"

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    using "tiles" not "staples" 2 Mar 2010 The group of Yan Liu and Hao Yan has discovered a way to scale up DNA origami using tiles not staples to pin the DNA into place. Their method has great potential for providing cheap access to complicated nanostructures. The research was recently published in Angewandte Chemie International Edition and is highlighted this week in Nature Materials. It is titled "A Route to Scale Up DNA Origami Using DNA Tiles as Folding Staples."

  19. Regulation of chloroplast number and DNA synthesis in higher plants. Final report, August 1995--August 1996

    SciTech Connect (OSTI)

    Mullet, J.E.

    1997-06-17

    The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focused on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The research focused on the isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

  20. Giant Protease TPP II's Structure, Mechanism Uncovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Giant Protease TPP II's Structure, Mechanism Uncovered Giant Protease TPP II's Structure, Mechanism Uncovered Print Wednesday, 23 February 2011 00:00 Tripeptidyl peptidase II (TPP II), the largest known eukaryotic enzyme that breaks down proteins (a protease), is implicated in numerous cellular processes including the degradation of the endogenous satiety agent cholecystokinin-8, making TPP II a target in the treatment of obesity. To gain insight into this molecular machine's mechanisms of

  1. PROJECT PROFILE: Mechanically Stacked Hybrid Photovoltaic Tandems |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Mechanically Stacked Hybrid Photovoltaic Tandems PROJECT PROFILE: Mechanically Stacked Hybrid Photovoltaic Tandems Funding Opportunity: SuNLaMP SunShot Subprogram: Photovoltaics Location: National Renewable Energy Laboratory, Golden, CO Amount Awarded: $999,999 Tandem cell architectures present a path toward higher module efficiencies over single junction designs. This project will develop a gallium indium phosphide (GaInP) on silicon mechanically stacked voltage-matched

  2. Eccentric crank variable compression ratio mechanism

    DOE Patents [OSTI]

    Lawrence, Keith Edward (Kobe, JP); Moser, William Elliott (Peoria, IL); Roozenboom, Stephan Donald (Washington, IL); Knox, Kevin Jay (Peoria, IL)

    2008-05-13

    A variable compression ratio mechanism for an internal combustion engine that has an engine block and a crankshaft is disclosed. The variable compression ratio mechanism has a plurality of eccentric disks configured to support the crankshaft. Each of the plurality of eccentric disks has at least one cylindrical portion annularly surrounded by the engine block. The variable compression ratio mechanism also has at least one actuator configured to rotate the plurality of eccentric disks.

  3. Thermal-Mechanical Technologies | Argonne National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of thermal-mechanical research includes: Single and two phase heat transfer Nanomaterial synthesis Heat transfer fluids Engine and power electronics cooling Thermal energy...

  4. Cost Mechanisms | OpenEI Community

    Open Energy Info (EERE)

    Cost Mechanisms Home Kyoung's picture Submitted by Kyoung(150) Contributor 9 July, 2013 - 20:57 GRR 3rd Quarter - Stakeholder Update Meeting Alaska analysis appropriations...

  5. CRAD, Nuclear Facility Construction - Mechanical Equipment -...

    Broader source: Energy.gov (indexed) [DOE]

    Nuclear Facility Construction - Mechanical Equipment Installation, (HSS CRAD 45-53, Rev. 0) This Criteria Review and Approach Document (HSS CRAD 45-53) establishes review criteria...

  6. Mechanical Characterization of Fuel Injector Piezoactuators and...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Mechanical Characterization of Fuel Injector Piezoactuators and their Piezoceramics 2007 Diesel Engine-Efficiency & Emissions Research Conference (DEER 2007). 13-16 August, 2007,...

  7. Clean Development Mechanism Pipeline | Open Energy Information

    Open Energy Info (EERE)

    Clean Development Mechanism Pipeline AgencyCompany Organization: UNEP-Risoe Centre, United Nations Environment Programme Sector: Energy, Land Topics: Finance, Implementation,...

  8. Financing Mechanisms for Renewable Energy Projects | Department...

    Broader source: Energy.gov (indexed) [DOE]

    A variety of renewable energy financing mechanisms are available for federal agencies to help meet the 30% of electricity from renewable energy sources by 2025 target established...

  9. CONTROL OF MECHANICALLY ACTIVATED POLYMERSOME FUSION: FACTORS...

    Office of Scientific and Technical Information (OSTI)

    MECHANICALLY ACTIVATED POLYMERSOME FUSION: FACTORS AFFECTING FUSION. Henderson, Ian M.; Paxton, Walter F Abstract not provided. Sandia National Laboratories (SNL-NM), Albuquerque,...

  10. Distinct Mechanisms of Recognizing Endosomal Sorting Complex...

    Office of Scientific and Technical Information (OSTI)

    Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains...

  11. Giant Protease TPP II's Structure, Mechanism Uncovered

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    endogenous satiety agent cholecystokinin-8, making TPP II a target in the treatment of obesity. To gain insight into this molecular machine's mechanisms of activation and...

  12. Metal inhibition of human alkylpurine-DNA-N-glycosylase activityin base excision repair

    SciTech Connect (OSTI)

    Wang, Ping; Guliaev, Anton B.; Hang, Bo

    2006-02-28

    Cadmium (Cd{sup 2+}), nickel (Ni{sup 2+}) and cobalt (Co{sup 2+}) are human and/or animal carcinogens. Zinc (Zn{sup 2+}) is not categorized as a carcinogen, and rather an essential element to humans. Metals were recently shown to inhibit DNA repair proteins that use metals for their function and/or structure. Here we report that the divalent ions Cd{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} can inhibit the activity of a recombinant human N-methylpurine-DNA glycosylase (MPG) toward a deoxyoligonucleotide with ethenoadenine (var epsilonA). MPG removes a variety of toxic/mutagenic alkylated bases and does not require metal for its catalytic activity or structural integrity. At concentrations starting from 50 to 1000 {micro}M, both Cd{sup 2+} and Zn{sup 2+} showed metal-dependent inhibition of the MPG catalytic activity. Ni{sup 2+} also inhibited MPG, but to a lesser extent. Such an effect can be reversed with EDTA addition. In contrast, Co{sup 2+} and Mg{sup 2+} did not inhibit the MPG activity in the same dose range. Experiments using HeLa cell-free extracts demonstrated similar patterns of inactivation of the var epsilonA excision activity by the same metals. Binding of MPG to the substrate was not significantly affected by Cd{sup 2+}, Zn{sup 2+}, and Ni{sup 2+} at concentrations that show strong inhibition of the catalytic function, suggesting that the reduced catalytic activity is not due to altered MPG binding affinity to the substrate. Molecular dynamics (MD) simulations with Zn{sup 2+} showed that the MPG active site has a potential binding site for Zn{sup 2+}, formed by several catalytically important and conserved residues. Metal binding to such a site is expected to interfere with the catalytic mechanism of this protein. These data suggest that inhibition of MPG activity may contribute to metal genotoxicity and depressed repair of alkylation damage by metals in vivo.

  13. Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells

    SciTech Connect (OSTI)

    Vrba, Lukas; Jensen, Taylor J.; Garbe, James C.; Heimark, Ronald L.; Cress, Anne E.; Dickinson, Sally; Stampfer, Martha R.; Futscher, Bernard W.

    2009-12-23

    BACKGROUND: The microRNA-200 family participates in the maintenance of an epithelial phenotype and loss of its expression can result in epithelial to mesenchymal transition (EMT). Furthermore, the loss of expression of miR-200 family members is linked to an aggressive cancer phenotype. Regulation of the miR-200 family expression in normal and cancer cells is not fully understood. METHODOLOGY/ PRINCIPAL FINDINGS: Epigenetic mechanisms participate in the control of miR-200c and miR-141 expression in both normal and cancer cells. A CpG island near the predicted mir-200c/mir-141 transcription start site shows a striking correlation between miR-200c and miR-141 expression and DNA methylation in both normal and cancer cells, as determined by MassARRAY technology. The CpG island is unmethylated in human miR-200/miR-141 expressing epithelial cells and in miR-200c/miR-141 positive tumor cells. The CpG island is heavily methylated in human miR-200c/miR-141 negative fibroblasts and miR-200c/miR-141 negative tumor cells. Mouse cells show a similar inverse correlation between DNA methylation and miR-200c expression. Enrichment of permissive histone modifications, H3 acetylation and H3K4 trimethylation, is seen in normal miR-200c/miR-141-positive epithelial cells, as determined by chromatin immunoprecipitation coupled to real-time PCR. In contrast, repressive H3K9 dimethylation marks are present in normal miR-200c/miR-141-negative fibroblasts and miR-200c/miR-141 negative cancer cells and the permissive histone modifications are absent. The epigenetic modifier drug, 5-aza-2'-deoxycytidine, reactivates miR-200c/miR-141 expression showing that epigenetic mechanisms play a functional role in their transcriptional control. CONCLUSIONS/ SIGNIFICANCE: We report that DNA methylation plays a role in the normal cell type-specific expression of miR-200c and miR-141 and this role appears evolutionarily conserved, since similar results were obtained in mouse. Aberrant DNA methylation of the miR-200c/141 CpG island is closely linked to their inappropriate silencing in cancer cells. Since the miR-200c cluster plays a significant role in EMT, our results suggest an important role for DNA methylation in the control of phenotypic conversions in normal cells.

  14. Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function

    SciTech Connect (OSTI)

    Polonskaya, Zhanna; Benham, Craig J.; Hearing, Janet . E-mail: jhearing@ms.cc.sunysb.edu

    2004-10-25

    The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component of oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.

  15. Modeling the mechanical response of PBX 9501

    SciTech Connect (OSTI)

    Ragaswamy, Partha; Lewis, Matthew W; Liu, Cheng; Thompson, Darla G

    2010-01-01

    An engineering overview of the mechanical response of Plastic-Bonded eXplosives (PBXs), specifically PBX 9501, will be provided with emphasis on observed mechanisms associated with different types of mechanical testing. Mechanical tests in the form of uniaxial tension, compression, cyclic loading, creep (compression and tension), and Hopkinson bar show strain rate and temperature dependence. A range of mechanical behavior is observed which includes small strain recoverable response in the form of viscoelasticity; change in stiffness and softening beyond peak strength due to damage in the form microcracks, debonding, void formation and the growth of existing voids; inelastic response in the form of irrecoverable strain as shown in cyclic tests, and viscoelastic creep combined with plastic response as demonstrated in creep and recovery tests. The main focus of this paper is to elucidate the challenges and issues involved in modeling the mechanical behavior of PBXs for simulating thermo-mechanical responses in engineering components. Examples of validation of a constitutive material model based on a few of the observed mechanisms will be demonstrated against three point bending, split Hopkinson pressure bar and Brazilian disk geometry.

  16. Durability Improvements Through Degradation Mechanism Studies | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy Improvements Through Degradation Mechanism Studies Durability Improvements Through Degradation Mechanism Studies Presented at the Department of Energy Fuel Cell Projects Kickoff Meeting, September 1 - October 1, 2009 PDF icon borup_lanl_kickoff.pdf More Documents & Publications FC-PAD Organization and Activities Fuel Cell Projects Kickoff Meeting The Science And Engineering of Duralbe Ultralow PGM Catalysts

  17. Thermoelectric Mechanical Reliability | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    09 DOE Hydrogen Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. PDF icon pm_10_wereszczak.pdf More Documents & Publications Thermoelectric Mechanical Reliability Thermoelectric Mechanical Reliability Thermoelectrics Theory and Structure

  18. Enhancement of mechanical properties of 123 superconductors

    DOE Patents [OSTI]

    Balachandran, U.

    1995-04-25

    A composition and method are disclosed of preparing YBa{sub 2}Cu{sub 3}O{sub 7{minus}x} superconductor. Addition of tin oxide containing compounds to YBCO superconductors results in substantial improvement of fracture toughness and other mechanical properties without affect on T{sub c}. About 5-20% additions give rise to substantially improved mechanical properties.

  19. Enhancement of mechanical properties of 123 superconductors

    DOE Patents [OSTI]

    Balachandran, Uthamalingam (Hinsdale, IL)

    1995-01-01

    A composition and method of preparing YBa.sub.2 Cu.sub.3 O.sub.7-x superconductor. Addition of tin oxide containing compounds to YBCO superconductors results in substantial improvement of fracture toughness and other mechanical properties without affect on T.sub.c. About 5-20% additions give rise to substantially improved mechanical properties.

  20. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    SciTech Connect (OSTI)

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.