National Library of Energy BETA

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. Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease,

    E-Print Network [OSTI]

    Monnat, Ray

    Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease, Brett Chevalier-SceI indicate that three catalytic divalent metal ions are distributed across a pair of overlapping active sites, with one shared metal participating in both strand cleavage reactions. These structures differ

  3. MECHANISM AND FUNCTION OF SPLICEOSOMAL CLEAVAGE IN FISSION YEAST

    E-Print Network [OSTI]

    Kannan, Ram

    2013-08-31

    MECHANISM AND FUNCTION OF SPLICEOSOMAL CLEAVAGE IN FISSION YEAST BY Ram Kannan B. Tech., PSG College Of Technology, 2007 Submitted to the graduate degree program in Molecular and Integrative Physiology and the Graduate Faculty of the University... The Dissertation Committee for Ram Kannan certifies that this is the approved version of the following dissertation: MECHANISM AND FUNCTION OF SPLICEOSOMAL CLEAVAGE IN FISSION YEAST ________________________________ Dr. Peter Baumann (Advisor...

  4. Mechanisms for ribotoxin-induced ribosomal RNA cleavage

    SciTech Connect (OSTI)

    He, Kaiyu [Department of Microbiology and Molecular Genetics (United States) [Department of Microbiology and Molecular Genetics (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Zhou, Hui-Ren [Food Science and Human Nutrition (United States)] [Food Science and Human Nutrition (United States); Pestka, James J., E-mail: pestka@msu.edu [Department of Microbiology and Molecular Genetics (United States); Food Science and Human Nutrition (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States)

    2012-11-15

    The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (? 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (? 10 ng/ml) and ribosome-inactivating protein ricin (? 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activated kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-? and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ? Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ? Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ? Ribotoxins induce rRNA cleavage via activation of p53, caspases and cathepsins. ? DON- and anisomycin-triggered rRNA cleavage is p38-dependent. ? SG- and ricin-induced rRNA cleavage is p38-independent.

  5. FeBABE-mediated hydroxyl radical cleavage assay DNA hybridization

    E-Print Network [OSTI]

    Auble, David

    BABE is obtained from Dojindo (catalog no: F279-10). Resuspend the yellowish powder in 50 µl of water (to a finalBABE conjugated DNA to beads 9. Wash 40 µl of Dynabeads M-280 Streptavidin (catalog no: 112.05D) for each reaction of Reaction mix+water (containing DTT). 15. Add 6 µl of 1 µM TBP (20nM final concentration). Incubate

  6. DNA Strand Cleavage by the Phenazine Di-N-oxide Natural Product Myxin under Both Aerobic and Anaerobic Conditions

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Strand Cleavage by the Phenazine Di-N-oxide Natural Product Myxin under Both Aerobic: Heterocyclic N-oxides are an interesting class of antitumor agents that selectively kill the hypoxic cells found in solid tumors. The hypoxia-selective activity of the lead compound in this class, tirapazamine

  7. FRONTIERS ARTICLE Mechanisms for SS and NCa bond cleavage in peptide ECD and ETD

    E-Print Network [OSTI]

    Simons, Jack

    FRONTIERS ARTICLE Mechanisms for S­S and N­Ca bond cleavage in peptide ECD and ETD mass [5­9] (ETD), one allows the parent ion to undergo collisions with an anion donor having low electron is the recombination energy released when the electron is captured, while, in ETD, this recombination energy is reduced

  8. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

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  9. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

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  10. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 toDepartment ofTopo II: AnTopo II:

  11. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 toDepartment ofTopo II: AnTopo

  12. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 toDepartment ofTopo II:

  13. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 toDepartment ofTopo II:Topoisomerase II

  14. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 toDepartment ofTopo II:Topoisomerase

  15. Mechanisms for peptide S-S and N-C bond cleavage in ECD/ETD mass spectroscopy-

    E-Print Network [OSTI]

    Simons, Jack

    Mechanisms for peptide S-S and N-C bond cleavage in ECD/ETD mass spectroscopy- Anions in Disguise. Skurski, M. Sobczyk, D.Neff http://simons.hec.utah.edu for references #12;How does ECD (or ETD) fragment

  16. Elastin Degradation by Matrix Metalloproteinases CLEAVAGE SITE SPECIFICITY AND MECHANISMS OF ELASTOLYSIS*

    E-Print Network [OSTI]

    Mecham, Robert

    elastin was characterized by temperature ef- fects and water requirements typical of common en- zyme, the energy requirements for elastolysis were not extraordinary, consistent with cleavage sites in elas- tin a wide distribution in nature and are found in animals as well as in plants and bacteria (4, 5

  17. Carbon Nanotube DNA Sensor and Sensing Mechanism

    E-Print Network [OSTI]

    Le Roy, Robert J.

    nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label for direct label-free detection of DNA hybridization in a biocompatible buffer solution. We also carried out is a field effect device, which has a typical on-current of 3-6 µA at 10 mV source- drain bias and an on-off

  18. 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...

  19. 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.

  20. 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.

  1. Bioconjugated Nanoparticles for DNA Protection from Cleavage Xiao-xiao He, Kemin Wang,* Weihong Tan, Bin Liu, Xia Lin, Chunmei He, Du Li,

    E-Print Network [OSTI]

    Tan, Weihong

    in water-in-oil microemulsion. Briefly, a well- distributed mixture of the two silanes (with volume ratio 1/Biosensing and Chemometrics, College of Chemistry & Chemical Engineering, Institute of Biological Technology, Hunan Uni and 4, plasmid DNA moved in the electric field, and amino-modified silica nanopar- ticles-plasmid DNA

  2. Kinetic Mechanism of Direct Transfer of Escherichia coli SSB Tetramers between Single-Stranded DNA Molecules

    E-Print Network [OSTI]

    Lohman, Timothy M.

    Kinetic Mechanism of Direct Transfer of Escherichia coli SSB Tetramers between Single-Stranded DNA tetramer forms transiently prior to the release of the acceptor DNA. When an initial 1:1 SSB-ssDNA complex tetramer to form a singly ligated complex. However, when an initial SSB-ssDNA complex is formed with (dT)35

  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...

  4. DNA Cleavage by Photogenerated Rh2(O2CCH3)4(H2O)2 Patty K.-L. Fu, Patricia M. Bradley, and Claudia Turro*

    E-Print Network [OSTI]

    Turro, Claudia

    the subject of intense investigation since, upon light activation, they can act as reporters of DNA structure and coordination of the dirhodium core to single-stranded oligonucleotides has been observed, the mode of binding-methylpyridinium tetrafluoroborate (py+),17 results in the formation of the one-electron-oxidized complex, Rh2(O2

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

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

    revealing the surprising mechanism behind FEN1's speed, accuracy, and versatility. A Recipe for Rigorous Replication Providing a duplicate copy of DNA for each new cell requires...

  6. A 1.9 Å 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.

  7. Mechanical Control of Enzymes Using DNA Molecular Springs

    E-Print Network [OSTI]

    Tseng, Chiao-Yu

    2013-01-01

    Responses of GK to Mechanical Stresses . . . . . . .4 Mechanical Control of Renilla116 Relation of Enzymatic Activity and Mechanical Stress

  8. A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

    E-Print Network [OSTI]

    Dinner, Aaron

    A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT Jie and the forces that promote it. In contrast to previously proposed flipping mechanisms, we observe a two and ``pulled'' by specific interactions in the active site (5, 6). Alternatively, more passive mechanisms

  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)

    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.

  10. 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

  11. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

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  12. Mechanism for Damage to DNA by Low-Energy Electrons Robyn Barrios, Piotr Skurski, and Jack Simons*

    E-Print Network [OSTI]

    Simons, Jack

    Mechanism for Damage to DNA by Low-Energy Electrons Robyn Barrios, Piotr Skurski, and Jack Simons electronic structure calculations on a portion of DNA, the results of which provide support for a mechanism that produces single-strand breaks (SSBs) with low-energy electrons. This mechanism involves attaching a low

  13. Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms

    E-Print Network [OSTI]

    Levine, Alex J.

    . This separation is mainly performed in gels, and a wide variety of migration mechanisms can come into play for Migration in High Fields 841 A. Direct simulations of a chain in an array of obstacles 842 B. Tube models fields 848 E. Return to analytics 849 1. Investigating the repton model in depth 849 2. Analytical models

  14. DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery

    E-Print Network [OSTI]

    Brickner, Jason

    ARTICLES DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery are recruited to the nuclear periphery after transcriptional activation. We have identified two gene recruitment sequences (GRS I and II) from the promoter of the INO1 gene that target the gene to the nuclear periphery

  15. A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

    E-Print Network [OSTI]

    Tesoro, S; Morozov, A N; Sulaiman, N; Marenduzzo, D

    2015-01-01

    The first level of folding of DNA in eukaryotes is provided by the so called '10nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging 'bead on a string' structure. In this work we present a one dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We consider both the case of homogeneous DNA, where the problem can be mapped to a Tonks gas, and that of genomic sheep DNA, where our modelling is informed by high-resolution nucleosome positioning data. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally, we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on ...

  16. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments

    E-Print Network [OSTI]

    Rocha, M S

    2015-01-01

    In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in special when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of the DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch the DNA-ligand complex...

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation ofAlbuquerque|SensitiveAprilPhotonStructure of DNA-Bound FEN1 Reveals Mechanism

  18. 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

  19. Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

    SciTech Connect (OSTI)

    Not Available

    1988-01-01

    The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.

  20. 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.

  1. 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.

  2. Investigation of the Effect of Hydrogel Pore Morphology on DNA Migration Mechanisms in Microchip Gel Electrophoresis 

    E-Print Network [OSTI]

    Shi, Nan

    2014-08-20

    Many efforts to develop advanced medical diagnostic capabilities rely on the ability to perform size-based separations of DNA and proteins. Miniaturized formats have potential to provide rapid integrated solutions, but ...

  3. To understanding of the mechanisms of DNA deactivation in ion therapy of cancer cells

    E-Print Network [OSTI]

    Piatnytskyi, D V; Perepelytsya, S M; Volkov, S N

    2015-01-01

    The changes of medium in the living cell during ion beam therapy are considered as the probable reason of disruption of the cancer cells functioning. As the most probable molecular product appeared in the cell after the passage of high energy ions, the hydrogen peroxide molecule is picked out. The possibility of the formation of stable complexes of hydrogen peroxide molecules with the sites of DNA nonspecific recognition (phosphate groups of the double helix backbone) is studied. Due to the negative charge on the oxygen atoms of PO$_{4}^{-}$ the counterions that under natural conditions neutralize the DNA double helix have been also taken into consideration. The complexes consisting of oxygen atoms of DNA phosphate group, H$_2$O$_2$ and H$_2$O molecules, and Na$^{+}$ counterion have been considered. The complex energies have been determined with accounting of electrostatic and van der Waals interactions in the framework of atom-atom potential functions. The stability of various configurations of molecular com...

  4. An investigation of crack-tip stress field criteria of predicting cleavage-crack initiation

    SciTech Connect (OSTI)

    Keeney-Walker, J.; Bass, B.R.; Landes, J.D. (Oak Ridge National Lab., TN (United States))

    1991-09-01

    Cleavage-crack initiation in large-scale wide-plate (WP) specimens could not be accurately predicted from small, compact (CT) specimens by using a linear-elastic fracture-mechanics, K{sub Ic}, methodology. In the wide-plate tests conducted by the Heavy-Section Steel Technology Program at Oak Ridge National Laboratory, crack initiation has consistently occurred at stress-intensity (K{sub I}) values ranging from two to four times those predicted by the CT specimens. Studies were initiated to develop crack-tip stress field criteria incorporating effects of geometry, size, and constraint that will lead to improved predictions of cleavage initiation in WP specimens from CT specimens. The work centers around nonlinear two-and three-dimensional finite-element analyses of the crack-tip stress fields in these geometries. Analyses were conducted on CT and WP specimens for which cleavage initiation fracture had been measured in laboratory tests. The local crack-tip field generated for these specimens were then used in the evaluation of fracture correlation parameters to augment the K{sub I} parameter for predicting cleavage initiation. Parameters of hydrostatic constraint and of maximum principal stress, measured volumetrically, are included in these evaluations. The results suggest that the cleavage initiation process can be correlated with the local crack-tip fields via a maximum principal stress criterion based on achieving a critical area within a critical stress contour. This criterion has been successfully applied to correlate cleavage initiation in 2T-CT and WP specimen geometries. 23 refs., 16 figs., 5 tabs.

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation ofAlbuquerque|SensitiveAprilPhotonStructure of DNA-Bound FEN1 Reveals

  6. Multiple Word DNA Computing on Surfaces Liman Wang, Qinghua Liu,, Robert M. Corn, Anne E. Condon,,# and

    E-Print Network [OSTI]

    Multiple Word DNA Computing on Surfaces Liman Wang, Qinghua Liu,,§ Robert M. Corn, Anne E. Condon words" is demonstrated, with applications to DNA computing. A new DESTROY operation to selectively enzyme cleavage, has been developed for multiple-word DNA computing. DNA polymerase is used to extend DNA

  7. 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.; Schär, 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.

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

    Office of Scientific and Technical Information (OSTI)

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

  9. 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.

  10. Redesigning the Specificity of ProteinDNA Interactions with Rosetta

    E-Print Network [OSTI]

    Baker, David

    +Business Media New York 2014 #12;266 DNA cleavage enzymes, such as LAGLIDADG endonucleases [4, 5], to sites specificity offer an efficient alternative to more labor-intensive experimental procedures, such as directed­DNA specificity.Each panel represents the structure with the mean energy from a set of 56 repacks done

  11. Non-Chromatographic Protein Purification via Mini-Intein Cleavage 

    E-Print Network [OSTI]

    Valdes, Najla

    2012-04-20

    NON-CHROMATOGRAPHIC PROTEIN PURIFICATION VIA MINI-INTEIN CLEAVAGE Major: Chemical Engineering May 2012 Submitted to Honors and Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation... as UNDERGRADUATE RESEARCH SCHOLAR A Senior Scholars Thesis by NAJLA EUNICE VALDES NON-CHROMATOGRAPHIC PROTEIN PURIFICATION VIA MINI-INTEIN CLEAVAGE Approved by: Research Advisor: Zhilei Chen Associate Director, Honors and Undergraduate Research...

  12. 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.

  13. Research Paper 85 The role of the cleavage site 2-hydroxyl in the Tetrahymena

    E-Print Network [OSTI]

    Herschlag, Dan

    Research Paper 85 The role of the cleavage site 2-hydroxyl in the Tetrahymena group I ribozyme-hydroxyl of U preceding the cleavage site, U(­1), in the Tetrahymena ribozyme reaction contributes 103-fold

  14. The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1

    SciTech Connect (OSTI)

    Nash, Rebekah Potts; Habibi, Sohrab; Cheng, Yuan; Lujan, Scott A.; Redinbo, Matthew (UNC)

    2010-11-15

    Bacteria expand their genetic diversity, spread antibiotic resistance genes, and obtain virulence factors through the highly coordinated process of conjugative plasmid transfer (CPT). A plasmid-encoded relaxase enzyme initiates and terminates CPT by nicking and religating the transferred plasmid in a sequence-specific manner. We solved the 2.3 {angstrom} crystal structure of the relaxase responsible for the spread of the resistance plasmid pCU1 and determined its DNA binding and nicking capabilities. The overall fold of the pCU1 relaxase is similar to that of the F plasmid and plasmid R388 relaxases. However, in the pCU1 structure, the conserved tyrosine residues (Y18,19,26,27) that are required for DNA nicking and religation were displaced up to 14 {angstrom} out of the relaxase active site, revealing a high degree of mobility in this region of the enzyme. In spite of this flexibility, the tyrosines still cleaved the nic site of the plasmid's origin of transfer, and did so in a sequence-specific, metal-dependent manner. Unexpectedly, the pCU1 relaxase lacked the sequence-specific DNA binding previously reported for the homologous F and R388 relaxase enzymes, despite its high sequence and structural similarity with both proteins. In summary, our work outlines novel structural and functional aspects of the relaxase-mediated conjugative transfer of plasmid pCU1.

  15. Nanotechnology with DNA DNA Nanodevices

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

  16. Cleavage of biphenyl moieties: An efficient new reaction pathway in catalytic hydrocracking

    SciTech Connect (OSTI)

    Klein, M.T.; Lapinas, A.T.; Gates, B.C.; Read, C.J.; Lyons, J.E. (Univ. of Delaware, Newark (United States)); Macris, A. (Sun Co., Marcus Hook, PA (United States))

    1992-10-01

    The hydrocracking of the five-carbon-membered-ring-containing PNA fluoranthsene (I) is qualitatively different from the classical pattern. A major reaction pathway involves hydrogenation to give tetrahydrofluoranthene (II), center ring opening to give phenyl tetralin (III), and biphenyl cleavage to give tetralin (IV) and benzene. This mechanism includes protonation of (III) followed by an internal 1,5-hydride shift to afford the carbenium ion III{sup +}, of III, represented in the benzylic form. A 1,3-hydride shift of a resonance form of III{sup +} affords benzene and a carbenium ion IV{sup +}, the deprotonation of which leads to an intermediate, dialin, which is rapidly hydrogenated to yield tetralin. The noteworthy reaction in the sequence, which is a net 1.5-shift of the benzylic hydride to the ring bearing the positively charged carbon, evidently takes place along a molecular topology that includes a strong biphenyl linkage. This suggests an apparent structural moiety for efficient cleavage of strong biphenyl linkages, which otherwise would require prior hydrogenation. Thus, the authors have investigated the catalytic hydrocracking of molecules that either contain this structural moiety, or can react to form it. Experiments were done to determine the hydrocracking pathways and kinetics of 9-ethyl fluorene, 9-phenyl anthracene, and 2-phenyl naphthalene in the presence of an equilibrated Ni-Mo/Al{sub 2}O{sub 3}-catalyst-containing ultra-stable Y-Zeolite at 310-380 C and 153 atm.

  17. DNA Mixture DNA Mixture

    E-Print Network [OSTI]

    ;Introductions J.M. Butler ­ Wisconsin DNA Mixture Training May 12, 2009 http://www.cstl.nist.gov/biotech.M. Butler ­ Wisconsin DNA Mixture Training May 12, 2009 http://www.cstl.nist.gov/biotech textbook (now in its 2nd Edition) · STRBase website: http://www.cstl.nist.gov/biotech/strbase/ · Family

  18. Carbon-Fluorine Bond Cleavage by Zirconium Metal Hydride Complexes

    E-Print Network [OSTI]

    Jones, William D.

    Carbon-Fluorine Bond Cleavage by Zirconium Metal Hydride Complexes Brian L. Edelbach, A. K. Fazlur, Rochester, New York 14627 Received April 8, 1999 The zirconium hydride dimer [Cp2ZrH2]2 reacts with C6F6. [Cp2ZrH2]2 reacts with C6F5H to give Cp2Zr(p-C6F4H)F, Cp2ZrF2, C6F4H2, and H2. The zirconium hydride

  19. Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under Physiologically Relevant

    E-Print Network [OSTI]

    Gates, Kent. S.

    Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under found that micromolar concentrations of H2S generated single-strand DNA cleavage. Mechanistic studies indicate that this process involved autoxidation of H2S to generate superoxide, hydrogen peroxide, and

  20. DEVELOPMENTALBIOLOGY120,270-283(198'7) Centrifugation Redistributes Factors Determining Cleavage

    E-Print Network [OSTI]

    Weisblat, David A.

    DEVELOPMENTALBIOLOGY120,270-283(198'7) Centrifugation Redistributes Factors Determining Cleavage/P, and Q) teloblasts. Here we report studies on the effects of centrifugation on cleavage pattern and protein composition of individual blastomeres of the leech HelobdeUu triswialis. Centrifugation partially

  1. 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.

  2. 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.

  3. The role of the de novo DNA methyltransferase Dnmt3a in the nervous system

    E-Print Network [OSTI]

    Nguyen, Suzanne Pham

    2007-01-01

    DNA methylation is an important mechanism of gene regulation. Evidence is mounting that epigenetic mechanisms including that of DNA methylation operate in the nervous system. Genetic disruption of the de novo DNA ...

  4. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09

    We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heterogeneity and finite temperature and discuss possible applications to determine the strength of colloidal nanoparticle assemblies functionalized by DNA.

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

    DOE Patents [OSTI]

    Kilbane, II, John J. (Woodstock, IL)

    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.

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

    DOE Patents [OSTI]

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

    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. A novel role for the transcriptional modulator NusA in DNA repair/damage tolerance pathways in Escherichia coli

    E-Print Network [OSTI]

    Cohen, Susan E., Ph. D. Massachusetts Institute of Technology

    2009-01-01

    All organisms must contend with the consequences of DNA damage, induced by a variety of both endogenous and exogenous sources. Mechanisms of DNA repair and DNA damage tolerance are crucial for cellular survival after DNA ...

  10. Atomistic characterization of stress-driven configurational instability and its activation mechanisms

    E-Print Network [OSTI]

    Zhu, Ting, 1971-

    2004-01-01

    Cleavage decohesion and shear dislocation nucleation are two basic modes of localized deformation in crystal lattices, which normally result from instability of the atomic configuration driven by mechanical forces. The ...

  11. Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA cleavage mechanism.

    E-Print Network [OSTI]

    Thomas, Brian C.; Li, Xinqiang; Gegenheimer, Peter Albert

    2000-01-01

    RNase P RNA is the sole catalytic component. In contrast, the RNase P activity isolated from spinach chloroplasts lacks an RNA component and appears to function as a catalytic protein. Nonetheless, the chloroplast enzyme recognizes a pre-tRNA substrate...

  12. Euler buckling and nonlinear kinking of double-stranded DNA

    E-Print Network [OSTI]

    Cohen, Adam E.

    physiological conditions: at high curvature, does the DNA bend smoothly, or does it kink like a drinking straw and damage). These aspects of DNA mechanics are likely to influence protein binding and DNA packaging, yet the effect of single-nucleotide mismatches on DNA bending. Our data support a model of linear elastic bending

  13. New Regioselectivity in the Cleavage of Histidine-Containing Peptides by Palladium(II) Complexes Studied by Kinetic Experiments

    E-Print Network [OSTI]

    Ullmann, G. Matthias

    New Regioselectivity in the Cleavage of Histidine-Containing Peptides by Palladium(II) Complexes, Germany ReceiVed July 6, 1998 Abstract: Palladium(II) complexes promote hydrolytic cleavage of amide bonds at the N-1 or N-3 atom of imidazole. Methylation controls coordination of imidazole to palladium

  14. StochasticModeling of the Independent Roles of Particle Size and Grain Size in Transgranular Cleavage Fracture

    E-Print Network [OSTI]

    Ritchie, Robert

    Cleavage Fracture TSANN LIN, A. G. EVANS, and R. O. RITCHIE The independent roles of grain size. INTRODUCTION CLEAVAGE fracture in most metals occurs by the nu- cleation of a microcrack, assisted by the local, concentrated, tensile stress exceeds some critical fracture stress. In mild steels, such microcracks were

  15. Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2

    E-Print Network [OSTI]

    Tullius, Thomas D.

    Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2 and Jason A Greenbaum2 Hydroxyl radical footprinting is a widely used method for following the folding of RNA molecules be followed simultaneously at single-nucleotide resolution. In recent work, hydroxyl radical footprinting has

  16. Cytokine secretion profiles in primary cultured cells and in mice stimulated with plasmid DNA

    E-Print Network [OSTI]

    Yoshida, Hiroyuki

    2006-10-27

    University Elimination of DNA by antigen presenting cells Gene therapy Infection Leakage Processing Macrophages and dendritic cells Apoptotic or necrotic cells Endogenous DNA DNA Virus Plasmid DNA Exogenous DNA CpG motif5?- Pur Pur CG Pyr Pyr -3? Danger... signal Naked CpG DNA DNA lipoplex Macrophages or dendritic cells ???? ???? Cytokine geneNF-?B AP-1 ???? ???? Endosome Nucleus ? TLR9 Interferon ?/? gene Inflammatory cytokines TNF-?, IL-6 etc. Type I interferon IFN-?, INF-? ? Mechanisms of immune response...

  17. Use of Plasmon Coupling to Reveal the Dynamics of DNA Bending and Cleavage by Single EcoRV Restriction Enzymes

    E-Print Network [OSTI]

    Reinhard, Bjorn; Sheikholeslami, Sassan; Mastroianni, Alexander; Alivisatos, A. Paul; Liphardt, Jan

    2006-01-01

    5000 rpm, 15 min) and resuspension in T40 (40mM NaCl, 10mMTris, pH8). After resuspension the gold particle5000 rpm, 15 min) and resuspension in T40. After two washing

  18. Roles of grain boundaries in cleavage cracking and thermal crack arrest experiments in iron-silicon alloy

    E-Print Network [OSTI]

    Qiao, Yu, 1972-

    2002-01-01

    High-angle grain boundaries in steel offer an important resistance to the propagation of cleavage cracks that affects the fracture toughness and can modulate the ductile-to-brittle transition temperature of fracture downward. ...

  19. CarbonCarbon Bond Cleavage and Dehydrogenation of Isobutane Over HZSM-5 at Low Pressures and Temperatures

    E-Print Network [OSTI]

    Tesfatsion, Leigh

    Acidic zeolite substrates, such as HZSM-5 are vital cata- lysts in the petrochemical industry, due-temperature activation for C­C bond cleavage to propene and methane, and dehydrogenation to isobutene and hydrogen

  20. 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.

  1. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30

    It has been previously shown that DNA computing can solve those problems currently intractable on even the fastest electronic computers. The algorithm design for DNA computing, however, is not straightforward. A strong background in both the DNA...

  2. 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.

  3. DNA Engine Thermal Cycler

    E-Print Network [OSTI]

    Raizada, Manish N.

    ® Peltier Thermal Cycler PTC-0200 DNA Engine Cycler Operations Manual Version 4.0 #12;ii Tech Support: 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi The DNA Engine® Peltier Thermal Cycler Introduction

  4. 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.

  5. Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage

    E-Print Network [OSTI]

    Pruteanu, Mihaela

    UV irradiation damages DNA and activates expression of genes encoding proteins helpful for survival under DNA stress. These proteins are often deleterious in the absence of DNA damage. Here, we investigate mechanisms used ...

  6. Conversion of the LIMA1 tumor suppressor into an oncogenic LMO-like protein by API2-MALT1 paracaspase cleavage in MALT lymphoma

    E-Print Network [OSTI]

    Nie, Zilin; Du, Ming-Qing; McAllister-Lucas, Linda M.; Lucas, Peter C.; Bailey, Nathanael G.; Hogaboam, Cory M.; Lim, Megan S.; Elenitoba-Johnson, Kojo S. J.

    2015-01-08

    lymphomagenesis by cleavage of LIMA1?. Finally, to demonstrate the clinical relevance of API2-MALT1 targeting LIMA1 in B cell oncogenesis, LIMA1 proteolytic cleavage was examined by Western blot in cell lysates obtained from patient-derived API2-MALT1 positive...

  7. Photoaffinity Labeling Reveals Nuclear Proteins That Uniquely Recognize Cisplatin?DNA Interstrand Cross-Links

    E-Print Network [OSTI]

    Zhu, Guangyu

    The DNA-binding inorganic compound cisplatin is one of the most successful anticancer drugs. The detailed mechanism by which cells recognize and process cisplatin?DNA damage is of great interest. Although the family of ...

  8. 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.

  9. 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.

  10. Circadian Regulation of the PhCCD1 Carotenoid Cleavage Dioxygenase Controls Emission of b-Ionone,

    E-Print Network [OSTI]

    Klee, Harry J.

    Circadian Regulation of the PhCCD1 Carotenoid Cleavage Dioxygenase Controls Emission of b rhythm in both leaves and flowers. b-Ionone emission by flowers occurred principally during daylight-ionone emission are likely regulated at the level of transcript. Apocarotenoids are a class of compounds derived

  11. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

    in Genome Functioning . Biological Role of Alternative DNA Structures Figure 1 A hypothetical circular DNA. 1ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net #12;topological

  12. Capstan friction model for DNA ejection from bacteriophages

    E-Print Network [OSTI]

    Sandip Ghosal

    2013-01-09

    Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell.The phage DNA is then transcribed by the cell's transcription machinery.A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection.In recent in vitro experiments, the speed of DNA translocation from a lambda phage capsid has been measured as a function of ejected length over the entire duration of the event.Here a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.

  13. Mechanism of the Acid-Catalyzed Si-O Bond Cleavage in Siloxanes and Siloxanols. A Theoretical Study

    E-Print Network [OSTI]

    Apeloig, Yitzhak

    Marek Cypryk*, and Yitzhak Apeloig Center of Molecular and Macromolecular Studies of Polish Academy. Introduction Acid-catalyzed condensation of silanol groups is the most important reaction leading considerable interest of theoreticians.5 Kinetic studies showed that in acidic media silanol condensation

  14. Activation of nucleic acid-sensing Toll-like receptors requires cleavage by endolysosomal proteases: a mechanism to avoid autoimmunity

    E-Print Network [OSTI]

    Ewald, Sarah Elisabeth

    2010-01-01

    activation. Immunity 28, Hacker, H. , and Karin, M. (2006).Sci STKE 2006, re13. Hacker, H. , Mischak, H. , Miethke,Embo J 17, 6230-6240. Hacker, H. , Redecke, V. , Blagoev,

  15. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

    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.

  16. 2006 Nature Publishing Group Mechanochemical analysis of DNA gyrase using

    E-Print Network [OSTI]

    Gore, Jeff

    -independent step at the end of the reaction cycle, and an ATP-binding step in the middle of the cycle, subsequent of DNA gyrase, which works against mechanical stresses to drive the genome into an elastically strained releasing the DNA substrate), the location of the rate-limiting step for the overall reaction cycle

  17. Mechanical forces such as cell traction control cell growth, differ

    E-Print Network [OSTI]

    Salaita, Khalid

    Mechanical forces such as cell traction control cell growth, differ entiation, motility, which bind integrins (transmembrane receptors that relay mechanical signals from the extracellular the contribution of mechanical forces to cell behaviour and function. Eytan Zlotorynski TECHNIQUE DNA hairpins

  18. 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.

  19. Cleavage specificity of chloroplast and nuclear tRNA 3'-processing nucleases.

    E-Print Network [OSTI]

    Oommen, A.; Li, X. Q.; Gegenheimer, Peter Albert

    1992-02-01

    step in forma- tion of functional mature tRNA molecules (11, 18, 27), since it is to the tRNA's 3'-terminal adenosine residue that amino acids are esterified during protein biosynthesis. Maturation of tRNA precursors requires at least two nucleolytic... from SPECIFICITY OF PLANT tRNA 3'-PROCESSING NUCLEASES 867 was selected, and the DNA sequence of its insert was determined. Plasmid DNA was prepared by a modification of standard protocols (29, 31). Cells were lysed by boiling; after acidic phenol...

  20. Advanced Review Mediators and dynamics of DNA

    E-Print Network [OSTI]

    Wang, Wei

    -wide classifies cell types uniquely and in several cases discriminates between healthy and cancerous cell types zinc fin- ger proteins, recognize the presence of methylated cytosines.4­13 DNMT1 maintains methylation mechanism that prevents the activation of these sequences.31­34 DNA methyla- tion is also present in genes

  1. Z .Mechanics of Materials 28 1998 247262 Experimental and computational study of fracturing in an

    E-Print Network [OSTI]

    Nemat-Nasser, Sia

    Z .Mechanics of Materials 28 1998 247­262 Experimental and computational study of fracturing, stress- and energy-based fracture criteria lead to fairly similar results. Theoretical studies show the fracture path along different cleavage planes. The experimental observations are compared

  2. Size and Temperature Effects on the Fracture Mechanisms of Silicon Nanowires: Molecular Dynamics

    E-Print Network [OSTI]

    Cai, Wei

    Size and Temperature Effects on the Fracture Mechanisms of Silicon Nanowires: Molecular Dynamics. The fracture behavior of the NWs depends both on temperature and NW diameter. For NWs of di- ameter larger than 4 nm, cleavage fracture on the transverse (1 1 0) plane are predominantly observed at temperatures

  3. Metal-Catalyzed C-C Bond Cleavage in Alkanes: Effects of Methyl Substitution on Transition-State Structures and Stability

    E-Print Network [OSTI]

    Iglesia, Enrique

    -C bonds via hydrogenolysis reactions during catalytic reforming and isomerization pro- cesses,1 which. Such interpretations and catalytic consequences of substitution seem also relevant to C-X cleavage (X = S, N, O

  4. Introduction: DNA Electrophoresis Fralin Life Science

    E-Print Network [OSTI]

    Hopkins, William A.

    .................................... 12 Student Pre-Lab Activity: What is DNA? DNA extraction from strawberry ..... Teacher guide: DNA extraction from strawberry.................................. 14 Student guide: DNA extraction from strawberry.................................. 16

  5. DNA nanotechnology: understanding and optimisation through simulation

    E-Print Network [OSTI]

    Thomas E. Ouldridge

    2014-11-07

    DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

  6. Kinetics of target site localization of a protein on DNA: a stochastic approach

    E-Print Network [OSTI]

    M. Coppey; O. Benichou; R. Voituriez; M. Moreau

    2005-02-23

    It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one--dimensional diffusion along a DNA segment, and long--range jumps coming from association/dissociation events. We propose here a stochastic model for this reaction which comprises a series of 1D diffusions of a restriction enzyme on non-specific DNA sequences interrupted by 3D excursions in the solution until the target sequence is reached. This model provides an optimal finding strategy which explains the fast association rate. Modeling the excursions by uncorrelated random jumps, we recover the expression of the mean time required for target site association to occur given by Berg & al. \\cite{berg81}, and we explicitly give several physical quantities describing the stochastic pathway of the enzyme. For competitive target sites we calculate two quantities: processivity and preference. By comparing these theoretical expressions to recent experimental data obtained for \\textit{Eco}RV--DNA interaction, we quantify: i) the mean residence time per binding event of \\textit{Eco}RV on DNA for a representative 1D diffusion coefficient, ii) the average lengths of DNA scanned during the 1D diffusion (during one binding event and during the overall process), iii) the mean time and the mean number of visits needed to go from one target site to the other. Further, we evaluate the dynamics of DNA cleavage with regard to the probability for the restriction enzyme to perform another 1D diffusion on the same DNA substrate following a 3D excursion.

  7. Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

    SciTech Connect (OSTI)

    Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E.; Wilson, Gerald M.

    2009-05-11

    The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

  8. 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.

  9. Processing of 3'-Phosphoglycolate-Terminated DNA Double-StrandBreaks by Artemis Nuclease

    SciTech Connect (OSTI)

    Povrik, Lawrence F.; Zhou, Tong; Zhou, Ruizhe; Cowan, Morton J.; Yannone, Steven M.

    2005-10-01

    The Artemis nuclease is required for V(D)J recombination and for repair of an as yet undefined subset of radiation-induced DNA double-strand breaks. To assess the possibility that Artemis functions on oxidatively modified double-strand break termini, its activity toward model DNA substrates, bearing either 3{prime}-hydroxyl or 3{prime}-phosphoglycolate moieties, was examined. A 3{prime}-phosphoglycolate had little effect on Artemis-mediated trimming of long 3{prime} overhangs (>9 nucleotides), which were efficiently trimmed to 4-5 nucleotides. However, 3{prime}-phosphoglycolates on overhangs of 4-5 bases promoted selective Artemis-mediated trimming of a single 3{prime}-terminal nucleotide, while at least 2 nucleotides were trimmed from identical hydroxyl-terminated substrates. Artemis also efficiently removed a single nucleotide from a phosphoglycolate-terminated 3-base 3{prime} overhang, while leaving an analogous hydroxyl-terminated overhang largely intact. Such removal was dependent upon Ku, DNA-dependent protein kinase, and ATP. Together, these data suggest that Artemis-mediated cleavage of 3{prime} overhangs requires a minimum of 2 nucleotides, or a nucleotide plus a phosphoglycolate, 3{prime} to the cleavage site. Shorter 3{prime}-phosphoglycolate-terminated overhangs and blunt ends were also processed by Artemis, but much less efficiently. Consistent with the in vitro substrate specificity of Artemis, human cells lacking Artemis exhibited hypersensitivity to X-rays, bleomycin and neocarzinostatin, which all induce 3{prime}-phosphoglycolate-terminated double-strand breaks. Collectively, these results suggest that 3{prime}-phosphoglycolate termini and/or specific classes of DNA ends that arise from such blocked termini are relevant Artemis substrates in vivo.

  10. Becky Hill Green Mountain DNA Conference LT-DNA Analysis

    E-Print Network [OSTI]

    Becky Hill ­ Green Mountain DNA Conference LT-DNA Analysis July 26, 2010 http of the Chief Medical Examiner, NYC Green Mountain DNA Conference Burlington, VT July 26, 2010 Low Template (LT generally aim for 0.5-2 ng 100 pg template 5 pg template #12;Becky Hill ­ Green Mountain DNA Conference LT

  11. 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.

  12. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M. (Boston, MA); Kieffer-Higgins, Stephen (Dorchester, MA)

    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. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

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

    Shaikh, Nizamuddin [Brookhaven National Laboratory, Chemistry Dept, Upton, NY (United States); Valiev, Marat [Pacific Northwest National Laboratory, William R. Wiley Environmental Molecular Sciences Laboratory, Richland, WA (United States); Lymar, Sergei V. [Brookhaven National Laboratory, Chemistry Dept, Upton, NY (United States)

    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 = single bondN(C2H5)2 (1), single bondN(C3H4NH2)2 (2), or single bondN(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 Nsingle bondN 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.

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

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

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

    2014-12-01

    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; 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. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH - group.« less

  15. 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.

  16. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

    Jonathan P. K. Doye; Thomas E. Ouldridge; Ard A. Louis; Flavio Romano; Petr Sulc; Christian Matek; Benedict E. K. Snodin; Lorenzo Rovigatti; John S. Schreck; Ryan M. Harrison; William P. J. Smith

    2013-08-18

    To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

  17. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

    Doye, Jonathan P K; Louis, Ard A; Romano, Flavio; Sulc, Petr; Matek, Christian; Snodin, Benedict E K; Rovigatti, Lorenzo; Schreck, John S; Harrison, Ryan M; Smith, William P J

    2013-01-01

    To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

  18. Insights into DNA-mediated interparticle interactions from a coarse-grained model

    E-Print Network [OSTI]

    Yajun Ding; Jeetain Mittal

    2015-03-05

    DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA- functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

  19. 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.

  20. Force steps during viral DNA packaging ?

    E-Print Network [OSTI]

    Prashant K. Purohit; Jane' Kondev; Rob Phillips

    2003-09-22

    Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process.

  1. 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.

  2. DNA repair: Dynamic defenders against cancer and aging

    SciTech Connect (OSTI)

    Fuss, Jill O.; Cooper, Priscilla K.

    2006-04-01

    You probably weren't thinking about your body's cellular DNA repair systems the last time you sat on the beach in the bright sunshine. Fortunately, however, while you were subjecting your DNA to the harmful effects of ultraviolet light, your cells were busy repairing the damage. The idea that our genetic material could be damaged by the sun was not appreciated in the early days of molecular biology. When Watson and Crick discovered the structure of DNA in 1953 [1], it was assumed that DNA is fundamentally stable since it carries the blueprint of life. However, over 50 years of research have revealed that our DNA is under constant assault by sunlight, oxygen, radiation, various chemicals, and even our own cellular processes. Cleverly, evolution has provided our cells with a diverse set of tools to repair the damage that Mother Nature causes. DNA repair processes restore the normal nucleotide sequence and DNA structure of the genome after damage [2]. These responses are highly varied and exquisitely regulated. DNA repair mechanisms are traditionally characterized by the type of damage repaired. A large variety of chemical modifications can alter normal DNA bases and either lead to mutations or block transcription if not repaired, and three distinct pathways exist to remove base damage. Base excision repair (BER) corrects DNA base alterations that do not distort the overall structure of the DNA helix such as bases damaged by oxidation resulting from normal cellular metabolism. While BER removes single damaged bases, nucleotide excision repair (NER) removes short segments of nucleotides (called oligonucleotides) containing damaged bases. NER responds to any alteration that distorts the DNA helix and is the mechanism responsible for repairing bulky base damage caused by carcinogenic chemicals such as benzo [a]pyrene (found in cigarette smoke and automobile exhaust) as well as covalent linkages between adjacent pyrimidine bases resulting from the ultraviolet (UV) component of sunlight. NER can be divided into two classes based on where the repair occurs. NER occurring in DNA that is not undergoing transcription (i.e., most of the genome) is called global genome repair (GGR or GGNER), while NER taking place in the transcribed strand of active genes is called transcription-coupled repair (TCR or TC-NER). We will explore NER in more detail below. Mismatch repair (MMR) is another type of excision repair that specifically removes mispaired bases resulting from replication errors. DNA damage can also result in breaks in the DNA backbone, in one or both strands. Single-strand breaks (SSBs) are efficiently repaired by a mechanism that shares common features with the later steps in BER. Double-strand breaks (DSBs) are especially devastating since by definition there is no intact complementary strand to serve as a template for repair, and even one unrepaired DSB can be lethal [3]. In cells that have replicated their DNA prior to cell division, the missing information can be supplied by the duplicate copy, or sister chromatid, and DSBs in these cells are faithfully repaired by homologous recombination involving the exchange of strands of DNA between the two copies. However, most cells in the body are non-dividing, and in these cells the major mechanism for repairing DSBs is by non-homologous end joining (NHEJ), which as the name implies involves joining two broken DNA ends together without a requirement for homologous sequence and which therefore has a high potential for loss of genetic information.

  3. Searching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase

    E-Print Network [OSTI]

    Drennan, Catherine L.

    To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, ...

  4. Protective effects of melittin on transforming growth factor-{beta}1 injury to hepatocytes via anti-apoptotic mechanism

    SciTech Connect (OSTI)

    Lee, Woo-Ram; Park, Ji-Hyun; Kim, Kyung-Hyun [Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu (Korea, Republic of); Park, Yoon-Yub [Department of Physiology, College of Medicine, Catholic University of Daegu, Daegu (Korea, Republic of); Han, Sang-Mi [Department of Agricultural Biology, National Institute of Agricultural Science and Technology, Suwon (Korea, Republic of); Park, Kwan-kyu, E-mail: kkpark@cu.ac.kr [Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu (Korea, Republic of)

    2011-10-15

    Melittin is a cationic, hemolytic peptide that is the main toxic component in the venom of the honey bee (Apis mellifera). Melittin has multiple effects, including anti-bacterial, anti-viral and anti-inflammatory, in various cell types. However, the anti-apoptotic mechanisms of melittin have not been fully elucidated in hepatocytes. Apoptosis contributes to liver inflammation and fibrosis. Knowledge of the apoptotic mechanisms is important to develop new and effective therapies for treatment of cirrhosis, portal hypertension, liver cancer, and other liver diseases. In the present study, we investigated the anti-apoptotic effect of melittin on transforming growth factor (TGF)-{beta}1-induced apoptosis in hepatocytes. TGF-{beta}1-treated hepatocytes were exposed to low doses (0.5 and 1 {mu}g/mL) and high dose (2 {mu}g/mL) of melittin. The low doses significantly protected these cells from DNA damage in TGF-{beta}1-induced apoptosis compared to the high dose. Also, melittin suppressed TGF-{beta}1-induced apoptotic activation of the Bcl-2 family and caspase family of proteins, which resulted in the inhibition of poly-ADP-ribose polymerase (PARP) cleavage. These results demonstrate that TGF-{beta}1 induces hepatocyte apoptosis and that an optimal dose of melittin exerts anti-apoptotic effects against TGF-{beta}1-induced injury to hepatocytes via the mitochondrial pathway. These results suggest that an optimal dose of melittin can serve to protect cells against TGF-{beta}1-mediated injury. - Highlights: > We investigated the anti-apoptotic effect of melittin on TGF-{beta}1-induced hepatocyte. > TGF-{beta}1 induces hepatocyte apoptosis. > TGF-{beta}1-treated hepatocytes were exposed to low doses and high dose of melittin. > Optimal dose of melittin exerts anti-apoptotic effects to hepatocytes.

  5. & Mechanical Engineering

    E-Print Network [OSTI]

    Zhou, Chongwu

    AME Aerospace & Mechanical Engineering #12;Aerospace and Mechanical Engineers design complex mechanical, thermal, uidic, acoustical, optical, and electronic systems, with characteristic sizes ranging and far underground, to near-Earth, planetary, interplanetary and galactic space. Aerospace and Mechanical

  6. DNA Structural Nanotechnology Duke University

    E-Print Network [OSTI]

    Reif, John H.

    DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran&Caltech Tube Lattices #12;Ned Seeman New York University, USA Ned Seeman: Father of DNA Nanotechnology His Initial Ideas & Motivation for DNA Nanotechnology #12;Cube Chen & Seeman, Nature350:631 (1991) Truncated

  7. DNA translocation through nanopores with salt gradients: The role of osmotic flow

    E-Print Network [OSTI]

    Hatlo, Marius M; van Roij, René

    2010-01-01

    Recent experiments of translocation of double stranded DNA through nanopores [M. Wanunu et al. Nature Nanotech. 5, 160 (2010)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoresis can quantitatively explain the experimental data on the capture rate. The osmotic flow is induced by the salt gradient across the nanopore, and can be the dominant mechanism for DNA translocation through nanopores with a salt gradient.

  8. Ionization Spectroscopy of a DNA Base: Vacuum-Ultraviolet Mass-Analyzed Threshold Ionization Spectroscopy of Jet-Cooled Thymine

    E-Print Network [OSTI]

    Kim, Sang Kyu

    to ionizing radiation.1-8 After the initial ionization of a nucleic acid base, the hole trapped in that base migrates along the DNA helix through hopping and/or tunneling mechanisms, resulting in various types-based molecular devices. According to the hopping mechanism, charge migration in DNA occurs through hole/electron

  9. Protein search for multiple targets on DNA

    E-Print Network [OSTI]

    Martin Lange; Maria Kochugaeva; Anatoly B. Kolomeisky

    2015-08-03

    Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.

  10. 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.

  11. DNA waves and water

    E-Print Network [OSTI]

    L. Montagnier; J. Aissa; E. Del Giudice; C. Lavallee; A. Tedeschi; G. Vitiello

    2010-12-23

    Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We discuss this phenomenon in the framework of quantum field theory. A scheme able to account for the observations is proposed. The reported phenomenon could allow to develop highly sensitive detection systems for chronic bacterial and viral infections.

  12. RESEARCH NOTE A proposed protocol for nomenclaturally effective DNA barcoding of microalgae

    E-Print Network [OSTI]

    RESEARCH NOTE A proposed protocol for nomenclaturally effective DNA barcoding of microalgae barcoding of microalgae. Phycologia 48: 70­74. DOI: 10.2216/08-70.1. A mechanism for giving DNA barcodes nomenclatural status in microalgae via culture-derived epitypes is demonstrated with reference to four species

  13. Adhesion-Induced DNA Naturation A. E. Allahverdyan,1,2

    E-Print Network [OSTI]

    Adhesion-Induced DNA Naturation A. E. Allahverdyan,1,2 Zh. S. Gevorkian,1,3,4 Chin-Kun Hu,4 and Th of the genetic information. We shall study the adsorption and surface (adhesion) induced naturation of a double some features of DNA (see below), our model predicts two mechanisms of adhesion-induced naturation

  14. High-Affinity DNA Base Analogs as Supramolecular, Nanoscale Promoters of Macroscopic Adhesion

    E-Print Network [OSTI]

    Sottos, Nancy R.

    High-Affinity DNA Base Analogs as Supramolecular, Nanoscale Promoters of Macroscopic Adhesion Cyrus Information ABSTRACT: Adhesion phenomena are essential to many biological processes and to synthetic adhesives adhesion mechanisms. Recently, supramolecular building blocks, such as synthetic DNA base- pair mimics

  15. AMEAerospace & Mechanical

    E-Print Network [OSTI]

    Wang, Hai

    , emerging fuel cell technolo- gies, computational fluid mechanics, ground vehicle aerodynamics, combustion students develop problem solving skills in the areas of mechanics, thermody- namics, fluid mechanics, heat advance our understanding of such areas as continuum and particulate fluid mechanics, flight mechanics

  16. Bohmian Mechanics

    E-Print Network [OSTI]

    Detlef Duerr; Sheldon Goldstein; Roderich Tumulka; Nino Zanghi

    2009-03-15

    Bohmian mechanics is a theory about point particles moving along trajectories. It has the property that in a world governed by Bohmian mechanics, observers see the same statistics for experimental results as predicted by quantum mechanics. Bohmian mechanics thus provides an explanation of quantum mechanics. Moreover, the Bohmian trajectories are defined in a non-conspiratorial way by a few simple laws.

  17. Design, fabrication, and characterization of a motion stage for scalable imprinting of DNA nanowires

    E-Print Network [OSTI]

    LaColla, John J. (John Joseph)

    2012-01-01

    This thesis work examines the scalability of an imprinting stage utilizing parallel self-aligning mechanisms in a DNA combing and imprinting (DCl) process. Scalability is vital in developing efficient, low-cost and high-yield ...

  18. Catalytic DNA (deoxyribozymes) for synthetic applications--current abilities and future prospects

    E-Print Network [OSTI]

    Silverman, Scott K.

    nanostructures,6­10 as the basis for nano- mechanical devices,11 and as rigid conformational control elements-term storage of genetic information, the antithesis of chemical reactivity? How can DNA actually do anything

  19. Suberoylanilide Hydroxyamic Acid Modification of Chromatin Architecture Affects DNA Break Formation and Repair

    SciTech Connect (OSTI)

    Singh, Sheetal; Le Hongan; Shih, S.-J.; Ho, Bay [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Vaughan, Andrew T., E-mail: andrew.vaughan@ucdmc.ucdavis.ed [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Department of Veterans Affairs, Mather, California 95655 (United States)

    2010-02-01

    Purpose: Chromatin-modifying compounds that inhibit the activity of histone deacetylases have shown potency as radiosensitizers, but the action of these drugs at a molecular level is not clear. Here we investigated the effect of suberoylanilide hydroxyamic acid (SAHA) on DNA breaks and their repair and induction of rearrangements. Methods and Materials: The effect of SAHA on both clonogenic survival and repair was assessed using cell lines SCC-25, MCF7, and TK6. In order to study unique DNA double-strand breaks, anti-CD95 antibody was employed to introduce a DNA double-strand break at a known location within the 11q23 region. The effects of SAHA on DNA cleavage and rearrangements were analyzed by ligation-mediated PCR and inverse PCR, respectively. Results: SAHA acts as radiosensitizer at 1 {mu}M, with dose enhancement factors (DEFs) at 10% survival of: SCC-25 - 1.24 +- 0.05; MCF7 - 1.16 +- 0.09 and TK6 - 1.17 +- 0.05, and it reduced the capacity of SCC-25 cells to repair radiation induced lesions. Additionally, SAHA treatment diffused site-specific fragmentation over at least 1 kbp in TK6 cells. Chromosomal rearrangements produced in TK6 cells exposed to SAHA showed a reduction in microhomology at the breakpoint between 11q23 and partner chromosomes. Conclusions: SAHA shows efficacy as a radiosensitizer at clinically obtainable levels. In its presence, targeted DNA strand breaks occur over an expanded region, indicating increased chromatin access. The rejoining of such breaks is degraded by SAHA when measured as rearrangements at the molecular level and rejoining that contributes to cell survival.

  20. DNA | Open Energy Information

    Open Energy Info (EERE)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIX E LISTStar EnergyLawler,CoalConcordiaConsumerLEDSEnergyDMS Company Ltd Jump to:DNA Jump

  1. Transcription factor search for a DNA promoter in a three-states model

    E-Print Network [OSTI]

    Juergen Reingruber; David Holcman

    2011-04-12

    To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF bound to the DNA), the TF further switches between a fast translocation state dominated by interaction with the DNA backbone, and a slow examination state where interaction with DNA base pairs is predominant. We derive a new formula for the mean search time, and show that it is faster and less sensitive to the binding energy fluctuations compared to the case of a single sliding state. We find that for an optimal search, the time spent bound to the DNA is larger compared to the 3D time in the nucleus, in agreement with recent experimental data. Our results further suggest that modifying switching via phosphorylation or methylation of the TF or the DNA can efficiently regulate transcription.

  2. 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 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. 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.

  3. Bohmian mechanics contradicts quantum mechanics

    E-Print Network [OSTI]

    Neumaier, Arnold

    Bohmian mechanics contradicts quantum mechanics Arnold Neumaier Institut fur Mathematik, Universit://solon.cma.univie.ac.at/#24;neum/ Abstract. It is shown that, for a harmonic oscillator in the ground state, Bohmian mechanics and quantum mechanics predict values of opposite sign for certain time correlations. The discrepancy can

  4. 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).

  5. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost Ground8 GasDEVELOPMENTS E P I IT h it

  6. Mechanical Control of Enzymes Using DNA Molecular Springs

    E-Print Network [OSTI]

    Tseng, Chiao-Yu

    2013-01-01

    or swirling the tube. Do not pipette or vortex the cells. 5.or swirling the tube. Do not pipette or vortex the cells. 5.microfuge tubes and store them at -80 ? C. Do not vortex the

  7. Mechanisms of initiation of DNA mismatch repair in Saccharomyces cerevisiae

    E-Print Network [OSTI]

    Shell, Scarlet Sara

    2008-01-01

    or the cisplatin-d(GpG) adduct. Proc Natl Acad Sci U S A 93,or the cisplatin-d(GpG) adduct. Proc Natl Acad Sci U S A 93,or the cisplatin-d(GpG) adduct. Proc Natl Acad Sci U S A 93,

  8. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    A2-, A3-, and B2-Box DNAs are colored yellow, green, and blue, respectively. How Do Microbes Reproduce? On the cellular level, self-replication by cell division is a hallmark of...

  9. Mechanical Control of Enzymes Using DNA Molecular Springs

    E-Print Network [OSTI]

    Tseng, Chiao-Yu

    2013-01-01

    constant measured by neutron scattering. Science, 288(5471):dynamics studied by neutron scattering. Quarterly Reviews ofconditions. Neutron scattering and x-ray scattering have di?

  10. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet Hanford Advisory Board6/23/2014DLFM

  11. Structure and mechanism of human DNA polymerase [eta] (Journal Article) |

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail. (Conference)Feedback System inStatus of theSciTechin aCrystals 2015,

  12. Molecular behavior of DNA in a cell-sized compartment coated by lipids

    E-Print Network [OSTI]

    T. Hamada; R. Fujimoto; S. F. Shimobayashi; M. Ichikawa; M. Takagi

    2015-04-13

    The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space. Globular DNA showed a cell-size-dependent unfolding transition after adsorption on the membrane. Furthermore, when DNA interacted with a two-phase membrane surface, DNA selectively adsorbed on the membrane phase, such as an ordered or disordered phase, depending on its conformation. We discuss the mechanism of these trends by considering the free energy of DNA together with a polyamine in the solution. The free energy of our model was consistent with the present experimental data. The cooperative interaction of DNA and polyamines with a membrane surface leads to the size-dependent behavior of molecular systems in a small space. These findings may contribute to a better understanding of the physical mechanism of molecular events and reactions inside a cell.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Mechanical Engineering 1 Mechanical Engineering

    E-Print Network [OSTI]

    Haller, Gary L.

    , for example, in novel gas turbine or electric hybrid vehicles--require that students understand the fundamentals of mechanics, thermodynamics, fluid mechanics, combustion, and materials science. In all members of the next generation of mechanical engineers. To implement this mission, the department adheres

  18. Physics of base-pairing dynamics in DNA

    E-Print Network [OSTI]

    Manoel Manghi; Nicolas Destainville

    2015-10-19

    As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque- driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain degrees of freedom can be integrated out, and the quasi- static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  19. Bohmian mechanics contradicts quantum mechanics

    E-Print Network [OSTI]

    Arnold Neumaier

    2000-02-16

    It is shown that, for a harmonic oscillator in the ground state, Bohmian mechanics and quantum mechanics predict values of opposite sign for certain time correlations. The discrepancy can be explained by the fact that Bohmian mechanics has no natural way to accomodate the Heisenberg picture, since the local expectation values that define the beables of the theory depend on the Heisenberg time being used to define the operators. Relations to measurement are discussed, too, and shown to leave no loophole for claiming that Bohmian mechanics reproduces all predictions of quantum mechanics exactly.

  20. Topics in Forensic DNA Analysis &

    E-Print Network [OSTI]

    chemistry from the University of Virginia. His dissertation research, which was conducted at the FBI Academy guest of the FBI's Scientific Working Group on DNA Analysis Methods (SWGDAM) and a member

  1. The probability of double-strand breaks in giant DNA decreases markedly as the DNA concentration increases

    E-Print Network [OSTI]

    Shimobayashi, Shunsuke F; Mori, Toshiaki; Yoshikawa, Kenichi

    2012-01-01

    DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production have not yet been clearly understood, and there is no established theory that can account for the statistics of their production, in particular, the number of DSBs per base pair per unit Gy, here denoted by P1, which is the most important parameter for evaluating the degree of risk posed by DSBs. Here, using the single-molecule observation method with giant DNA molecules (166 kbp), we evaluate the number of DSBs caused by gamma-ray irradiation. We find that P1 is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. A simple model that accounts for the marked decrease of P1 shows that it is necessary to consider the characteristics of giant DNA molecules as semiflexible polymers to interpret the intrinsic mechanism of DSBs.

  2. Compliant mechanisms 

    E-Print Network [OSTI]

    Venkataraghavan, Janarthanan T

    2001-01-01

    and a few mechanisms like a magneto active peristaltic pump, have been designed and tested for the first time using this material. In this mechanism, the pumping action is obtained when a moving magnetic field produces peristaltic waves in the magneto...

  3. MECHANICAL ENGINEERING What is Mechanical

    E-Print Network [OSTI]

    power plant energy conversion and generating systems; design, development, and manufactureof consumer of the broadest engineering fields. Mechanical engineers are found in virtually all productive industries, from

  4. Quantum Confinement in Hydrogen Bond of DNA and RNA

    E-Print Network [OSTI]

    da Silva dos Santos; Elso Drigo Filho; Regina Maria Ricotta

    2015-02-09

    The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics.

  5. Quantum Confinement in Hydrogen Bond of DNA and RNA

    E-Print Network [OSTI]

    Santos, da Silva dos; Ricotta, Regina Maria

    2015-01-01

    The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics.

  6. Characterization of nanoparticle-DNA conjugate and control of DNA conformation on particle surface

    E-Print Network [OSTI]

    Park, Sunho, 1976-

    2009-01-01

    Nano-science has exploited the hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively ...

  7. Regulation of DNA damage tolerance : studies of the translesion synthesis DNA ploymerase eta in Saccharomyces cerevisiae

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01

    All organisms must control the effects of DNA damage to protect the integrity of their genomes. In addition to DNA repair, this requires DNA damage tolerance pathways, which allow the continuation of essential processes ...

  8. DNA damage responses in the context of the cell division cycle

    E-Print Network [OSTI]

    Giunta, Simona

    2010-11-16

    cycle describes the process whereby a cell replicates its DNA and divides to produce two genetically identical daughter cells. Essentially, two types of cell cycle control mechanisms exist: a cascade of protein phosphorylations that act as an “engine... and inducing displacement of base pairing (Patel and Picha, 2000). (3) In the ‘rotatory pump model’, similarly to the torsional model, MCM acts as rotary motor but the rotatory movement along the DNA helical axis occurs at a distance from the replication...

  9. Magnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to study DNA motorsDNA motorsDNA motorsDNA motors

    E-Print Network [OSTI]

    Ritort, Felix

    to study DNA motorsDNA motorsDNA motorsDNA motors MariaMariaMariaMaria MañosasMañosasMañosasMañosas Ritort) · Applications: 1. Tracking DNA motors: (i) Helicases (ii) Annealing motor 2. Studying a multiprotein system: DNA hexamers (Dong et al, JBC 1995) Tracking DNA motors: (i) Helicases #12;Passive: helicase behaves

  10. Genomic DNA methylation in various developmental stages of two plant pathogenic fungi 

    E-Print Network [OSTI]

    Schliesing, Laura Jo

    1990-01-01

    showing Southern hybridization of pRW614a to a blot of S. rolfsii mycelial DNA digested with HpaII and Mspl. Autoradiogram showing Southern hybridization of pRW614a to a blot of P. omnivorum mycelial and sclerotial DNA digested with Sau3AI and Mbo...I. Autoradiogram showing Southern hybridization of pRW614a to a blot of S. rolfsii mycelial and sclerotial DNA digested with Sau3AI and MboI. Page 27 28 29 31 34 I. INTRODUCTION To date, the molecular mechanisms responsible for the activity of genes...

  11. Mechanical memory

    DOE Patents [OSTI]

    Gilkey, Jeffrey C. (Albuquerque, NM); Duesterhaus, Michelle A. (Albuquerque, NM); Peter, Frank J. (Albuquerque, NM); Renn, Rosemarie A. (Alburquerque, NM); Baker, Michael S. (Albuquerque, NM)

    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.

  12. Mechanical memory

    DOE Patents [OSTI]

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

    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.

  13. The Structure of DNA within Cationic Lipid/DNA Complexes

    E-Print Network [OSTI]

    Braun, Chad S.; Jas, Gouri S.; Choosakoonriang, Sirirat; Koe, Gary S.; Smith, Janet G.; Middaugh, C. Russell

    2003-02-01

    hexagonal phase of cationic liposome-DNA complexes related to DNA release and delivery. Science. 281:78–81. Koppel, D. E. 1972. Analysis of macromolecular polydispersity in inten- sity correlation spectroscopy: the method of cumulants. J. Chem. Phys. 57:4814..., DOTAP, 1,2-dioleoyl-sn-glycero-3-phosphatidyletha- nolamine, and cholesterol were purchased from Avanti Polar Lipids (Alabaster, AL). Poly(dG) Æ poly(dC) (4 kbp), poly(dA) Æ poly(dT) (;229 bp), poly(dGdC) Æ poly(dGdC) (724 bp), and poly(dAdT) Æ poly(d...

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

  16. Direct measurement of DNA-mediated adhesion between lipid bilayers

    E-Print Network [OSTI]

    S. F. Shimobayashi; B. M. Mognetti; L. Parolini; D. Orsi; P. Cicuta; L. Di Michele

    2015-04-16

    Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous artificial materials have been synthesised by functionalising the outer surface of compliant Brownian units, for example emulsion droplets and lipid vesicles, with selective linkers, in particular short DNA sequences. This development extended the range of applicability of DNA as a selective glue, originally applied to solid nano and colloidal particles. On very deformable lipid vesicles, the coupling between statistical effects of multivalent interactions and mechanical deformation of the membranes gives rise to complex emergent behaviours, as we recently contributed to demonstrate [Parolini et al., Nature Communications, 2015, 6, 5948]. Several aspects of the complex phenomenology observed in these systems still lack a quantitative experimental characterisation and fundamental understanding. Here we focus on the DNA-mediated multivalent interactions of a single liposome adhering to a flat supported bilayer. This simplified geometry enables the estimate of the membrane tension induced by the DNA-mediated adhesive forces acting on the liposome. Our experimental investigation is completed by morphological measurements and the characterisation of the DNA-melting transition, probed by in-situ F\\"{o}rster Resonant Energy Transfer spectroscopy. Experimental results are compared with the predictions of an analytical theory that couples the deformation of the vesicle to a full description of the statistical mechanics of mobile linkers. With at most one fitting parameter, our theory is capable of semi-quantitatively matching experimental data, confirming the quality of the underlying assumptions.

  17. 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; Šulc, 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.

  18. Molecular behavior of DNA in a cell-sized compartment coated by lipids

    E-Print Network [OSTI]

    Hamada, T; Shimobayashi, S F; Ichikawa, M; Takagi, M

    2015-01-01

    The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space. Globular DNA showed a cell-size-dependent unfolding transition after adsorption on the membrane. Furthermore, when DNA interacted with a two-phase membrane surface, DNA selectively adsorbed on the membrane phase, such as an ordered or disordered phase, depending on its conformation. We discuss the mechanism of these trends by considering the free energy of DNA together with a polyamine in the solution. The free energy of our model was consistent with the present experimental data. The cooperative interaction of DNA and polyamines with a membrane surface leads to the size-dependent behavior of molec...

  19. Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

    E-Print Network [OSTI]

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

    2015-05-19

    We introduce an extended version of oxDNA, a coarse-grained model of 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$^+$]=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.

  20. 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.

  1. 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 ? (Pol ?) in the ternary complex with anmore »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.« less

  2. The Initiation of Bacterial DNA Replication

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

    for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior,...

  3. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01

    Numerous agents are capable of interacting with DNA and damaging it. Permanent changes in the DNA structure can be both mutagenic and cytotoxic; therefore, methods to measure the susceptibility of cells to mutations are ...

  4. Towards Privacy Preserving of Forensic DNA Databases 

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14

    Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

  5. 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).

  6. The Future of Forensic DNA

    E-Print Network [OSTI]

    History and Mission · National Institute of Standards and Technology (NIST) was created in 1901The Future of Forensic DNA John M. Butler, PhD National Institute of Standards and Technology.S. Department of Commerce with a mission to develop and promote measurement, standards, and technology

  7. Origami DNA model Mountain fold

    E-Print Network [OSTI]

    Csürös, Miklós

    Origami DNA model Mountain fold Solid lines are "mountains" and are to be folded away from you with the peak pointing towards you. 1. Fold all solid lines going lengthwise down the page into "mountain folds fold 2. Fold all dashed lines going lengthwise down the page into "valley folds". Mountain folds along

  8. The Future of Forensic DNA

    E-Print Network [OSTI]

    ;Checks and Controls on DNA Results Community FBI Quality Assurance Standards (and interlaboratory studies Washington D.C. Dulles Airport Reagan National Airport BWI Airport NIST FBI Lab Baltimore, MD Richmond, VA Materials (SRMs) Helps meet FBI QAS and ISO 17025 requirements Traceable standards to ensure accurate

  9. DNA Mixture Interpretation & Statistical Analysis

    E-Print Network [OSTI]

    of Standards and Technology Gaithersburg, Maryland John M. Butler CIB Forensic Science Center Training Seminar Mixture Workshop This workshop is for analysts, technical reviewers and technical leaders performing) National recommendations of the technical UK DNA working group on mixture interpretation for the NDNAD

  10. DNA sequencing protocols BN Danforth

    E-Print Network [OSTI]

    Danforth, Bryan Nicholas

    in the degradation of DNA. (7) Spin the tubes down at the end to remove condensation from tops of tubes. B. Extraction and RNA digestion. NOTE: We now skip the Rnase step. You will need: Phenol and gently invert several times. This step removes the phenol from the previous extraction. Spin

  11. Biological Physics of DNA Typeset by FoilTEX 1

    E-Print Network [OSTI]

    Potsdam, Universität

    fragments to ssDNA Labelling: eg radioact probe fragm & Xray film http;Packaging of DNA in bacteria 11 #12;DNA melting 12 #12;Polymerase chain reaction Heating dsDNA sample 2

  12. DNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps

    E-Print Network [OSTI]

    extraction methods were compared to determine their efficacy in isolating DNA. Success of each methodDNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps GUDRUN DITTRICH, South Africa Abstract DNA extraction from minute hymenopterans and their larvae is difficult

  13. DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays

    E-Print Network [OSTI]

    DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays mismatches with the complements of all the other members in the set. These "DNA word" sets are denoted as nbm. To achieve good discrimination between each DNA word in each set generated using the template-map strategy

  14. 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.

  15. MATERIALS AND METHODS 1) DNA extraction

    E-Print Network [OSTI]

    Collins, Gary S.

    MATERIALS AND METHODS 1) DNA extraction · DNA was extracted from the ileo-cecal nodes of 475 Holstein cows from two herds using the Qiagen DNA extraction kit (Valencia, CA). 2) Map detection · Map was extracted from ileo-cecal nodes using Ambion's MagMAX Total Nucleic Acid Isolation kit (Austin, TX

  16. 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

  17. Calculation of complex DNA damage induced by ions

    E-Print Network [OSTI]

    Eugene Surdutovich; David C. Gallagher; Andrey V. Solov'yov

    2012-01-27

    This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The analysis and assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms may not be sufficiently effective. We studied the flux of secondary electrons through the surface of nucleosomes and calculated the radial dose and the distribution of clustered damage around the ion's track. The calculated radial dose distribution is compared to simulations. The radial distribution of the complex damage is found to be different from that of the dose. Comparison with experiments may solve the question of what is more lethal for the cell, damage complexity or absorbed energy. We suggest a way to calculate the probability of cell death based on the complexity of the damage. This work is done within the framework of the phenomenon-based multiscale approach to radiation damage by ions.

  18. Direct measurement of DNA-mediated adhesion between lipid bilayers

    E-Print Network [OSTI]

    Shimobayashi, S F; Parolini, L; Orsi, D; Cicuta, P; Di Michele, L

    2015-01-01

    Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous artificial materials have been synthesised by functionalising the outer surface of compliant Brownian units, for example emulsion droplets and lipid vesicles, with selective linkers, in particular short DNA sequences. This development extended the range of applicability of DNA as a selective glue, originally applied to solid nano and colloidal particles. On very deformable lipid vesicles, the coupling between statistical effects of multivalent interactions and mechanical deformation of the membranes gives rise to complex emergent behaviours, as we recently contributed to demonstrate [Parolini et al., Nature Communications, 2015, 6, 5948]. Several aspects of the complex phenomenology observed in these systems still lack a quantitative experimental characterisation and fundamental...

  19. 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.

  20. 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.

  1. Electromagnetic Signals from Bacterial DNA

    E-Print Network [OSTI]

    A. Widom; J. Swain; Y. N. Srivastava; S. Sivasubramanian

    2012-02-09

    Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.

  2. 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.

  3. 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.

  4. Mechanical Engineering ME 3720 FLUID MECHANICS

    E-Print Network [OSTI]

    Panchagnula, Mahesh

    Mechanical Engineering ME 3720 FLUID MECHANICS Pre-requisite: ME 2330 Co-requisite: ME 3210) to develop an understanding of the physical mechanisms and the mathematical models of fluid mechanics of fluid mechanics problems in engineering practice. The basic principles of fluid mechanics

  5. The dynamic interplay between DNA damage and metabolism : the metabolic fate and transport of DNA lesions and novel DNA damage derived from intermediary metabolism

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01

    The work presented in this thesis explores two novel and complementary facets of endogenous DNA damage: the development of biomarkers of inflammation based on metabolites of DNA damage products and the formation of DNA ...

  6. Elongational-flow-induced scission of DNA nanotubes in laminar flow Rizal F. Hariadi*

    E-Print Network [OSTI]

    Winfree, Erik

    -induced scission are pro- foundly affected by the fluid flow and the polymer bond strengths. In this paper, laminarElongational-flow-induced scission of DNA nanotubes in laminar flow Rizal F. Hariadi* Department libraries in shotgun ge- nome sequencing 2­4 . The fluid-flow-induced mechanical shearing of prion fibrils

  7. Torsional regulation of hRPA-induced unwinding of double-stranded DNA

    E-Print Network [OSTI]

    Dekker, Cees

    and mechanism of the unwinding and rewinding reaction through single-molecule experiments. Human RPA (h Department of Cell Biology and Genetics, Cancer Genomic Center and 3 Department of Radiation OncologyDNA. Here, we study the dynamics of human RPA (hRPA) activity on topolog- ically constrained ds

  8. 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.

  9. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering An experimental methodology is presented for mechanism verification of physics-based prognosis of mechanical damage, such as fatigue. The proposed experimental methodology includes multi-resolution in-situ mechanical testing, advanced imaging analysis, and mechanism

  10. 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

  11. 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.

  12. 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.

  13. DNA

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost Ground8 GasDEVELOPMENTS E P I IT h it cdrives

  14. DNA

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

    blueprint of a bacterium's "molecular machinery," showing how bacterial immune systems fight off the viruses that infect them. By tracking down how bacterial defense systems work,...

  15. Base Excision by Thymine DNA Glycosylase Mediates DNA-Directed Cytotoxicity of 5-Fluorouracil 

    E-Print Network [OSTI]

    Selfridge J.; Schar P.; Lettieri T.; Schuermann D.; Saito Y.; Focke F.; Kunz C.

    2009-04-01

    5-Fluorouracil (5-FU), a chemotherapeutic drug commonly used in cancer treatment, imbalances nucleotide pools, thereby favoring misincorporation of uracil and 5-FU into genomic DNA. The processing of these bases by DNA repair activities was proposed...

  16. Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids

    E-Print Network [OSTI]

    Podgornik, Rudolf

    Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids Ame (13), or the virus capsid itself (14­16), either upon addition of spermine (Spm4þ ) or in a monovalent

  17. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01

    of DNA recognition by p53 tetramers. Mol Cell 22, 741-753.site as a self-assembled tetramer. Structure 18, 246- Chene,structure of a p53 core tetramer bound to DNA. Oncogene 28,

  18. Mechanical Buckling: Mechanics, Metrology, and Stretchable Electronics

    E-Print Network [OSTI]

    Rogers, John A.

    Mechanical Buckling: Mechanics, Metrology, and Stretchable Electronics By Dahl-Young Khang, John A of wrinkling is in aging human skin. All such phenomena originate from the same mechanism, i.e., mechanical of the wave, or their wavelength, depends upon the film thickness and/or mechanical properties of materials

  19. Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

    SciTech Connect (OSTI)

    Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)] [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: leesmill@ucalgary.ca [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)

    2013-07-01

    DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.

  20. 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.

  1. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

    Kaplan, Matt (University of Arizona Genetics Core) [University of Arizona Genetics Core

    2011-03-29

    Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. Dr. Kaplan starts with a short general review of human genetics and the biology behind this form of DNA testing. He looks at how DNA testing is performed and how samples are processed in the University of Arizona laboratory. He also examines examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, he describes the newest project in the UA laboratory, the DNA Shoah Project.

  2. 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

  3. SnapShot: DNA Polymerases II Mammals

    E-Print Network [OSTI]

    Foti, James J.

    DNA polymerases ensure the faithful duplication of genetic information inside the nuclease and mitochondria of eukaryotic cells and the nucleoid of prokaryotic cells. These remarkable enzymes synthesize polynucleotide ...

  4. 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.

  5. DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding

    E-Print Network [OSTI]

    Meller, Amit

    a 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical for drug development, necessitating new in vitro methods for rapid and low-cost assessment of the binding molecules, which give the DNA/intercalator complex a bulkier structure than that of native DNA. Furthermore

  6. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor?

    E-Print Network [OSTI]

    Nielsen, Rasmus

    Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal

  7. Dellaporta DNA Extraction Citation: Stephen L. Dellaporta,Jonathan Wood , James B. Hicks. A plant DNA

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    1 Dellaporta DNA Extraction Citation: Stephen L. Dellaporta,Jonathan Wood , James B. Hicks. A plant supernatant and lightly dry DNA pellets by inverting the tubes on paper towels for 10 min. #12;4 12. Redissolve each DNA pellet with 0.7 mL EB2. May need to let sit overnight at 4°C if having trouble dissolving

  8. MECHANICAL ENGINEERING Curriculum Notes

    E-Print Network [OSTI]

    Mohan, Chilukuri K.

    MECHANICAL ENGINEERING Curriculum Notes 2013-2014 1. Mechanical engineering students must complete of technical electives. 2. Technical electives must be taken within the Mechanical and Aerospace Engineering

  9. Physicalism versus quantum mechanics

    E-Print Network [OSTI]

    Stapp, Henry P; Theoretical Physics Group; Physics Division

    2009-01-01

    Foundations of Quantum Mechanics. (Princeton UniversityMind, Matter, and Quantum Mechanics, (Springer, Berlin & NewMindful Universe: Quantum Mechanics and the Participating

  10. Sandia Energy - Mechanical Testing

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

    Mechanical Testing Home Stationary Power Nuclear Fuel Cycle Advanced Nuclear Energy Nuclear Energy Systems Laboratory (NESL) Brayton Lab Mechanical Testing Mechanical...

  11. 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

  12. DNA Nanomechanical Switches under Folding Kinetics Control

    E-Print Network [OSTI]

    Meller, Amit

    DNA Nanomechanical Switches under Folding Kinetics Control Virgile Viasnoff,, Amit Meller operate at equilibrium under changes in solution composition. We propose an alternative DNA switch design after heat denaturation drives the switch to its lowest energy conformation, while rapid cooling (>100

  13. Dynamics and control of DNA sequence amplification

    SciTech Connect (OSTI)

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-10-28

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  14. 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.

  15. Prospects & Overviews Integrating DNA barcode data and

    E-Print Network [OSTI]

    DeSalle, Rob

    , and description Paul Z. Goldstein and Rob DeSalleà DNA barcodes, like traditional sources of taxonomic information interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance

  16. Slow closure of denaturation bubbles in DNA: twist matters

    E-Print Network [OSTI]

    Anil Kumar Dasanna; Nicolas Destainville; John Palmeri; Manoel Manghi

    2013-04-24

    The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $\\kappa_\\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\\kappa_\\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.

  17. Elastic and Proton Dynamics of the DNA

    E-Print Network [OSTI]

    V. L. Golo

    2008-03-28

    The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could accommodate the intrinsic structure of the DNA. In this respect studying the interplay among the elastic system and the protons of the DNA, is of interest, for it could accommodate the inter-strand as well as the tunneling modes of protons. Following this direction, we come to the conclusion that the elastic-proton dynamics may have a bearing on biophysics of the DNA. The phenomenon of point mutations is discussed within this framework.

  18. Programmable DNA-mediated multitasking processor

    E-Print Network [OSTI]

    Shu, Jian-Jun; Yong, Kian-Yan; Shao, Fangwei; Lee, Kee Jin

    2015-01-01

    Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.

  19. 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.

  20. 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.

  1. Particulate Carrier Systems for Mucosal DNA Vaccine Delivery

    E-Print Network [OSTI]

    Borchard, Gerrit

    2006-10-26

    Streptomyces griseus Stop solution: 1M KOH In humans: degradation by lysozyme Incubation with chitosanase (1) GPEN 2006 Free DNA chitoplexes Incubation with chitosanase, 37?C Intact DNA ? Degraded chitosan Intact DNA ? Extraction with phenol: chloroform... Streptomyces griseus Stop solution: 1M KOH In humans: degradation by lysozyme Incubation with chitosanase (1) GPEN 2006 Free DNA chitoplexes Incubation with chitosanase, 37?C Intact DNA ? Degraded chitosan Intact DNA ? Extraction with phenol: chloroform...

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Ductile failure in structural materials has been a problem the Temple Foundation Professorship in the Department of Aerospace Engineering and Engineering Mechanics, multiscale experimental mechanics, mechanics of polymers. He is a fellow of the American Society

  3. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering seminar Three Dimensional Traction Force Microscopy with Applications in Cell Mechanics abstract The interactions between biochemical and mechanical signals during-dimensional measurement techniques are needed to investigate the effect of mechanical properties of the substrate

  4. Research Review Mechanical Engineering

    E-Print Network [OSTI]

    Theune, Mariët

    Research Review Mechanical Engineering University of Twente #12;QANU / Research Review Mechanical;QANU / Research Review Mechanical Engineering / University of Twente 3 Report on the research assessment of Mechanical Engineering at the University of Twente Contents Preface

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

    Office of Scientific and Technical Information (OSTI)

    Conference: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid...

  6. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    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...

  7. IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY...

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

    IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL IN VITRO MUTAGENIC AND DNA...

  8. 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

  9. 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.

  10. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C. (Los Alamos, NM); Kuske, Cheryl R. (Los Alamos, NM); Mullen, Kenneth I. (Los Alamos, NM)

    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.

  11. Nanopores formed by DNA origami: a review

    E-Print Network [OSTI]

    Bell, Nicholas A. W.; Keyser, Ulrich F.

    2014-06-10

    , coated with hydrophobic moieties, into a lipid bilayer. Recent work in these two branches is now discussed. Hybrid nanopores formed by trapping DNA origami onto a solid state nanopore The combination of DNA origami and solid state nanopores was first... (1982) Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–47. 28 Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440, 297– 302. 29 Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Högele A, Simmel FC...

  12. Bipedal nanowalker by pure physical mechanisms

    E-Print Network [OSTI]

    Cheng, Juan; Hou, Ruizheng; Efremov, Artem; Liu, Ruchuan; van der Maarel, Johan RC; Wang, Zhisong

    2013-01-01

    Artificial nanowalkers are inspired by biomolecular counterparts from living cells, but remain far from comparable to the latter in design principles. The walkers reported to date mostly rely on chemical mechanisms to gain a direction; they all produce chemical wastes. Here we report a light-powered DNA bipedal walker based on a design principle derived from cellular walkers. The walker has two identical feet and the track has equal binding sites; yet the walker gains a direction by pure physical mechanisms that autonomously amplify an intra-site asymmetry into a ratchet effect. The nanowalker is free of any chemical waste. It has a distinct thermodynamic feature that it possesses the same equilibrium before and after operation, but generates a truly non-equilibrium distribution during operation. The demonstrated design principle exploits mechanical effects and is adaptable for use in other nanomachines.

  13. The androgen receptor independent mechanism of toxicity of the novel anti-tumor agent 11[beta]-dichloro

    E-Print Network [OSTI]

    Fedele?, Bogdan I

    2009-01-01

    Inspired by the toxicity mechanism of cisplatin in testicular cancer, a series of bi-functional genotoxicants has been designed that supplement their DNA damaging properties with the ability to interact with tumor specific ...

  14. Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

    E-Print Network [OSTI]

    R. Gutierrez; R. Caetano; P. B. Woiczikowski; T. Kubar; M. Elstner; G. Cuniberti

    2009-10-02

    Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.

  15. 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.

  16. 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

  17. Casting inorganic structures with DNA molds

    E-Print Network [OSTI]

    Sun, Wei

    We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nanomold” that ...

  18. Deoxyribose oxidation chemistry and endogenous DNA adducts

    E-Print Network [OSTI]

    Zhou, Xinfeng

    2006-01-01

    Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ...

  19. Ubiquitylation, neddylation and the DNA damage response

    E-Print Network [OSTI]

    Brown, Jessica S.; Jackson, Stephen P.

    2015-04-01

    , collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating...

  20. NIJ-Funded Research in Forensic DNA

    E-Print Network [OSTI]

    Standards Funding from the FBI S&T Branch through NIST Information Access Division httpDNA) · Technology Evaluation and Development ­ Rapid multiplex PCR protocols* (PCR: 3 hr to FBI

  1. Intriguing DNA Editor Has a Structural Trigger

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

    "plug in" very specific snippets of DNA coding for a variety of reasons. For example, microbes could be re-engineered to consume specific environmental toxins or to produce better...

  2. Linear Thermodynamics of Rodlike DNA Filtration

    E-Print Network [OSTI]

    Li, Zirui

    Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex ...

  3. 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.

  4. The unholy trinity: taxonomy, species delimitation and DNA barcoding

    E-Print Network [OSTI]

    DeSalle, Rob

    The unholy trinity: taxonomy, species delimitation and DNA barcoding Rob DeSalle*, Mary G. Egan are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can framework for interweaving classical taxonomy with the goals of `DNA barcoding'. Keywords: DNA barcoding

  5. Synopsis: Repulsion Helps Virus Pack DNA APS/Joan Tycko

    E-Print Network [OSTI]

    Smith, Douglas E.

    Synopsis: Repulsion Helps Virus Pack DNA APS/Joan Tycko Repulsive DNA-DNA Interactions Accelerate, and Douglas E. Smith Phys. Rev. Lett. 112, 248101 (2014) Published June 17, 2014 Featured in Physics Editors reported in Physical Review Letters show that, surprisingly, switching the DNA self-interaction from

  6. DNA Concentration By UV Spectrophotometry Measure Absorption

    E-Print Network [OSTI]

    Aris, John P.

    DNA Concentration By UV Spectrophotometry Measure Absorption: 1. Dilute DNA to 0.5 to 50 µg/ml in TE buffer or dH2O. Plan to use a quartz cuvette or a UV-transparent plastic (disposable) cuvette (1 2. Measure absorption at 260 nm (A260). Start by zeroing instrument with TE buffer or dH2O alone

  7. Overview of DNA Programs at NIST

    E-Print Network [OSTI]

    .nist.gov/mml/bmd/genetics/applied_genetics_pubs.cfm Pete Vallone Erica Butts DNA Biometrics Team Funding from the FBI S&T Branch through NIST Information http://www.cstl.nist.gov/strbase/NISTpub.htm +FBI-funding (DNA biometrics) Workshops 0 0 0 1 2 7 9 6 11) measurement calibration Required under FBI Quality Assurance Standard 9.5.5 for labs connected to the national

  8. Mechanical & Biomedical Engineering

    E-Print Network [OSTI]

    Barrash, Warren

    Mechanical & Biomedical Engineering Department BACHELOR OF SCIENCE IN MECHANICAL ENGINEERING COURSE 105 Mechanical Engineering Graphics 3 CHEM 111L College Chemistry Lab (DLN) 1 ENGL 102 English PHYS 211 Mechanics, Waves & Heat (DLN) 4 UF 100 Intellectual Foundations 3 PHYS 211L Mechanics, Waves

  9. Mechanical Engineering & Thermal Group

    E-Print Network [OSTI]

    Mojzsis, Stephen J.

    LASP's mechanical analysts also lead mechanical verification testing including: random vibration, forceMechanical Engineering & Thermal Group The Mechanical Engineering (ME) & Thermal Group at LASP has, and ground- based mechanical systems. Instrument Design Building on decades of design experience that has

  10. Denaturation of DNA at high salt concentrations

    E-Print Network [OSTI]

    Maity, Arghya; Singh, Navin

    2015-01-01

    Cations present in the solution are important for the stability of two negative strands of DNA molecules. Experimental as well as theoretical results show that the DNA molecule is more stable as the concentration of salt (or cations) increases. It is known that the two strands of DNA molecule carry negative charge due to phosphate group along the strands. These cations act as a shielding particles to the two like charge strands. Recently, in an experiment it is shown that there is a critical value in the concentration of salts (or cations) that can stabilize the helical structure of DNA. If one add more salt in the solution beyond this critical value, the stability of the DNA molecule will disrupt. In this work we study the stability of DNA molecules at higher concentrations. How the stability at higher concentration can be explained through some theoretical calculations is the aim of this manuscript. We consider the PBD model with proper modifications that can explain the negative stability of the molecule a...

  11. Denaturation of DNA at high salt concentrations

    E-Print Network [OSTI]

    Arghya Maity; Amar Singh; Navin Singh

    2015-08-19

    Cations present in the solution are important for the stability of two negative strands of DNA molecules. Experimental as well as theoretical results show that the DNA molecule is more stable as the concentration of salt (or cations) increases. It is known that the two strands of DNA molecule carry negative charge due to phosphate group along the strands. These cations act as a shielding particles to the two like charge strands. Recently, in an experiment it is shown that there is a critical value in the concentration of salts (or cations) that can stabilize the helical structure of DNA. If one add more salt in the solution beyond this critical value, the stability of the DNA molecule will disrupt. In this work we study the stability of DNA molecules at higher concentrations. How the stability at higher concentration can be explained through some theoretical calculations is the aim of this manuscript. We consider the PBD model with proper modifications that can explain the negative stability of the molecule at higher concentration. Our findings are in close match with the experimental results.

  12. 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.

  13. Mechanical, Industrial & Manufacturing

    E-Print Network [OSTI]

    Balasubramanian, Ravi

    Mechanical, Industrial & Manufacturing Engineering (MIME) COLLEGE OF ENGINEERING FY2013 Oregon graduate degrees (MS, MEng, PhD) in mechanical engineering, industrial engineering, and materials science. We offer bachelor's degrees in mechanical, industrial, manufacturing, and energy systems engineering

  14. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Despite an enormous range of applications and centuries. Nicholas Ouellette is an Associate Professor in the Department of Mechanical Engineering & Materials Structures in Turbulent Flow Nicholas Ouellette Department of Mechanical Engineering & Material Sciences Yale

  15. Mechanical Systems Signal Processing

    E-Print Network [OSTI]

    Verleysen, Michel

    Mechanical Systems and Signal Processing Mechanical Systems and Signal Processing 22 (2008) 155 Department of Mechanical Engineering, University of Sheffield, Mappin Street S1 3JD Sheffield, UK Received 27

  16. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering This presentation presents the stability analysis of time- delay of the Department of Mechanical and Industrial Engineering, Southern Illinois University Edwardsville, where he has Gu Dept. of Mechanical & Industrial Engineering Southern Illinois University, Edwardsville March 27

  17. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering With the increases in computational power and numerical methods a series of research challenges. These challenges involve many branches of mechanical engineering: mechanics, dynamics, tribology, statistical modeling, experimentation, and numerical methods. During

  18. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

    Mechanical & Industrial Engineering 1 Welcome MIE Industrial Advisory Board October 15, 2010 #12;Mechanical & Industrial Engineering 2 MIE Dorothy Adams Undergraduate/Graduate Secretary David Schmidt Associate Professor & Graduate Program Director #12;Mechanical & Industrial Engineering 3 MIE James Rinderle

  19. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Today's design environments take advantage of powerful professor of Mechanical Engineering at Carnegie Mellon University. He is the founder of Visual Design award and American Society of Mechanical Engineers Design Automation Society Young Investigator Award

  20. Department of Mechanical & Aerospace

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    in mechanics, electrical theory, kinematics, thermodynamics, fluid mechanics, heat transfer and materials dynamics, fluid dynamics, propulsion and structures. While each program features a solid technicalDeveloping Leaders of Innovation Department of Mechanical & Aerospace Engineering #12;Emphasizing

  1. ACETYL-COA CLEAVAGE AND SYNTHESIS IN METHANOGENS; CHARACTERIZATION OF SUBOMPONENT INTERACTIONS IN THE ACETYL-COA DECARBONYLASE/SYNTHASE MULTIENZYME COMPLEX

    SciTech Connect (OSTI)

    GRAHAM, DAVID A.

    2013-10-10

    The work reported resulted in much new insight into unusual mechanisms of metalloenzymes involved in anaerobic metabolism in methanogens, other archaea, and bacteria.

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The gap between `advanced' prosthetic technology was educated in Mechanical and Biomedical Engineering at the University of Illinois and Northwestern University

  3. Mechanical Performance Extreme Conditions

    E-Print Network [OSTI]

    Mechanical Performance ­ Extreme Conditions METALS This project provides property data, metrology information using the image correlation technique. With this instrument, high strain rate mechanical testing

  4. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering In the pursuit of developing manned, reusable hypersonic will experience thermal and mechanical loads. The research presented will discuss advancements in structural

  5. In vivo and in vitro effects of ethanol on the incorporation and cleavage of sialic acid moieties in the brain before, during and after withdrawal from a chronic ethanol diet 

    E-Print Network [OSTI]

    Acevedo-Pabon, Nestor Enrique

    1988-01-01

    . F ye (M e Gerald R. Bratton (Head of Department) December 1988 ABSTRACT In Vivo and in Vitro Effects of Ethanol on the Incorporation and Cleavage of Sialic Acid Moieties in the Brain Before, During and After Withdrawal from a Chronic Ethanol... C ACI D MO IETIES IN THE BRAIN BEFORE g DURING AND AFTER WITHDRAWAL FROM A CHRONIC ETHANOL DIET A Thesis by NESTOR ENRIQUE ACEVEDO-PABON Approved as to style and content by: W. R. Klemm (Chair of Committee) Newell McArthur (Member) G raid...

  6. Mechanical Engineering Graduate Student

    E-Print Network [OSTI]

    Wisconsin at Madison, University of

    Mechanical Engineering Graduate Student Handbook January 2015 Department of Mechanical Engineering University of Wisconsin-Madison #12;1 Mechanical Engineering Web Page: http://www.engr.wisc.edu/me Graduate & Terrace Chairs) and Samantha Stepp (ME Building) #12;2 Department of Mechanical Engineering AGUIDE

  7. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Bone is a biological material with excellent material properties the properties at lower level serve as inputs for modeling at the next structural level. Mechanical properties and applied mechanics at Northwestern University. Prior to joining the faculty of mechanical engineering

  8. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Strategic Plan 2014-2018 College of Engineering, Architecture & Technology #12;Mechanical and Aerospace Engineering at Oklahoma State University was organized as Mechanical the strongest in the nation. MAE is proud to continue in this fine tradition, forging high quality mechanical

  9. Mechanical Engineering David Sumner

    E-Print Network [OSTI]

    Saskatchewan, University of

    Mechanical Engineering David Sumner david.sumner@usask.ca #12;Mechanical Engineering? · Design, production and use of mechanical systems that control and transform energy · Focused on engineering systems that involve heat, energy and motion · The broadest engineering discipline #12;Subject Areas · Fluid mechanics

  10. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

    Mechanical & Industrial Engineering 1 Welcome MIE Industrial Advisory Board May 5th, 2011 #12;Mechanical & Industrial Engineering 2 IAB 2010-2011 · David K. Anderson ­ Alden Research Laboratory, Inc went on for three weeks Mechanical & Industrial Engineering 6 #12;Reza Shahbazian Yassar Mechanical

  11. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The science of robotics is a unique combination of mechanical in Dayton, OH. Dr. Sodemann received a PhD in Mechanical Engineering from the Georgia Institute to recent advances in the science of robotics, and thus the machines perform primarily as mechanical devices

  12. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Nanocrystal superlattices are materials formed by assembly Professor in the Department of Mechanical Engineering and Applied Mechanics at the University her B.S. in Mechanical Engineering magna cum laude from Rice University in 1994 and was elected to Phi

  13. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering This talk concerns the effective behavior of heterogeneous media Science as well as the Executive Officer for Mechanical and Civil Engineering at the California Institute in Applied Mechanics from the American Society of Mechanical Engineers in 2004. He is currently an Editor

  14. INTRODUCTION TO THE MECHANICS

    E-Print Network [OSTI]

    Kaminski, Edouard

    INTRODUCTION TO THE MECHANICS OF A CONTINUOUS MEDIUM Lawrence E. Malvern Professor of Mechanics princi- ples common to all branches of solid and fluid mechanics, designed to appeal to the intuition science. The book arose from the need to provide a general preparation in contin- uum mechanics

  15. 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.

  16. Conditions for positioning of nucleosomes on DNA

    E-Print Network [OSTI]

    Michael Sheinman; Ho-Ryun Chung

    2015-04-29

    Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single nucleosome to different locations along the DNA and some as interactions between neighboring nucleosomes. In this study we analyzed how well nucleosomes are positioned along the DNA as a function of strength of the preferential binding, correlation length of the binding energy landscape, interactions between neighboring nucleosomes and others relevant system properties. We analyze different scenarios: designed energy landscapes and generically disordered ones and derive conditions for good positioning. Using analytic and numerical approaches we find that, even if the binding preferences are very weak, synergistic interplay between the interactions and the binding preferences is essential for a good positioning of nucleosomes, especially on correlated energy landscapes. Analyzing empirical energy landscape, we discuss relevance of our theoretical results to positioning of nucleosomes on DNA \\emph{in vivo.}

  17. 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.

  18. MechanicalEngineering The Department of Mechanical

    E-Print Network [OSTI]

    for the informed development and optimization of materials. This talk will present our recent work on exploring, Ph.D. Associate Professor Department of Mechanical Engineering Department of Materials Science to thermo-mechanical loads is a fundamental requirement in the characterization of materials and structures

  19. DNA analysis conference in Santa Fe

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet Hanford Advisory Board6/23/2014DLFM libraryDNA OrigamiDNA

  20. 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.

  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. Analysis of the structural changes caused by positive DNA supercoiling

    E-Print Network [OSTI]

    Barth, Marita Christine

    2007-01-01

    The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) ...

  3. Engineering of DNA-mediated assemblies for biosensing applications /

    E-Print Network [OSTI]

    Xu, Phyllis F.

    2013-01-01

    OF THE DISSERTATION Engineering of DNA-mediated assembliesCALIFORNIA, SAN DIEGO Engineering of DNA-mediated assembliesMaterials Science and Engineering by Phyllis F. Xu Committee

  4. Manipulation of cellular DNA repair by early adenovirus proteins

    E-Print Network [OSTI]

    Orazio, Nicole Ise

    2010-01-01

    The function of BLM in the DDR and in processing of DNA endscellular DNA damage response (DDR) functions to inhibit thespecific components of the DDR, and provides insight into

  5. DNA hybridization : fundamental studies and applications in directed assembly

    E-Print Network [OSTI]

    Bajaj, Manish G. (Manish Gopal)

    2005-01-01

    Programmed self-assembly using non-covalent DNA-DNA interactions is a promising technique for the creation of next-generation functional devices for electronic, optical, and magnetic applications. This thesis develops the ...

  6. Genome scanning : an AFM-based DNA sequencing technique

    E-Print Network [OSTI]

    Elmouelhi, Ahmed (Ahmed M.), 1979-

    2003-01-01

    Genome Scanning is a powerful new technique for DNA sequencing. The method presented in this thesis uses an atomic force microscope with a functionalized cantilever tip to sequence single stranded DNA immobilized to a mica ...

  7. Defining functional DNA elements in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

    With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements ...

  8. THE NEW YORK BOTANICAL GARDEN DNA BANK ACQUISITIONS POLICY

    E-Print Network [OSTI]

    Law, Wayne

    THE NEW YORK BOTANICAL GARDEN DNA BANK ACQUISITIONS POLICY The DNA Bank of The New York Botanical herbarium. Please contact Lisa M. Campbell, Plant Research Laboratory, The New York Botanical Garden, Bronx

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

    Office of Scientific and Technical Information (OSTI)

    constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4and a coiling period of...

  10. Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device 

    E-Print Network [OSTI]

    Lo, Chih-Cheng

    2009-05-15

    -throughput DNA gel electrophoresis. However, further progress toward dramatic improvements of separation performance over ultra-short distances requires a much more detailed understanding of the physics of DNA migration in the sieving gel matrix than is currently...

  11. Enhancement of in vitro Translation by Gold Nanoparticle – DNA Conjugates

    E-Print Network [OSTI]

    Park, Sunho

    Gold nanoparticle (AuNP)?DNA conjugates can enhance in vitro translation of a protein. Enhancement occurs via a combination of nonspecific adsorption of translation-related molecules and the ribosome to the AuNP?DNA and ...

  12. Role of DNA repair protein ERCC1 in skin cancer 

    E-Print Network [OSTI]

    Song, Liang

    2009-01-01

    Nucleotide excision repair (NER) is one of the major repair systems for removal of DNA lesions. The NER pathway has evolved mainly to repair UV-induced DNA damage and is also active against a broad range of endogenously ...

  13. A model for sample stacking in microcapillary DNA electrophoresis

    E-Print Network [OSTI]

    Srivastava, Alok Kumar, 1967-

    2002-01-01

    Sanger's method of chain termination is the method of choice in DNA sequencing, where electrophoresis is used to separate the different sized DNA. In the past decade, microfabricated capillary devices have been developed ...

  14. 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)

  15. Photoelectrochemical array platform for genomic scale DNA synthesis

    E-Print Network [OSTI]

    Emig, Christopher Joseph

    2006-01-01

    Molecular and synthetic biologists have increasing demand for large, high-fidelity constructs of synthetic DNA. Recent developments in harvesting oligonucleotides from DNA microarrays has proven that these can be assembled ...

  16. Single cell trapping and DNA damage analysis using microwell arrays

    E-Print Network [OSTI]

    Wood, David

    With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from ...

  17. Mitigating security issues in the evolving DNA synthesis industry

    E-Print Network [OSTI]

    Turlington, Ralph Donald, III

    2013-01-01

    DNA synthesis technologies are advancing at exponential rates, with production of ever longer, more complex, and less expensive sequences of double stranded DNA. This has fostered development of industrial scale design, ...

  18. Alternative Methods for Human Identification: Mitochondrial DNA Base Composition Profiling

    E-Print Network [OSTI]

    Applied Genetics Alternative Methods for Human Identification: Mitochondrial DNA Base Composition · Evaluation Experiments · Future directions #12;Applied Genetics Mitochondrial DNA · Mitochondria are organelles within cells ­ Produce energy via the Krebs Cycle · Separate genome from the nucleus ­ 16,569 bp

  19. The Genetic Structure of the Kuwaiti Population: Mitochondrial DNA Markers

    E-Print Network [OSTI]

    Theyab, Jasem

    2010-06-14

    the expansion of early Homo sapiens out of Africa. Kuwait is located in the Northeast portion of the Arabian Peninsula. This thesis investigated the mitochondrial DNA (mtDNA) genetic variation in 117 unrelated individuals to determine the genetic structure...

  20. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V. (Okemos, MI)

    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.

  1. International Standards in Forensic DNA and

    E-Print Network [OSTI]

    documentary (technical) standards physical (measurement) standards Certified reference material to aidInternational Standards in Forensic DNA and Recent Forensic Science Activities in the United States John M. Butler, Ph.D. National Institute of Standards and Technology NIST Fellow & Special Assistant

  2. Isolation of Yeast DNA Prepare in advance

    E-Print Network [OSTI]

    Aris, John P.

    Isolation of Yeast DNA Prepare in advance: · 2.0 ml microfuge tubes containing 0.25 g of 0.5 mm600 ~1, or 1 ml saturated YPD culture at OD600 ~10). Centrifuge for 5 minutes at 2000 rpm. Discard will thaw during centrifugation. Transfer supernatant (200-225 µl) to a fresh 1.5 ml tube. Avoid

  3. Rewritable Memory by Controllable Nanopatterning of DNA

    E-Print Network [OSTI]

    Pierce, Niles A.

    ABSTRACT Fabricating a nanostructure capable of reversibly patterning molecules is a fundamental goal within nanotechnology, underlying diverse processes such as information storage, scaffold functioning of the device as rewritable memory. The bit state of each address is controlled by specific DNA

  4. Research Article DNA sequencing by microchip

    E-Print Network [OSTI]

    Barron, Annelise E.

    .1002/elps.200800389 1 Introduction The completion of the Human Genome Project [1, 2] has led to tremendous of the reasons for the early completion of the Human Genome Project was the technological advance- ment in DNA of personalized medicine based on the human genome cannot be fully realized until the cost of full human genome

  5. Identification of animal images based on DNA

    E-Print Network [OSTI]

    Wolf, Lior

    ongus ? Given mtDNA, the algorithm identifies the correct unseen image #12;Data sets Fishes of Australia Regularized CCA #12;Results · 93 fish species, 82 for training, 11 for testing · Significantly better than chance or NN #12;Results Fish: 90% correct Birds: 72% correct Dorsal: 59% correct Head: 56% correct

  6. Conserved Steps in Eukaryotic DNA Replication

    E-Print Network [OSTI]

    Blow, J. Julian

    and 50 car- bons of deoxyribose. The 10 carbon of the deoxyribose is linked to one of four different of DNA contains all the information necessary to produce new second strands through complementary base the input of chemical energy to break the hydrogen bonds. This energy is derived from hydrolysis of ATP

  7. Studies of the chemical mechanisms of flavoenzymes 

    E-Print Network [OSTI]

    Sobrado, Pablo

    2004-09-30

    Flavocytochrome b2 catalyzes the oxidation of lactate to pyruvate. Primary deuterium and solvent kinetic isotope effects have been used to determine the relative timing of cleavage of the lactate OH and CH bonds by the wild type enzyme, a mutant...

  8. MechanicalEngineering Colloquium The Department of Mechanical

    E-Print Network [OSTI]

    MechanicalEngineering Colloquium The Department of Mechanical Engineering PRESENTS John C. Bischof Distinguished Professor Mechanical and Biomedical Engineering Chair, Mechanical Engineering University in the Departments of Mechanical and Biomedical Engineering and the inaugural Carl and Janet Kuhrmeyer Chair

  9. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    E-Print Network [OSTI]

    Bernstein, Bradley E.

    The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to

  10. Structural basis for the inhibition of human alkyladenine DNA by 3,N4-ethenocytosine containing DNA

    E-Print Network [OSTI]

    Lingaraju, Gondichatnahalli M.

    Reactive oxygen and nitrogen species, generated by neutrophils and macrophages in chronically inflamed tissues, readily damage DNA, producing a variety of potentially genotoxic etheno base lesions; such inflammation-related ...

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

    E-Print Network [OSTI]

    Greulich-Bode, Karin

    2009-01-01

    two linked P1 clones (‘3012’, ‘3015’) that contain one orcircular DNA molecule (‘3012’) as well as the RGB image (J)overlap between clones ‘3012’ and ‘3015’ and the location of

  12. RhoJ Regulates Melanoma Chemoresistance by Suppressing Pathways that Sense DNA Damage

    E-Print Network [OSTI]

    Ho, Hsiang; Aruri, Jayavani; Kapadia, Rubina; Mehr, Hootan; White, Michael A.; Ganesan, Anand K.

    2012-01-01

    Pathways that Sense DNA Damage $watermark-text Hsiang Ho 1 ,16. Roos WP, Kaina B. DNA damage-induced apoptosis: FromDNA lesions to the DNA damage response and apoptosis. Cancer

  13. An Investigation on Gel Electrophoresis with Quantum Dots End-labeled DNA 

    E-Print Network [OSTI]

    Chen, Xiaojia

    2009-05-15

    explored manipulating DNA fragments by end labeling DNA molecules with quantum dot nanocrystals. The quantum dot-DNA conjugates can be further modified through binding interactions with biotinylated single-stranded DNA primers. Single molecule visualization...

  14. Generation of Full-Length cDNA Library

    E-Print Network [OSTI]

    Chuong, Cheng-Ming

    Generation of Full- Length cDNA Library from Single Human Prostate Cancer Cells BioTechniques 27 are performed on fixed and per- meabilized cells. Subsequent RT-PCR generates full-length cDNA libraries. Flowchart of current method for generating a full-length cDNA library from single cells. Cell fixation

  15. Mechanochemistry of a Viral DNA Packaging Motor , Jeffrey Moffitt1

    E-Print Network [OSTI]

    Oster, George

    Mechanochemistry of a Viral DNA Packaging Motor Jin Yu1 , Jeffrey Moffitt1 , Craig L. Hetherington1 The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage 29 virus capsid to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while

  16. 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)

  17. Footprinting proteinDNA complexes using the hydroxyl radical

    E-Print Network [OSTI]

    Tullius, Thomas D.

    Footprinting protein­DNA complexes using the hydroxyl radical Swapan S Jain & Thomas D Tullius.2008.72 Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA­protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent

  18. Single-DNA Molecule Nanomotor Regulated by Photons

    E-Print Network [OSTI]

    Tan, Weihong

    Single-DNA Molecule Nanomotor Regulated by Photons Huaizhi Kang, Haipeng Liu, Joseph A. Phillips the design of a single-molecule nanomotor driven by photons. The nanomotor is a DNA hairpin photonic wires,8 enzyme assemblies,9 and functional DNA probes.10,11 Similar to RNA or protein

  19. Advances in DNA Testing for Genealogy and Anthropology

    E-Print Network [OSTI]

    Aazhang, Behnaam

    Advances in DNA Testing for Genealogy and Anthropology Join the MIT Enterprise Forum of Texas that are affecting Genealogy, Anthropology, Medicine, and more. In the second half of the program, Russ Capper company in the world for Genealogy (Family Tree DNA). Family Tree DNA has collaborated with other

  20. Metal Ion Binding and Enzymatic Mechanism of Methanococcus jannaschii RNase Bing Lai, Ying Li, Aoneng Cao, and Luhua Lai*

    E-Print Network [OSTI]

    Luhua, Lai

    Metal Ion Binding and Enzymatic Mechanism of Methanococcus jannaschii RNase HII Bing Lai, Ying Li the RNA moiety in DNA:RNA hybrid in a divalent metal ion dependent manner. It is essential to understand the role of metal ion in enzymatic mechanism. One of the key points in this study is how many metal ions

  1. 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: Förster 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@QD–DNA 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 Förster 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.

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering We introduce phonon recycling (local reabsorption of emitted) is Professor in Department of Mechanical Engineering and in Applied Physics Program, University of Michigan of Mechanical Engineering University of Michigan November 1, 2013 at 1:30pm in SCOB 228 School for Engineering

  3. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering seminar Manipulation of Energy and Mass Transport at Micro as an assistant professor in the Department of Mechanical Engineering and was promoted to an associate professor award in 2007. Dr. Deyu Li Department of Mechanical Engineering Vanderbilt University January 20, 2012

  4. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Thermal transport plays an important role in energy conversion conductivity and phonon transport mechanisms over the past 2 decades, owing much to the challenging needs Faculty Fellow in Engineering and an Associate Professor of Mechanical Engineering directing the Nano

  5. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Interfacial flows are multi-material flows comprised of two and Solid Mechanics group in the Theoretical Division. Her research focuses on the development of numerical, and nuclear energy. She is a member of the American Society of Mechanical Engineers (ASME), Fluids Engineering

  6. Department of Mechanical and

    E-Print Network [OSTI]

    Huang, Jianwei

    Department of Mechanical and Automation Engineering #12;4 2 3 1 Contents Messages in the souvenir publication of the Department of Mechanical and Automation Engineering of The Chinese University of Mechanical and Automation Engineering have also played a significant part in equipping businesses

  7. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Much of past research in structural dynamics (and many other the University of Liege, Belgium, in 1983 and his Ph.D. in mechanical engineering from Rice University in 1987. He then joined the rather newly formed Department of Mechanical and Aerospace Engineering at ASU

  8. TOWARDS MECHANICAL METAMATHEMATICS

    E-Print Network [OSTI]

    Boyer, Robert Stephen

    TOWARDS MECHANICAL METAMATHEMATICS N. Shankar Technical Report 43 December 1984 Institute application of certain mechanical rules of inference. The derivations of theorems from the axioms are termed of a valid mathematical argument. Another advantage of formal proofs is that they can be mechanically checked

  9. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering It has been demonstrated that the color pattern of the human received the B.A. degree in physics from Houghton College, Houghton, NY, and the B.S. degree in mechanical in mechanical engineering from the Massachusetts Institute of Technology (MIT), Cambridge, MA, in 1997 and 2002

  10. A mechanical encapsulatio n

    E-Print Network [OSTI]

    Jackson, Trachette L.

    A mechanical mo delo f tumo r encapsulatio n and transcapsular spread Trachette L. Jackso n a 48109­1109, USA b Division of Theoretical Mechanics, School of Mathematical Sciences, University rmatio n, such investigatio ns being ideally suited to o ur mechanical mo del. The mo del simulatio ns

  11. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Fragmentation is a process in which structures fail in a very Engineering at Duke University, where he directs the Duke Computational Mechanics Laboratory. Professor Dolbow received his BS in Mechanical Engineering from the University of New Hampshire in 1995, and his Ph

  12. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The miniaturization of structural components to the sub progress in strain-gradient continuum theories to model the mechanical behavior of metallic systems at small length scales, these theories fail to represent the variety of physical mechanisms involved

  13. Mechanical Engineering Assistant Professor

    E-Print Network [OSTI]

    Chandy, John A.

    Mechanical Engineering Xu Chen Assistant Professor xchen@uconn.edu http://xchen.lab.uconn.edu From Engineering Ingredients of Kung Pao Chicken Marinade · 1 tablespoon soy sauce · 2 teaspoons Chinese rice wine of Diana Kuan #12;Mechanical Engineering The Cooking Procedure #12;Mechanical Engineering The Difference

  14. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

    Mechanical & Industrial Engineering Mario A. Rotea Professor and Department Head #12;2Mechanical & Industrial Engineering Outline · Undergraduate Degree Programs · Graduate Degree Programs · The Faculty · The Research · Summary #12;3Mechanical & Industrial Engineering Undergraduate Programs ­ BSME & BSIE 0 20 40 60

  15. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Pool boiling heat transfer enhancement is taking a dramatic turn Mechanical Engineering Rochester Institute of Technology September 5, 2014 at 1:30pm in SCOB 210 School from the classical area enhancement and nucleation cavity augmentation to mechanism based

  16. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering Energetic materials that include nano-scale aluminum (Al and joined the faculty in the Mechanical Engineering Department at Texas Tech University in 2000 Pantoya Dept. of Mechanical Engineering Texas Tech University April 19, 2013 at 1:30pm in LSE 106 School

  17. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The presentation will first review emerging joint time in Mechanical Engineering and Engineering Science from the Technical University in Athens, Greece and his, vehicle engineering, bio-mechanics, and composite materials. He is Editor-in-Chief of the International

  18. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The state of the art in Quantification of Margin and UncertaintyD in Engineering Mechanics from the University of Wisconsin in 1978. He then worked in research laboratories of the University of Wisconsin as a Senior Scientist. In March of this year, he joined the Mechanical Engineering

  19. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering seminar From Jumping Drops to Thermal Diodes Abstract Scholar and Assistant Professor of Mechanical Engineering and Materials Science at Duke University since.D. degree in Mechanical Engineering from Stanford University (2004). Dr. Chen is a recipient of numerous

  20. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering seminar Some Forward-Looking Assistive Devices to Improve. Biosketch Michael Goldfarb, PhD, is the H. Fort Flowers Professor of Mechanical Engineering and the director in Mechanical Engineering from the University of Arizona in 1988, and received his SM and PhD degrees

  1. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering seminar Plasma Actuators for Aerodynamic Flow Control.D. in Mechanical Engineering from The Ohio State University in 2004, 2005 and 2010 respectively. He joined the Department of Aerospace and Mechanical Engineering at the University of Arizona in 2010 as an Assistant

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The atomization of a liquid jet by a high speed cross.S.E. degree in mechanical engineering from Amirkabir University of Technology in 2006 and M.S. degree in mechanical engineering from Sharif University of Technology in 2009. He is currently a Ph.D. candidate

  3. QUICK QUANTUM MECHANICS ---Introduction ---

    E-Print Network [OSTI]

    Jackson, Andrew D.

    QUICK QUANTUM MECHANICS --- Introduction --- The following notes are intended to be a supplement to your study of Liboff's ``Introductory Quantum Mechanics.'' They are not an alternative! My purpose here of Classical Mechanics After Newton found his equations of motion, physicists knew they would have to wait

  4. Introduction to Quantum Mechanics

    E-Print Network [OSTI]

    Eduardo J. S. Villaseñor

    2008-04-23

    The purpose of this contribution is to give a very brief introduction to Quantum Mechanics for an audience of mathematicians. I will follow Segal's approach to Quantum Mechanics paying special attention to algebraic issues. The usual representation of Quantum Mechanics on Hilbert spaces is also discussed.

  5. Mechanical Systems Signal Processing

    E-Print Network [OSTI]

    Carvalho, João B.

    , Northern Illinois University, DeKalb, IL 60115, USA c Department of Mechanical Engineering & VibrationMechanical Systems and Signal Processing Mechanical Systems and Signal Processing 21 (2007) 2715 Federal de Rio Grande do Sul, Brazil b Department of Mathematical Sciences & Vibration and Acoustic Center

  6. Can we model DNA at the mesoscale ? Comment on: Fluctuations in the DNA double helix: A critical review

    E-Print Network [OSTI]

    Peyrard, Michel

    2015-01-01

    Comment on "Fluctuations in the DNA double helix: A critical review" by Frank-Kamenetskii and Prakash

  7. DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA with restriction enzymes, here

    E-Print Network [OSTI]

    Doering, Tamara

    Liu 4/2004 DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA in molecular biology (3.1.1-3.1.2) Materials: · DNA sample in water or TE buffer · 10x digestion buffer.1 to 4 µg 10x Digestion buffer 2 µl 5 µl Enzyme ? ? Water Rest of volume Rest of volume 2. Add the enzyme

  8. Carrier DNA For Yeast Transformation Preparation of high molecular weight single stranded carrier DNA for yeast transformations.

    E-Print Network [OSTI]

    Aris, John P.

    minute pulses. Chill on ice for 1 minute in between. The DNA solution should not heat above room into ice bucket to cool quickly. Keep on ice. This denaturation step also sterilizes the DNA. 10. Freeze to collect solution at bottom of tube. Place on ice. 3. Sonicate DNA solution in tube with tip sonifier

  9. T4 DNA condensation in water-alcohol media

    E-Print Network [OSTI]

    M. O. Gallyamov; O. A. Pyshkina; V. G. Sergeyev; I. V. Yaminsky

    2011-07-21

    The process of compaction of high molecular weight DNA T4 is investigated directly in a AFM liquid cell. The AFM-images of globules formed by DNA molecules in the result of compaction in water-alcohol environments at high izopropanol concentration (80%) are received; it is found that at intermediate concentration of izopropanol (40-50%) the DNA molecules form partially compacted formations in which the separate coils of macromolecules twist in toroidal structures. It is shown using the technique of deconvolution of the AFM-images that the globule include only one closely packed DNA molecule. The model of DNA packing is proposed on the basis of AFM experiment.

  10. 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 5–10 minutes.

  11. 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.

  12. 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.

  13. Inhibition of DNA ejection from bacteriophage by Mg+2 counterions

    E-Print Network [OSTI]

    SeIl Lee; C. V. Tran; T. T. Nguyen

    2010-11-09

    The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg$^{+2}$ multivalent counterions. As Mg$^{+2}$ concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg$^{+2}$ concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA$-$DNA short range attraction energies, mediated by Mg$^{+2}$, is found to be $-$0.004 $k_BT$ per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in aggreement qualitatively with values for tri- and tetra-valent counterions.

  14. 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

  15. Fast DNA Sequencing via Transverse Electronic Transport

    E-Print Network [OSTI]

    Johan Lagerqvist; Michael Zwolak; Massimiliano Di Ventra

    2006-03-01

    A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, e.g., orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict and cure diseases from the perspective of the genetic makeup of each individual.

  16. 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.

  17. Fractional Classical Mechanics

    E-Print Network [OSTI]

    Nick Laskin

    2013-02-03

    Fractional classical mechanics has been introduced and developed as a classical counterpart of the fractional quantum mechanics. Lagrange, Hamilton and Hamilton-Jacobi frameworks have been implemented for the fractional classical mechanics. The Lagrangian of fractional classical mechanics has been introduced, and equation of motion has been obtained. Fractional oscillator model has been launched and solved in 1D case. A new equation for the period of oscillations of fractional classical oscillator has been found. The interplay between the energy dependency of the period of classical oscillations and the non-equidistant distribution of the energy levels for fractional quantum oscillator has been discussed. We discuss as well, the relationships between new equations of fractional classical mechanics and the well-known fundamental equations of classical mechanics.

  18. Mechanical Properties of Nanocrystal Supercrystals

    E-Print Network [OSTI]

    Tam, Enrico

    2010-01-01

    and Its Impact on Mechanical Properties. MacromoleculesO. L. ; Minor, A. M. , Mechanical annealing and source-Mechanical Properties of Nanocrystal Supercrystals Enrico

  19. Statistical mechanics of the cytoskeleton

    E-Print Network [OSTI]

    Wang, Shenshen

    2012-01-01

    mechanics . . . . . . . . . . . . . . . . . . . . . . 2.1bottom-up approach to cell mechanics. Nat. Phys. [6] Fabry,Wolynes, P. G. Statistical mechanics of a cat’s cradle. New

  20. Hard Evidence and Mechanism Design

    E-Print Network [OSTI]

    Watson, Joel; Bull, Jesse

    2006-01-01

    J. , 2003. Contract, mechanism design, and technologicalSeverinov, S. , 2001. Mechanism design and communicationveri?able information and mechanism design. Rev. Econ. Stud.

  1. Hard Evidence and Mechanism Design

    E-Print Network [OSTI]

    Bull, J; Watson, J

    2007-01-01

    J. , 2003. Contract, mechanism design, and technologicalSeverinov, S. , 2001. Mechanism design and communicationveri?able information and mechanism design. Rev. Econ. Stud.

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The development of high-energy storage devices has been one in portable electronic devices, satellites, and electric vehicles. Silicon (Si) is an attractive anode

  3. 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.

  4. 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.

  5. Structural Mechanics & Solid Mechanics A finite element toolbox to MATLAB

    E-Print Network [OSTI]

    Ehrhardt, Matthias

    Structural Mechanics & Solid Mechanics Department of Mechanics and Materials CALFEM A finite.3 Copyright © 1999 by Structural Mechanics, LTH, Sweden. Printed by JABE Offset, Lund, Sweden. ISRN LUTVDG/TVSM--99/9001--SE (1-265) ISSN 0281-6679 Department of Mechanics and Materials Structural Mechanics #12;The

  6. Mechanical Engineering Department Seminar Series

    E-Print Network [OSTI]

    Awtar, Shorya

    Mechanical Engineering Department Seminar Series Mechanics of a Mosquito Professor of Mechanical Engineering Clemson University Tuesday, March 24, 2015 4:00 ­ 5:00 pm Room 1303 EECS Abstract: The mechanics of a fascicle insertion into the skin

  7. MECHANICAL ENGINEERING Program of Study

    E-Print Network [OSTI]

    Thomas, Andrew

    MECHANICAL ENGINEERING Program of Study Correspondence The Department of Mechanical Engineering offers graduate programs in the fields of thermal science and engineering mechanics. Current areas of research activity include Biomedical Engineering, Biomimetics, Composite Materials, Computational Mechanics

  8. Removal of N-Alkyl Modifications from N[superscript 2]-Alkylguanine and N[superscript 4]-Alkylcytosine in DNA by the Adaptive Response Protein AlkB

    E-Print Network [OSTI]

    Li, Deyu

    The AlkB enzyme is an Fe(II)- and ?-ketoglutarate-dependent dioxygenase that repairs DNA alkyl lesions by a direct reversal of damage mechanism as part of the adaptive response in E. coli. The reported substrate scope of ...

  9. Seesaw mechanism and leptogenesis

    E-Print Network [OSTI]

    D. Falcone

    2006-12-05

    A brief overview of the phenomenology related to the seesaw mechanism and the baryogenesis via leptogenesis is presented. In particular, it is explained how large but not maximal lepton mixing can be achieved within the type II seesaw mechanism. Moreover, the consequences for leptogenesis are explored, including flavor effects.

  10. Mecanica Clasica (Classical Mechanics)

    E-Print Network [OSTI]

    Rosu, H C

    1999-01-01

    First Internet undergraduate course on Classical Mechanics in Spanish (Castellano). This is about 80% of the material I covered during the January-June 1999 semester at IFUG in the Mexican city of Leon. English and Romanian versions are in (slow) progress and hopefully will be arXived. For a similar course on Quantum Mechanics, see physics/9808031

  11. Geometrization of Quantum Mechanics

    E-Print Network [OSTI]

    J. F. Carinena; J. Clemente-Gallardo; G. Marmo

    2007-03-23

    We show that it is possible to represent various descriptions of Quantum Mechanics in geometrical terms. In particular we start with the space of observables and use the momentum map associated with the unitary group to provide an unified geometrical description for the different pictures of Quantum Mechanics. This construction provides an alternative to the usual GNS construction for pure states.

  12. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering It is a new beginning for innovative fundamental and applied and energy applications. Dr. Mark A. Tschopp is a materials engineer at the U.S. Army Research Laboratory and Mechanical Properties Mark Tschopp Materials Engineer U.S. Army Research Laboratory September 12, 2014 at 1

  13. Mechanical Systems Signal Processing

    E-Print Network [OSTI]

    Ray, Asok

    Mechanical Systems and Signal Processing Mechanical Systems and Signal Processing 21 (2007) 866 and analytical models. This paper attempts to address this inadequacy by taking advantage of advanced signal processing and pattern recognition tools. Since a vast majority of structural components that are prone

  14. Strong cooperativity and inhibitory effects in DNA multi-looping processes

    E-Print Network [OSTI]

    Artur Garcia-Saez; J. Miguel Rubi

    2009-03-23

    We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance of another. The underlying loop selection mechanism is analyzed by means of a Hamiltonian model from which the looping free energy and the corresponding repression level can be computed. We show significant differences between the probability of single and multiple loop formation. The consequences that these collective effects might have on gene regulation processes are outlined.

  15. Mechanical code comparator

    DOE Patents [OSTI]

    Peter, Frank J. (Albuquerque, NM); Dalton, Larry J. (Bernalillo, NM); Plummer, David W. (Albuquerque, NM)

    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.

  16. Molecular mechanisms of transcription regulation by non-coding RNAs and the DNA helicase RECQL5

    E-Print Network [OSTI]

    Kassube, Susanne Anke

    2013-01-01

    b) EM micrograph of the uranyl formate–stained complex.and electron micrographs of a uranyl formate–stained Pol II–set collected from the uranyl formate–stained sample was

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect PhotovoltaicsStructure and Receptor Specificity of anStructure

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect PhotovoltaicsStructure and Receptor Specificity of anStructureStructure of

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect PhotovoltaicsStructure and Receptor Specificity of anStructureStructure

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

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(JournalspectroscopyReport) | SciTechelement method inBook:ConnectandArticle) |[eta]

  1. 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.

  2. 07SCHOOL OF MECHANICAL ENGINEERING

    E-Print Network [OSTI]

    Dimitrova, Vania

    07SCHOOL OF MECHANICAL ENGINEERING UNDERGRADUATE DEGREES School of Mechanical Engineering FACULTY OF ENGINEERING Undergraduate Degrees 2015 #12;www.engineering.leeds.ac.uk/mechanical UNDERGRADUATE DEGREES SCHOOL OF MECHANICAL ENGINEERING The School of Mechanical Engineering offers both a broad mechanical engineering degree

  3. 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.

  4. 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.

  5. Capillarity Theory for the Fly-Casting Mechanism

    E-Print Network [OSTI]

    E. Trizac; Y. Levy; P. G. Wolynes

    2010-01-04

    Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this flycasting mechanism based on the capillarity approximation and polymer chain statistics. The model shows that flycasting is most effective when the protein unfolding barrier is small and the part of the chain which extends towards the target is relatively rigid. These features are often seen in known examples of flycasting in protein-DNA binding. Simulations of protein-DNA binding based on well-funneled native-topology models with electrostatic forces confirm the trends of the analytical theory.

  6. DNA Methylation as a Biomarker for Preeclampsia

    SciTech Connect (OSTI)

    Anderson, Cindy M.; Ralph, Jody L.; Wright, Michelle L.; Linggi, Bryan E.; Ohm, Joyce E.

    2014-10-01

    Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

  7. Extremely low-frequency electromagnetic fields cause DNA strand breaks in normal Vero cells

    E-Print Network [OSTI]

    Cosmin Teodor Miha; Gabriela Vochita; Florin Brinza; Pincu Rotinberg

    2013-01-23

    Extremely low frequency electromagnetic fields aren't considered as a real carcinogenic agent despite the fact that some studies have showed impairment of the DNA integrity in different cells lines. The aim of this study was evaluation of the late effects of a 100 Hz and 5.6 mT electromagnetic field, applied continuously or discontinuously, on the DNA integrity of Vero cells assessed by alkaline Comet assay and by cell cycle analysis. Normal Vero cells were exposed to extremely low frequency electromagnetic fields (100 Hz, 5.6 mT) for 45 minutes. The Comet assay and cell cycle analysis were performed 48 hours after the treatment. Exposed samples presented an increase of the number of cells with high damaged DNA as compared with non-exposed cells. Quantitative evaluation of the comet assay showed a significantly ($cells. Cell cycle analysis showed an increase of the frequency of the cells in S phase, proving the occurrence of single strand breaks. The most probable mechanism of induction of the registered effects is the production of different types of reactive oxygen species.

  8. 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.

  9. Collective behavior of minus-ended motors in mitotic microtubule asters gliding towards DNA

    E-Print Network [OSTI]

    Chaitanya A. Athale; Ana Dinarina; Francois Nedelec; Eric Karsenti

    2014-02-17

    Microtubules (MTs) nucleated by centrosomes form star-shaped structures referred to as asters. Aster motility and dynamics is vital for genome stability, cell division, polarization and differentiation. Asters move either towards the cell center or away from it. Here, we focus on the centering mechanism in a membrane independent system of Xenopus cytoplasmic egg extracts. Using live microscopy and single particle tracking, we find that asters move towards chromatinized DNA structures. The velocity and directionality profiles suggest a random walk with drift directed towards DNA. We have developed a theoretical model that can explain this movement as a result of a gradient of MT length dynamics and MT gliding on immobilized dynein motors. In simulations, the antagonistic action of the motor species on the radial array of MTs leads to a tug-of-war purely due to geometric considerations and aster motility resembles a directed random-walk. Additionally our model predicts that aster velocities do not change greatly with varying initial distance from DNA. The movement of asymmetric asters becomes increasingly super-diffusive with increasing motor density, but for symmetric asters it becomes less super-diffusive. The transition of symmetric asters from superdiffusive to diffusive mobility is the result of number fluctuations in bound motors in the tug-of-war. Overall, our model is in good agreement with experimental data in Xenopus cytoplasmic extracts and predicts novel features of the collective effects of motor-MT interactions.

  10. Allosteric Modulation of DNA by Small Molecules

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 OutreachProductswsicloudwsiclouddenDVA N C E D B L O O D S TA I N P A T TSorbentsAllosteric Modulation of DNA by

  11. DNA Origami: A History and Current Perspective

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet Hanford Advisory Board6/23/2014DLFM libraryDNA Origami

  12. A DNA tweezer-actuated enzyme nanoreactor

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.TheoryTuesday, August 10, 20102016 News Below are4BElectron---neutrinoAA CleanAAA DNA

  13. Intriguing DNA Editor Has a Structural Trigger

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATION PLANIsProcessRegulationRadiativeIntriguing DNA Editor Has a

  14. Intriguing DNA Editor Has a Structural Trigger

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATION PLANIsProcessRegulationRadiativeIntriguing DNA Editor Has

  15. Overview of Bohmian Mechanics

    E-Print Network [OSTI]

    Xavier Oriols; Jordi Mompart

    2013-01-09

    This chapter provides a comprehensive overview of the Bohmian formulation of quantum mechanics. It starts with a historical review of the difficulties found by Louis de Broglie, David Bohm, and John S. Bell to convince the scientific community about the validity and utility of Bohmian mechanics. Then, a formal explanation of Bohmian mechanics for nonrelativistic, single-particle quantum systems is presented. The generalization to many-particle systems, where the exchange interaction and the spin play an important role, is also presented. After that, the measurement process in Bohmian mechanics is discussed. It is emphasized that Bohmian mechanics exactly reproduces the mean value and temporal and spatial correlations obtained from the standard, that is the Copenhagen or orthodox, formulation. The ontological characteristics of Bohmian mechanics provide a description of measurements as another type of interaction without the need for introducing the wave function collapse. Several solved problems are presented at the end of the chapter, giving additional mathematical support to some particular issues. A detailed description of computational algorithms to obtain Bohmian trajectories from the numerical solution of the Schrodinger or the Hamilton-Jacobi equations are presented in an appendix. The motivation of this chapter is twofold: first, as a didactic introduction to Bohmian formalism, which is used in the subsequent chapters, and second, as a self-contained summary for any newcomer interested in using Bohmian mechanics in his or her daily research activity.

  16. Ergonomics in DNA Sequencing: Standing Down to Ergonomics

    E-Print Network [OSTI]

    Naca, Christine

    2009-01-01

    Ergonomics in DNA SequencingStanding Down to Ergonomics Presented at the COEH 2009We Do: Introduction • How We Work: Ergonomics Challenges in

  17. High-Performance Integrated Genetic Analyzers for Forensic DNA Typing

    E-Print Network [OSTI]

    Liu, Peng

    2009-01-01

    in nanoliter volumes. Analytical Chemistry 72, 5507-5512 (genetic analysis. Analytical Chemistry 78, 5474-5479 (2006).DNA sequencing. Analytical Chemistry 78, 3632-3637 (2006).

  18. Effect of salt concentration on the stability of heterogeneous DNA

    E-Print Network [OSTI]

    Amar Singh; Navin Singh

    2015-09-28

    We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard-Bishop-Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.

  19. Ionic switch controls the DNA state in phage ?

    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 ? 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 ? 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 ?-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 ? 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

  20. Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate...

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

    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...

  1. 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.

  2. 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.

  3. Selective chemical labelling of natural T modifications in DNA

    E-Print Network [OSTI]

    Hardisty, Robyn E.; Kawasaki, Fumiko; Sahakyan, Aleksandr B.; Balasubramanian, Shankar

    2015-05-06

    enriched, we carried out experiments exploiting the selective reactions developed for probes 1, 2, and 3. A double-stranded 80-mer bearing two modifications per strand was used as a model for 5-fU (fU-DNA), while an analogous ODN containing 5-fC (f... C-DNA) and a non-modified ODN (GCAT-DNA) were used as controls (Supporting Information, Table S1). These ODNs were subjected to the biotinylation reaction followed by affinity enrichment using streptavidin- coated magnetic beads. fU-DNA was enriched over f...

  4. 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.

  5. 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.

  6. 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.

  7. Quantum Mechanics Without Observers

    E-Print Network [OSTI]

    W. H. Sulis

    2013-03-03

    The measurement problem and the role of observers have plagued quantum mechanics since its conception. Attempts to resolve these have introduced anthropomorphic or non-realist notions into physics. A shift of perspective based upon process theory and utilizing methods from combinatorial games, interpolation theory and complex systems theory results in a novel realist version of quantum mechanics incorporating quasi-local, nondeterministic hidden variables that are compatible with the no-hidden variable theorems and relativistic invariance, and reproduce the standard results of quantum mechanics to a high degree of accuracy without invoking observers.

  8. Advanced Mechanics. Mathematical Introduction

    E-Print Network [OSTI]

    G. Giachetta; L. Mangiarotti; G. Sardanashvily

    2010-01-20

    Classical non-relativistic mechanics in a general setting of time-dependent transformations and reference frame changes is formulated in the terms of fibre bundles over the time-axis R. Connections on fibre bundles are the main ingredient in this formulation of mechanics which thus is covariant under reference frame transformations. The basic notions of a non-relativistic reference frame, a relative velocity, a free motion equation, a relative acceleration, an external force are formulated. Newtonian, Lagrangian, Hamiltonian mechanical systems and the relations between them are defined. Lagrangian and Hamiltonian conservation laws are considered.

  9. Electronic door locking mechanism

    DOE Patents [OSTI]

    Williams, Gary Lin (428 E. Third Ave., Kennewick, WA 99336); Kirby, Patrick Gerald (1010 W. Fifteenth Pl., Kennewick, WA 99337)

    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. 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.

  11. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

    E-Print Network [OSTI]

    Deniz, Özgen; Flores, Oscar; Battistini, Federica; Pérez, Alberto; Soler-López, Montserrat; Orozco, Modesto

    2011-01-01

    al. : Physical properties of naked DNA influence nucleosomeAccess Physical properties of naked DNA influence nucleosomeelusive. Results: Naked (histone-free) and nucleosomal DNA

  12. 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.

  13. Mechanical Engineering Achievement Awards 

    E-Print Network [OSTI]

    Unknown

    2011-08-17

    In this research, least-squares based finite element formulations and their applications in fluid mechanics are presented. Least-squares formulations offer several computational and theoretical advantages for Newtonian as ...

  14. Mechanics in medicine

    E-Print Network [OSTI]

    Bao, Gang

    Over decades, the theoretical and applied mechanics community has developed sophisticated approaches for analysing the behaviour of complex engineering systems. Most of these approaches have targeted systems in the ...

  15. Ultralight, ultrastiff mechanical metamaterials

    E-Print Network [OSTI]

    Zheng, Xiaoyu

    The mechanical properties of ordinary materials degrade substantially with reduced density because their structural elements bend under applied load. We report a class of microarchitected materials that maintain a nearly ...

  16. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    this chemistry in CFD codes. Finally, I will consider three different applications: ignition by a hot surface) and combustion. Guillaume Blanquart is an Assistant Professor in the Mechanical and Civil Engineering department

  17. Boosted Statistical Mechanics

    E-Print Network [OSTI]

    Massimo Testa

    2015-07-30

    Based on the fundamental principles of Relativistic Quantum Mechanics, we give a rigorous, but completely elementary, proof of the relation between fundamental observables of a statistical system when measured relatively to two inertial reference frames, connected by a Lorentz transformation.

  18. Failure mechanisms in MEMS.

    SciTech Connect (OSTI)

    Walraven, Jeremy Allen

    2003-07-01

    MEMS components by their very nature have different and unique failure mechanisms than their macroscopic counterparts. This paper discusses failure mechanisms observed in various MEMS components and technologies. MEMS devices fabricated using bulk and surface micromachining process technologies are emphasized. MEMS devices offer uniqueness in their application, fabrication, and functionality. Their uniqueness creates various failure mechanisms not typically found in their bulk or IC counterparts. In ICs, electrical precautions are taken to mitigate failure. In MEMS, both electrical and mechanical precautions must be enacted to reduce the risk of failure and increased reliability. Unlike ICs, many MEMS components are designed to interact with their environment, making the fabrication, testing, and packaging processes critical for the success of the device.

  19. Renewable Auction Mechanism (RAM)

    Broader source: Energy.gov [DOE]

    The Renewable Auction Mechanism (RAM), approved by the California Public Utilities Commission (CPUC) in December 2010, is expected to result in 1,299 megawatts (MW) of new distributed generation ...

  20. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization

    SciTech Connect (OSTI)

    Costes, Sylvain V; Chiolo, Irene; Pluth, Janice M.; Barcellos-Hoff, Mary Helen; Jakob, Burkhard

    2009-09-15

    DNA damage sensing proteins have been shown to localize to the sites of DSB within seconds to minutes following ionizing radiation (IR) exposure, resulting in the formation of microscopically visible nuclear domains referred to as radiation-induced foci (RIF). This review characterizes the spatio-temporal properties of RIF at physiological doses, minutes to hours following exposure to ionizing radiation, and it proposes a model describing RIF formation and resolution as a function of radiation quality and nuclear densities. Discussion is limited to RIF formed by three interrelated proteins ATM (Ataxia telangiectasia mutated), 53BP1 (p53 binding protein 1) and ?H2AX (phosphorylated variant histone H2AX). Early post-IR, we propose that RIF mark chromatin reorganization, leading to a local nuclear scaffold rigid enough to keep broken DNA from diffusing away, but open enough to allow the repair machinery. We review data indicating clear kinetic and physical differences between RIF emerging from dense and uncondensed regions of the nucleus. At later time post-IR, we propose that persistent RIF observed days following exposure to ionizing radiation are nuclear ?scars? marking permanent disruption of the chromatin architecture. When DNA damage is resolved, such chromatin modifications should not necessarily lead to growth arrest and it has been shown that persistent RIF can replicate during mitosis. Thus, heritable persistent RIF spanning over tens of Mbp may affect the transcriptome of a large progeny of cells. This opens the door for a non DNA mutation-based mechanism of radiation-induced phenotypes.

  1. 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 k–d 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.

  2. Time in quantum mechanics 

    E-Print Network [OSTI]

    Chapin, Kimberly R.

    1997-01-01

    TIME IN QUANTUM MECHANICS A Thesis by KIMBERLY R. CHAPIN Submitted to Texas A8M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved as to style and content by: Marian O. Scully (Chair... of Committee) Edward S. Fry (Member) aan Laane (Member) Thomas W. Adair, III (Head of Department) August 1997 Major Subject: Physics TIME IN QIJANTUM MECHANICS A Thesis by KIMBERLY R. CHAPIN Submitted to the Oflice of Graduate Studies of Texas A...

  3. 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.

  4. 126 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE)

    E-Print Network [OSTI]

    Kostic, Milivoje M.

    126 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE) Acting Chair: Kyuil Kim professor, Ph.D., P.E., University of Dayton Master of Science in Mechanical Engineering The Department of Mechanical Engineering offers a program leading to the M.S. in mechanical engineering. The program

  5. Mechanical Engineering Is Mechanical Engineering right for me?

    E-Print Network [OSTI]

    Martin, Ralph R.

    Mechanical Engineering Is Mechanical Engineering right for me? If you are interested in the wide range of principles related to mechanical systems then Mechanical Engineering is well suited to you. A Mechanical Engineering degree programme will focus on aspects such as analysis, design, manufacture

  6. The Role of Micro-Mechanics in Soil Mechanics

    E-Print Network [OSTI]

    Bolton, Malcolm

    The Role of Micro-Mechanics in Soil Mechanics M.D.Bolton CUED/D-Soils/TR313 September 2000;1 The Role of Micro-Mechanics in Soil Mechanics Malcolm Bolton Summary It is suggested that observations of the changing microstructure of soils will permit the selection and refinement of relevant micro-mechanisms

  7. Physicochemical characterization of immortal strand DNA

    E-Print Network [OSTI]

    Lansita, Janice A. (Janice Ann), 1975-

    2004-01-01

    Adult tissue differentiation involves the generation of distinct cell types from adult stem cells (ASCs). Current understanding of tissue differentiation mechanisms is based on studies of protein and RNAs that asymmetrically ...

  8. Mechanical locks Some of you may have a mechanical

    E-Print Network [OSTI]

    Shoubridge, Eric

    Mechanical locks Some of you may have a mechanical combination style lock securing your office. We collected and returned, and · codes to mechanical locks changed. REDUCE YOUR RISK OF THEFT REGARDING CASH

  9. JAB1 regulates unphosphorylated STAT3 DNA-binding activity through protein–protein interaction in human colon cancer cells

    SciTech Connect (OSTI)

    Nishimoto, Arata, E-mail: anishimo@yamaguchi-u.ac.jp [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan); Kugimiya, Naruji; Hosoyama, Toru; Enoki, Tadahiko [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan); Li, Tao-Sheng [Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523 (Japan)] [Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523 (Japan); Hamano, Kimikazu [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)] [Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 (Japan)

    2013-08-30

    Highlights: •JAB1 interacted with unphosphorylated STAT3 in the nucleus. •JAB1 knockdown tended to increase nuclear STAT3 expression. •JAB1 knockdown significantly decreased unphosphorylated STAT3 DNA-binding activity. •JAB1 knockdown significantly decreased MDR1, NANOG, and VEGF expressions. •Nuclear JAB1, but not nuclear STAT3, correlated with STAT3 DNA-binding activity. -- Abstract: Recent studies have revealed that unphosphorylated STAT3 forms a dimer, translocates to the nucleus, binds to the STAT3 binding site, and activates the transcription of STAT3 target genes, thereby playing an important role in oncogenesis in addition to phosphorylated STAT3. Among signaling steps of unphosphorylated STAT3, nuclear translocation and target DNA-binding are the critical steps for its activation. Therefore, elucidating the regulatory mechanism of these signaling steps of unphosphorylated STAT3 is a potential step in the discovery of a novel cancer drug. However, the mechanism of unphosphorylated STAT3 binding to the promoter of target genes remains unclear. In this study, we focused on Jun activation domain-binding protein 1 (JAB1) as a candidate protein that regulates unphosphorylated STAT3 DNA-binding activity. Initially, we observed that both unphosphorylated STAT3 and JAB1 existed in the nucleus of human colon cancer cell line COLO205 at the basal state (no cytokine stimulation). On the other hand, phosphorylated STAT3 did not exist in the nucleus of COLO205 cells at the basal state. Immunoprecipitation using nuclear extract of COLO205 cells revealed that JAB1 interacted with unphosphorylated STAT3. To investigate the effect of JAB1 on unphosphorylated STAT3 activity, RNAi studies were performed. Although JAB1 knockdown tended to increase nuclear STAT3 expression, it significantly decreased unphosphorylated STAT3 DNA-binding activity. Subsequently, JAB1 knockdown significantly decreased the expression levels of MDR1, NANOG, and VEGF, which are STAT3 target genes. Furthermore, the expression level of nuclear JAB1, but not nuclear STAT3, correlated with unphosphorylated STAT3 DNA-binding activity between COLO205 and LoVo cells. Taken together, these results suggest that nuclear JAB1 positively regulates unphosphorylated STAT3 DNA-binding activity through protein–protein interaction in human colon cancer cell line COLO205.

  10. ORIGINAL ARTICLE Forensic DNA databasesEthical and legal

    E-Print Network [OSTI]

    Noble, William Stafford

    number of innocent people's records to be kept, became highly controversial.1­3 * Corresponding author Authority. #12;Under former UK Prime Minister Tony Blair, legislation was introduced as part of the Criminal's DNA profiles to be retained on what was previously a criminal DNA database, overturning the pre

  11. Molecular Devices A Unidirectional DNA Walker That Moves

    E-Print Network [OSTI]

    Yin, Peng

    a designated path. The successful construction of self-assembled DNA nanostructures provides a solid structural,2] In particular, recent years have seen remarkable success in the construction of both self-assembled that moves along a DNA track. The self-assembled track contains three anchor- ages at which the walker, a six

  12. Alternative Methods for Human Identification: Mitochondrial DNA Base Composition Profiling

    E-Print Network [OSTI]

    Perkins, Richard A.

    of nucleotides ­ Base composition of a DNA molecule can be inferred ­ An empirical formula of numbers of A, G, C) · Fully automated ­ Plate stacker holds up to 15 PCR plates ­ Desalting by magnetic bead cleanup · Cleanup are dissociated on injection · DNA molecular masses are measured ­ Forward and reverse strands measured separately

  13. 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

  14. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

    DNA topology confers sequence specificity to nonspecific architectural proteins Juan Weia , Luke proteins into tightly organized 3D struc- tures. The bacterial heat-unstable (HU) protein builds up. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which

  15. Short communication The evolution of DNA databases--Recommendations

    E-Print Network [OSTI]

    Short communication The evolution of DNA databases--Recommendations for new European STR loci Peter from 7 to 10. # 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: National DNA database; STR; Evolution; European standards 1. Introduction The European Network of Forensic Science Institutes (ENFSI

  16. Shape and energetics of DNA plectonemes Prashant K. Purohit

    E-Print Network [OSTI]

    Purohit, Prashant

    , including single molecule experiments, and it is known that the average bending modulus of a random sequence scales of few hundred nanometers is described by a fluctuating elastic rod model. In this paper we couple that the twisting modulus of DNA is around Kt = 431pNnm2 [12]. The fact that DNA is a twist storing polymer allows

  17. 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.

  18. DNA barcoding and the renaissance of taxonomy Scott E. Miller*

    E-Print Network [OSTI]

    DNA barcoding and the renaissance of taxonomy Scott E. Miller* Office of the Under Secretary representing field ecology, molecular genetics, and morphological taxonomy presents data in this issue of PNAS). The work of Smith et al. (2) is a display of integrated taxonomy, demon- strating how DNA barcoding

  19. Google matrix analysis of DNA sequences Vivek Kandiah1

    E-Print Network [OSTI]

    Shepelyansky, Dima

    1 Google matrix analysis of DNA sequences Vivek Kandiah1 , Dima L. Shepelyansky1, 1 Laboratoire de.quantware.ups-tlse.fr/dima Abstract For DNA sequences of various species we construct the Google matrix G of Markov tran- sitions between nearby words composed of several letters. The statistical distribution of matrix elements

  20. Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging

    E-Print Network [OSTI]

    Straight, Aaron

    Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging Thesis by Andrew James of perfectly flexible and perfectly rigid polymer chains; however, many polymers, for example DNA, are somewhere in between these two limiting cases. Such polymers are termed semiflexible, and their molecular

  1. Investigating the Role of Vitamin D and DNA Repair in Influencing Cancer Presentation and Outcomes 

    E-Print Network [OSTI]

    Syed, Moinuddin Mohammed

    2014-09-26

    differences in DNA repair genes exist, which may in turn contribute to underlying differences in DNA repair capacity. These genes with high Fst value represent all six known common DNA repair pathways and DDR response. This supports our hypothesis...

  2. Telomere Regulation in Arabidopsis thaliana by the CST Capping Complex and DNA Damage Response Proteins 

    E-Print Network [OSTI]

    Boltz, Kara A.

    2013-09-11

    The ends of chormosomes are capped by telomeres, which distinguish the termini from damaged DNA. Paradoxically, DNA repair proteins are also required for telomere maintenance. How DNA repair pathways are regulated to ...

  3. Morphological taxonomy, DNA barcoding, and species diversity in southern Rocky Mountain headwater streams

    E-Print Network [OSTI]

    Zamudio, Kelly R.

    Morphological taxonomy, DNA barcoding, and species diversity in southern Rocky Mountain headwater and Conditions #12;MOLECULAR APPROACHES IN FRESHWATER ECOLOGY Morphological taxonomy, DNA barcoding, and species: diversity, elevation, DNA barcoding, taxonomy, aquatic insect, EPT, southern Rocky Mountain Elevation

  4. Extending the realm of SuNS to DNA nanoarrays and peptide features

    E-Print Network [OSTI]

    Akbulut Halatci, Özge

    2010-01-01

    Intense research on DNA arrays has been fostered by their applications in the field of biomedicine. DNA microarrays are composed of several different DNA sequences to be analyzed in parallel allowing high throughput ...

  5. Crystal Structure of E. coli RecE Protein Reveals a Toroidal Tetramer for Processing Double-Stranded DNA Breaks

    SciTech Connect (OSTI)

    Zhang, Jinjin; Xing, Xu; Herr, Andrew B.; Bell, Charles E.; (OSU); (UCIN)

    2009-07-21

    Escherichia coli RecE protein is part of the classical RecET recombination system that has recently been used in powerful new methods for genetic engineering. RecE binds to free double-stranded DNA (dsDNA) ends and processively digests the 5{prime}-ended strand to form 5{prime}-mononucleotides and a 3{prime}-overhang that is a substrate for single strand annealing promoted by RecT. Here, we report the crystal structure of the C-terminal nuclease domain of RecE at 2.8 {angstrom} resolution. RecE forms a toroidal tetramer with a central tapered channel that is wide enough to bind dsDNA at one end, but is partially plugged at the other end by the C-terminal segment of the protein. Four narrow tunnels, one within each subunit of the tetramer, lead from the central channel to the four active sites, which lie about 15 {angstrom} from the channel. The structure, combined with mutational studies, suggests a mechanism in which dsDNA enters through the open end of the central channel, the 5{prime}-ended strand passes through a tunnel to access one of the four active sites, and the 3{prime}-ended strand passes through the plugged end of the channel at the back of the tetramer.

  6. Entangled Mechanical Oscillators

    E-Print Network [OSTI]

    J. D. Jost; J. P. Home; J. M. Amini; D. Hanneke; R. Ozeri; C. Langer; J. J. Bollinger; D. Leibfried; D. J. Wineland

    2009-01-29

    Hallmarks of quantum mechanics include superposition and entanglement. In the context of large complex systems, these features should lead to situations like Schrodinger's cat, which exists in a superposition of alive and dead states entangled with a radioactive nucleus. Such situations are not observed in nature. This may simply be due to our inability to sufficiently isolate the system of interest from the surrounding environment -- a technical limitation. Another possibility is some as-of-yet undiscovered mechanism that prevents the formation of macroscopic entangled states. Such a limitation might depend on the number of elementary constituents in the system or on the types of degrees of freedom that are entangled. One system ubiquitous to nature where entanglement has not been previously demonstrated is distinct mechanical oscillators. Here we demonstrate deterministic entanglement of separated mechanical oscillators, consisting of the vibrational states of two pairs of atomic ions held in different locations. We also demonstrate entanglement of the internal states of an atomic ion with a distant mechanical oscillator.

  7. Computer Vision in Fluid Mechanics

    E-Print Network [OSTI]

    Aminfar, AmirHessam

    2015-01-01

    layers," Journal of Fluid Mechanics, vol. 30, no. 04, pp.M. Princevac, "Fundamental fluid mechanics," 2014. C. W.Computer Vision in Fluid Mechanics A Thesis submitted in

  8. Continuous Improvement Plan Mechanical Engineering

    E-Print Network [OSTI]

    Fernandez, Eduardo

    Continuous Improvement Plan Mechanical Engineering Undergraduate Curriculum #12;Plan for the Assessment and Continuous Improvement of the Mechanical Engineering Undergraduate Curriculum Department of Ocean and Mechanical Engineering Florida Atlantic University April 4, 2001 (latest modification 3

  9. STATISTICAL MECHANICS AND FIELD THEORY

    E-Print Network [OSTI]

    Samuel, S.A.

    2010-01-01

    1. L. 1. Schiff, Quantum Mechanics, third edition (McGraw-two-dimensional quantum mechanics problem vith a potential,Theory Methods to Statistical Mechanics Chapter I The Use of

  10. Waldyr Muniz Oliva Geometric Mechanics

    E-Print Network [OSTI]

    Natário, José

    Waldyr Muniz Oliva Geometric Mechanics February 1, 2002 Springer Berlin Heidelberg New mechanics : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 51 4.1 Galilean space-time structure and Newton equations . . . . . . . . 51 4.2 Critical remarks on Newtonian mechanics

  11. Computer Vision in Fluid Mechanics

    E-Print Network [OSTI]

    Aminfar, AmirHessam

    2015-01-01

    layers," Journal of Fluid Mechanics, vol. 30, no. 04, pp.Fundamental fluid mechanics," 2014. C. W. Enderlin, "MacroComputer Vision in Fluid Mechanics A Thesis submitted in

  12. EROSION MECHANISM IN DUCTILE METALS

    E-Print Network [OSTI]

    Bellman Jr., Robert

    2013-01-01

    England. Mayvflle, fL A. , "Mechanism of fV1aterial RemovalSubmitted to WEAR EROSION MECHANISM IN DUCTILE METALS Robertmetals. ace and erosion rate mechanism is a signifi- mic in

  13. A chemiosmotic mechanism of symport

    E-Print Network [OSTI]

    Kaback, HR

    2015-01-01

    HR (2003) Probing the mechanism of a membrane transportGJ, Kaback HR (1979) Mechanism of lactose translocation inDE, Kaback HR (1979) Mechanism of lactose translocation in

  14. 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

    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 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 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/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.« less

  15. 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

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

    Carrasco, Javier [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain); CIC Energigune, Minana, Alava (Spain); Rodriguez, Jose A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Stony Brook Univ., NY (United States); Lopez-Duran, David [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain); CIC Energigune, Minana, Alava (Spain); Liu, Zongyuan [Brookhaven National Lab. (BNL), Upton, NY (United States); Stony Brook Univ., NY (United States); Duchon, Tomas [Charles Univ., Praha (Czech Republic); Evans, Jaime [Univ. Central de Venezuela, Caracas (Venezuela); Senanayake, Sanjaya D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Crumlin, Ethan J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Matolin, Vladimir [Charles Univ., Praha (Czech Republic); Ganduglia-Pirovano, M. Veronica [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain)

    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 Ni²? 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.

  16. 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.

  17. Mechanisms in knockout reactions

    E-Print Network [OSTI]

    D. Bazin; R. J. Charity; R. T. de Souza; M. A. Famiano; A. Gade; V. Henzl; D. Henzlova; S. Hudan; J. Lee; S. Lukyanov; W. G. Lynch; S. McDaniel; M. Mocko; A. Obertelli; A. M. Rogers; L. G. Sobotka; J. R. Terry; J. A. Tostevin; M. B. Tsang; M. S. Wallace

    2009-02-16

    We report on the first detailed study of the mechanisms involved in knockout reactions, via a coincidence measurement of the residue and fast proton in one-proton knockout reactions, using the S800 spectrograph in combination with the HiRA detector array at the NSCL. Results on the reactions $^9$Be($^9$C,$^8$B+X)Y and $^9$Be($^8$B,$^7$Be+X)Y are presented. They are compared with theoretical predictions for both the diffraction and stripping reaction mechanisms, as calculated in the eikonal model. The data shows a clear distinction between the two reaction mechanisms, and the observed respective proportions are very well reproduced by the reaction theory. This agreement supports the results of knockout reaction analyses and their applications to the spectroscopy of rare isotopes.

  18. Transformable topological mechanical metamaterials

    E-Print Network [OSTI]

    D. Zeb Rocklin; Shangnan Zhou; Kai Sun; Xiaoming Mao

    2015-10-21

    Mechanical metamaterials are engineered materials that gain their remarkable mechanical properties, such as negative Poisson's ratios, negative compressibility, phononic bandgaps, and topological phonon modes, from their structure rather than composition. Here we propose a new design principle, based on a uniform soft deformation of the whole structure, to allow metamaterials to be immediately and reversibly transformed between states with contrasting mechanical and acoustic properties. These properties are protected by the topological structure of the phonon band of the whole structure and are thus highly robust against disorder and noise. We discuss the general classification of all structures that exhibit such soft deformations, and provide specific examples to demonstrate how to utilize soft deformations to transform a system between different regimes such that remarkable changes in their properties, including edge stiffness and speed of sound, can be achieved.

  19. Grassmann Matrix Quantum Mechanics

    E-Print Network [OSTI]

    Dionysios Anninos; Frederik Denef; Ruben Monten

    2015-12-11

    We explore quantum mechanical theories whose fundamental degrees of freedom are rectangular matrices with Grassmann valued matrix elements. We study particular models where the low energy sector can be described in terms of a bosonic Hermitian matrix quantum mechanics. We describe the classical curved phase space that emerges in the low energy sector. The phase space lives on a compact Kahler manifold parameterized by a complex matrix, of the type discovered some time ago by Berezin. The emergence of a semiclassical bosonic matrix quantum mechanics at low energies requires that the original Grassmann matrices be in the long rectangular limit. We discuss possible holographic interpretations of such matrix models which, by construction, are endowed with a finite dimensional Hilbert space.

  20. Grassmann Matrix Quantum Mechanics

    E-Print Network [OSTI]

    Anninos, Dionysios; Monten, Ruben

    2015-01-01

    We explore quantum mechanical theories whose fundamental degrees of freedom are rectangular matrices with Grassmann valued matrix elements. We study particular models where the low energy sector can be described in terms of a bosonic Hermitian matrix quantum mechanics. We describe the classical curved phase space that emerges in the low energy sector. The phase space lives on a compact Kahler manifold parameterized by a complex matrix, of the type discovered some time ago by Berezin. The emergence of a semiclassical bosonic matrix quantum mechanics at low energies requires that the original Grassmann matrices be in the long rectangular limit. We discuss possible holographic interpretations of such matrix models which, by construction, are endowed with a finite dimensional Hilbert space.

  1. Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments

    E-Print Network [OSTI]

    Missirian, Victor; Comai, Luca; Filkov, Vladimir

    2011-01-01

    S, Pe’er I: Overlapping pools for high-throughput targetedSequenced Overlapping DNA Pools in TILLING Experiments. BMCgeneration resequencing of DNA pools. Bioinformatics 2010,

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

    DOE Patents [OSTI]

    Bryant, Jennifer E. (Albuquerque, NM); Hutchings, Kent G. (Albuquerque, NM); Moyzis, Robert K. (Corona Del Mar, CA); Griffith, Jeffrey K. (Cedar Crest, NM)

    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.

  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. Experimental unsaturated soil mechanics

    E-Print Network [OSTI]

    Delage, Pierre

    2008-01-01

    In this general report, experimental systems and procedures of investigating the hydro-mechanical behaviour of unsaturated soils are presented. The water retention properties of unsaturated soils are commented and linked to various physical parameters and properties of the soils. Techniques of controlling suction are described together with their adaptation in various laboratory testing devices. Some typical features of the mechanical behaviour of unsaturated soils are presented within an elasto-plastic framework. An attempt to describe the numerous and significant recent advances in the investigation of the behaviour of unsaturated soils, including the contributions to this Conference, is proposed.

  5. 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...

  6. Quantum Chaos and Statistical Mechanics

    E-Print Network [OSTI]

    Mark Srednicki

    1994-06-14

    We briefly review the well known connection between classical chaos and classical statistical mechanics, and the recently discovered connection between quantum chaos and quantum statistical mechanics.

  7. Quantum Mechanics and Black Holes

    E-Print Network [OSTI]

    Jose N. Pecina-Cruz

    2005-11-27

    This paper discusses the existence of black holes from the foundations of quantum mechanics. It is found that quantum mechanics rule out a possible gravitational collapse.

  8. 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.

  9. MECHANICAL ENGINEERING 121 Department of Mechanical Engineering (MEE)

    E-Print Network [OSTI]

    Kostic, Milivoje M.

    MECHANICAL ENGINEERING 121 Department of Mechanical Engineering (MEE) *Available for general education credit. The Department of Mechanical Engineering offers an upper- division curriculum which leads to a B.S. in mechanical engineering. The curriculum is based on a strong foundation of fundamental

  10. 114 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE)

    E-Print Network [OSTI]

    Kostic, Milivoje M.

    114 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE) *Available for general education credit. The Department of Mechanical Engineering offers an upper- division curriculum which leads to a B.S. in mechanical engineering. The curriculum is based on a strong foundation of fundamental

  11. Mechanism Design for an Agnostic Planner: universal mechanisms, logarithmic equilibrium

    E-Print Network [OSTI]

    Cvitanic, Jaksa

    Mechanism Design for an Agnostic Planner: universal mechanisms, logarithmic equilibrium payoffs consider the problem of Bayesian mechanism design when the respondents share a com- mon prior about which concerned with the first issue, which connects our results to the literature on robust mechanism design

  12. Program Transformation Mechanics A Classification of Mechanisms for Program Transformation

    E-Print Network [OSTI]

    Utrecht, Universiteit

    Program Transformation Mechanics A Classification of Mechanisms for Program Transformation with a Survey of Existing Transformation Systems Jonne van Wijngaarden Eelco Visser UU-CS-2003-048 Institute Transformation Mechanics A Classification of Mechanisms for Program Transformation with a Survey of Existing

  13. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Reisslein, Martin

    conductivity. Coupled with its low thermal conductivity, polymer thermoelectric composites are attractive and thermoelectric applications. I will show that the thermal conductivity of ultra-thin polymer films can both conductivity and phonon transport mechanisms over the past 2 decades, owing much to the challenging needs

  14. Journal of applied mechanics

    E-Print Network [OSTI]

    Nov 11, 2009 ... Location: Engineering (Periodicals) ... wave propagation in such systems is examined in reference (4). Gassman (5, 6) has ... Now Research Scientist at Missile. Systems ... Presented at the Applied Mechanics Division Summer Conference,. Berkeley ..... This will be true in some cases for a water- saturated ...

  15. 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.

  16. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    advantage over solar collectors that require tracking mechanisms to follow the sun and they can also capture and concentrating sunlight onto specially made collector tubes at the UC Solar Lab at UC Merced. The latest external CPC collector (XCPC) is being used in Mongolia and Dubai with great success. XCPC's offer a big cost

  17. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    and lithium ion batteries. Our interest is to understand how solid diffusion generates mechanical stresses in lithium batteries. Using input from ab initio and molecular dynamic simulations, we investigated to the presence of ionic fluxes. The second example is on the insertion of lithium into silicon in silicon anodes

  18. COVER IMAGE Mechanical metamaterials

    E-Print Network [OSTI]

    Loss, Daniel

    COVER IMAGE Mechanical metamaterials are artificial structures whose properties originate from a range of structural deformations. Letter p153; News & Views p95 IMAGE: JAYSON PAULOSE COVER DESIGN in elementary optical excitations of monolayer WSe2 Ajit Srivastava, Meinrad Sidler, Adrien V. Allain, Dominik S

  19. STUDENT HANDBOOK MECHANICAL ENGINEERING

    E-Print Network [OSTI]

    Krstic, Miroslav

    accredited programs) Aerospace and Mechanical Engineering: · An ability to apply knowledge of mathematics-long learning. · A knowledge of contemporary issues. · An ability to use modern engineering techniques, skills, and computing tools necessary for engineering practice. Additionally: Aerospace Engineering · Knowledge of key

  20. LABORATORY II MECHANICAL OSCILLATIONS

    E-Print Network [OSTI]

    Minnesota, University of

    Lab II - 1 LABORATORY II MECHANICAL OSCILLATIONS Most of the laboratory problems so far have was constant. In this set of laboratory problems, the total force acting on an object, and thus its's oscillation frequency. OBJECTIVES: After successfully completing this laboratory, you should be able to