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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 Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this molecular model provide evidence for the chemical mechanism by which type II topoisomerases (topo IIs) and a related topo family (topo IA) accomplish DNA cleavage. The structure also reveals how the enzyme avoids dissociating when DNA is cleaved, preventing the aberrant formation of mutagenic genomic lesions.

2

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

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

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this molecular model provide evidence for the chemical mechanism by which type II topoisomerases (topo IIs) and a related topo family (topo IA) accomplish DNA cleavage. The structure also reveals how the enzyme avoids dissociating when DNA is cleaved, preventing the aberrant formation of mutagenic genomic lesions.

3

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

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

Topoisomerase II Structure Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Wednesday, 26 January 2011 00:00 Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this molecular model provide evidence for the chemical mechanism by which type II topoisomerases (topo IIs) and a related topo family (topo IA) accomplish DNA cleavage. The structure also reveals how the enzyme avoids dissociating when DNA is cleaved, preventing the aberrant formation of mutagenic genomic lesions.

4

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

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

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this molecular model provide evidence for the chemical mechanism by which type II topoisomerases (topo IIs) and a related topo family (topo IA) accomplish DNA cleavage. The structure also reveals how the enzyme avoids dissociating when DNA is cleaved, preventing the aberrant formation of mutagenic genomic lesions.

5

The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the cleavage of AP site and its synthetic analogs  

Science Journals Connector (OSTI)

Abstract The mechanism of hydrolysis of the apurinic/apyrimidinic (AP) site and its synthetic analogs by using tyrosyl-DNA phosphodiesterase 1 (Tdp1) was analyzed. Tdp1 catalyzes the cleavage of AP site and the synthetic analog of the AP site, 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran (THF), in DNA by hydrolysis of the phosphodiester bond between the substituent and 5? adjacent phosphate. The product of Tdp1 cleavage in the case of the AP site is unstable and is hydrolyzed with the formation of 3?- and 5?-margin phosphates. The following repair demands the ordered action of polynucleotide kinase phosphorylase, with XRCC1, DNA polymerase ?, and DNA ligase. In the case of THF, Tdp1 generates break with the 5?-THF and the 3?-phosphate termini. Tdp1 is also able to effectively cleave non-nucleotide insertions in DNA, decanediol and diethyleneglycol moieties by the same mechanism as in the case of THF cleavage. The efficiency of Tdp1 catalyzed hydrolysis of AP-site analog correlates with the DNA helix distortion induced by the substituent. The following repair of 5?-THF and other AP-site analogs can be processed by the long-patch base excision repair pathway.

Natalia A. Lebedeva; Nadejda I. Rechkunova; Alexander A. Ishchenko; Murat Saparbaev; Olga I. Lavrik

2013-01-01T23:59:59.000Z

6

MDC1 Cleavage by Caspase-3: A Novel Mechanism for Inactivating the DNA Damage Response during Apoptosis  

Science Journals Connector (OSTI)

...double-strand break repair and may be a novel therapeutic...commonly used or are in the pipeline, yet virtually all pancreatic...these lines, the DNA repair pathway is an attractive...timely drug development pipeline. Therefore, the model...components of the DNA repair complex (31, 33...

Stéphanie Solier and Yves Pommier

2011-02-01T23:59:59.000Z

7

Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments: EcoRII endonuclease cleavage of substrates with repeated natural and modified recognition sites  

Science Journals Connector (OSTI)

Interaction of EcoRII restriction endonuclease with a set of synthetic concatemer DNA duplexes with natural and modified sites for this enzyme has been studied. DNA duplexes with repeated natural sites are cleaved by EcoRII. Substitution of central AT-pair in the recognition site for a non-complementary TT- or AA-pair reduces the rate of cleavage, this effect being much more pronounced in the last case. Absence of site flanking in one strand from the 5?-terminus also results in very slow cleavage. The results obtained testify to the interaction of EcoRII with both strands of the substrate.

A.A. Yolov; E.S. Gromova; E.A. Romanova; T.S. Oretskaya; A.A. Oganov; Ya.I. Buryanov; Z.A. Shabarova

1984-01-01T23:59:59.000Z

8

Carbon Nanotube DNA Sensor and Sensing Mechanism  

E-Print Network [OSTI]

Carbon Nanotube DNA Sensor and Sensing Mechanism Xiaowu Tang,*,, Sarunya Bansaruntip, Nozomi; Revised Manuscript Received June 7, 2006 ABSTRACT We report the fabrication of single-walled carbon nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label

Le Roy, Robert J.

9

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

E-Print Network [OSTI]

DNA-EcoRV restriction enzyme complexes the DNA retains a Babout 1.6 pN could act on the enzyme-DNA complex. Wuite andcompare Fig. S2): the enzyme is bound to the plasmon rulers

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

2006-01-01T23:59:59.000Z

10

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

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

DNA-Binding Mechanism in DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere site (parS) on the plasmid DNA and two proteins, ParA and ParB. The initial formation of the so-called partition complex between ParB and the centromere is a critical step in partition. To understand the DNA-binding mechanism utilized by ParB, Schumacher and Funnell determined crystal structures of the C-terminal region of ParB, known as ParB(142-333), bound to centromere sites.

11

Cleavage of nucleic acids  

DOE Patents [OSTI]

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.

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)

2007-12-11T23:59:59.000Z

12

-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism  

Science Journals Connector (OSTI)

Structural analysis of apo and DNA-bound HU from S. aureus (SHU) revealed that conformational changes occur in both the protein and DNA upon DNA binding. Base-readout and shape-readout mechanisms are involved in DNA binding and recognition by SHU, in which -arm flexibility is a major determinant.

Kim, D.-H.

2014-11-28T23:59:59.000Z

13

Ensuring Productive Resolution by the Junction-Resolving Enzyme RuvC: Large Enhancement of the Second-Strand Cleavage Rate  

Science Journals Connector (OSTI)

Table 1:? Rates of Cleavage of Synthetic DNA Junctions by RuvCa ... Table 2:? Rates of Cleavage by RuvC of Synthetic DNA Junctions Containing Oligoadenine Bulges at the Point of Strand Exchangea ...

Jonathan M. Fogg; David M. J. Lilley

2000-12-01T23:59:59.000Z

14

Mechanism of Interaction of CC-1065 (NSC 298223) with DNA  

Science Journals Connector (OSTI)

...interaction of CC-1065 with synthetic DNA polymers indicated a specificity...interaction of CC-1065 with synthetic DNA polymers indicated a specificity...interaction of CC-1065 with synthetic DNA polymers indicated a specificity...

David H. Swenson; Li H. Li; Laurence H. Hurley; J. Stefan Rokem; Gary L. Petzold; Brian D. Dayton; Tanya L. Wallace; Alice H. Lin; William C. Krueger

1982-07-01T23:59:59.000Z

15

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 Structure of DNA-Bound FEN1 Reveals Mechanism of Action Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print Tuesday, 24 January 2012 11:30 DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by researchers from Berkeley Lab and the Scripps Research Institute has solved the structure of human FEN1 bound to DNA using ALS Beamline 12.3.1, revealing the surprising mechanism behind FEN1's speed, accuracy, and versatility.

16

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 Structure of DNA-Bound FEN1 Reveals Mechanism of Action Print DNA replication is a critical step in the life of all organisms, insuring that each new cell gets an accurate copy of the genome. Among the legions of proteins required to do this work, the DNA-slicing "flap endonuclease" FEN1 plays a key role. Much of FEN1's structure was solved previously, but the DNA-free structure failed to expose information about the mechanics of how it works. An international team of scientists led by researchers from Berkeley Lab and the Scripps Research Institute has solved the structure of human FEN1 bound to DNA using ALS Beamline 12.3.1, revealing the surprising mechanism behind FEN1's speed, accuracy, and versatility. A Recipe for Rigorous Replication

17

Mechanical Control of Enzymes Using DNA Molecular Springs  

E-Print Network [OSTI]

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

Tseng, Chiao-Yu

2013-01-01T23:59:59.000Z

18

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA  

E-Print Network [OSTI]

Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive 'rezipping' of the solution-phase protein onto DNA sites liberated by 'unzipping' of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.

Simona Cocco; John F. Marko; Remi Monasson

2014-05-26T23:59:59.000Z

19

DNA  

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

directed directed assembly of nanoparticle linear structure for nanophotonics Baoquan Ding, aÍ’ Stefano Cabrini, bÍ’ Ronald N. Zuckermann, and Jeffrey Bokor Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720 Í‘Received 17 June 2008; accepted 22 December 2008; published 2 February 2009Í’ Assemblies of metal nanospheres have shown interesting properties for nanophotonics. Here the authors describe a method to use robust DNA multicrossover molecules to organize Au nanoparticles with different sizes to form well controlled linear chain structures with desired distance below 10 nm between the particles. Au particles with only one piece of DNA attached are purified individually. Three different sizes DNA-Au conjugates then hybridize with five other DNA strands to form the stiff triple crossover Í‘TXÍ’ motif. The linkage position

20

Brittle to ductile transition in cleavage fracture  

SciTech Connect (OSTI)

The problem of interpretation of fracture transition from brittle to ductile or vice versa is the subject of study. An instrumented tapered double cantilever beam (TDCB) has been developed as a definitive tool in the study of the intrinsic mechanism in single crystalline samples. In this experiment, the crack velocity is directly proportional to actuator velocity. In experiments performed on TDCB shaped Si single crystals, oriented for cleavage on either [l brace]111[r brace] or [l brace]110[r brace] planes, a number of troubling features of jerky carck extension were encountered. Evidence suggests that nucleation of dislocation loops from crack tip is easier than moving these dislocations away from crack tip. 14 refs, 1 fig.

Argon, A.S.; Berg, Q.

1992-09-30T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Elucidation of the Mechanism of Gene Silencing using Small Interferin RNA: DNA Hybrid Molecules  

SciTech Connect (OSTI)

The recent discovery that short hybrid RNA:DNA molecules (siHybrids) induce long-term silencing of gene expression in mammalian cells conflicts with the currently hypothesized mechanisms explaining the action of small, interfering RNA (siRNA). As a first step to elucidating the mechanism for this effect, we set out to quantify the delivery of siHybrids and determine their cellular localization in mammalian cells. We then tracked the segregation of the siHybrids into daughter cells after cell division. Markers for siHybrid delivery were shown to enter cells with and without the use of a transfection agent. Furthermore, delivery without transfection agent only occurred after a delay of 2-4 hours, suggesting a degradation process occurring in the cell culture media. Therefore, we studied the effects of nucleases and backbone modifications on the stability of siHybrids under cell culture conditions.

Dugan, L

2006-02-08T23:59:59.000Z

22

A novel synthetic DNA minor groove binder, MS-247: antitumor activity and cytotoxic mechanism  

Science Journals Connector (OSTI)

Purpose: MS-247 is a novel synthetic compound possessing a DNA-binding moiety and a DNA-alkylating residue, chlorambucil. In this study, ... murine tumor cell lines and its effects on DNA molecul...

Y. Matsuba; H. Edatsugi; I. Mita; A. Matsunaga…

2000-06-01T23:59:59.000Z

23

Two-Color DNA Nanoprobe of Intracellular Dynamics  

Science Journals Connector (OSTI)

We have developed a correlation microscopy technique to follow the dynamics of quantum dot labeled DNA within living cells. ... The intracellular environment imposes a variety of mechanical constraints and engenders interactions both from molecular crowding to a range of motor-driven activity responsible for transcription, replication, cargo transport, cytoskeletal rearrangement, chromosomal remodeling, and so on. ... Other future applications of this method could be to witness a variety of cellular processes, such as chromosomal rearrangement or DNA cleavage, so long as the correlated motion of the two labels is altered during the dynamics. ...

Joshua N. Milstein; Mike Chu; Krishnan Raghunathan; Jens-Christian Meiners

2012-04-02T23:59:59.000Z

24

5-fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase  

SciTech Connect (OSTI)

5-Fluorodeoxycytidine (FdCyd) was incorporated into a synthetic DNA polymer containing the GCGC recognition sequence of HhaI methylase to give a polymer with about 80% FdCyd. In the absence of AdoMet, poly(FdC-dG) bound competitively with respect to poly(dG-dC). In the presence of AdoMet, the analogue caused a time-dependent, first-order inactivation of the enzyme. There is an ordered mechanism of binding in which enzyme first binds to poly(FdC-dG), then binds to AdoMet, and subsequently forms stable, inactive complexes. The complexes did not dissociate over the course of 3 days and were stable to heat (95/sup 0/C) in the presence of 1% SDS. Gel filtration of a complex formed with HhaI methylase, poly(FdC-dG), and (methyl-/sup 3/H)AdoMet gave a peak of radioactivity eluting near the void volume. Digestion of the DNA in the complex resulted in a reduction of the molecular weight to the size of the methylase, and the radioactivity in this peak was shown to be associated with protein. These data indicate that the complexes contain covalently bound HhaI methylase, poly(FdC-dG), and methyl groups and that 5-fluorodeoxycytidine is a mechanism-based inactivator of the methylase. By analogy with other pyrimidine-modifying enzymes and recent studies on the mechanism of HhaI methylase, these results suggest that an enzyme nucleophile attacks FdCyd residues at C-6, activating the 5-position for one-carbon transfer. Subsequent transfer of the methyl group of AdoMet to the activated FdCyd forms a stable complex in which the enzyme is covalently bound to the 6-position of FdCyd in the polymer and a methyl group is attached to C-5. The effect of 5-fluorodeoxycytidine on the inhibition of DNA-cytosine methyltransferases is thus due to irreversible, covalent inactivation.

Osterman, D.G.; DePillis, G.D.; Wu, J.C.; Matsuda, A.; Santi, D.V.

1988-07-12T23:59:59.000Z

25

Atomistic Details of the Associative Phosphodiester Cleavage in Human Ribonuclease H  

SciTech Connect (OSTI)

During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O30 oxygen to generate the product state. During the reaction mechanism two Mg2+ ions support the formation of a stable associated in-line SN2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol*1 is in excellent agreement with experimental findings (20.5 kcal mol*1). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.

Elsasser, Brigitta M.; Fels, Gregor

2010-07-30T23:59:59.000Z

26

A DNA Damage-Induced, SOS-Independent Checkpoint Regulates Cell Division in Caulobacter crescentus  

E-Print Network [OSTI]

Cells must coordinate DNA replication with cell division, especially during episodes of DNA damage. The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the ...

Modell, Joshua W.

27

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA , J.F. Marko2  

E-Print Network [OSTI]

- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments processes. In [1] a single DNA was stretched out, and spontaneous dissociation of fluorescently-labeled Fis Fis or another DNA-binding protein, e.g., HU) was added, the fluorescent protein unbound rapidly

Cocco, Simona

28

DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms  

Science Journals Connector (OSTI)

...assembly process and contributes to complex stability. Both TFIIF and TFIIE are a2b2 heterotetramers...RNA-DNA hybrid and the transcription bubble. Wrapping of DNA upstream of elongating...complex. The extent of the transcription bubble prior to initiation has been determined...

Benoit Coulombe; Zachary F. Burton

1999-06-01T23:59:59.000Z

29

“Synthetic Lethality”: Molecular Co-targeting to Restore the DNA Repair Mechanisms in Prostate Cancer Cells  

Science Journals Connector (OSTI)

To this end, PARP inhibitors are the well-known class of drugs that have recently been proposed to reach synthetic lethality in DNA repair-defective, radio-resistant prostate tumors.

Gennaro Ilardi; Stefania Staibano

2013-01-01T23:59:59.000Z

30

MOLECULAR MECHANISMS OF THE DNA DAMAGE RESPONSE INDUCED DURING PARVOVIRUS INFECTION  

E-Print Network [OSTI]

DNA damage response (DDR) is a critical safeguarding system to protect genomic stability and integrality through a cascade of phosphorylation events of three PI-3-kinase-like kinases: ATM (ataxia telangiectasia mutated), ATR (ATM and Rad3 related...

Luo, Yong

2012-12-31T23:59:59.000Z

31

Structure of DNA-Bound FEN1 Reveals Mechanism of Action  

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

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

32

Mechanisms that prevent DNA re-replication in the yeast Saccharomyces cerevisiae  

E-Print Network [OSTI]

Every time a cell divides it must faithfully duplicate its genome before the cell divides. If replication initiates a second time (re-replication) before cytokinesis, cells can accumulate extensive DNA damage, which results ...

Tanny, Robyn E

2006-01-01T23:59:59.000Z

33

Cationic Lipid-Nucleic Acid Complexes for Gene Delivery And Silencing: Pathways And Mechanisms for Plasmid Dna And Sirna  

SciTech Connect (OSTI)

Motivated by the promises of gene therapy, there is great interest in developing non-viral lipid-based vectors for therapeutic applications due to their low immunogenicity, low toxicity, ease of production, and the potential of transferring large pieces of DNA into cells. In fact, cationic liposome (CL) based vectors are among the prevalent synthetic carriers of nucleic acids (NAs) currently used in gene therapy clinical trials worldwide. These vectors are studied both for gene delivery with CL-DNA complexes and gene silencing with CL-siRNA (short interfering RNA) complexes. However, their transfection efficiencies and silencing efficiencies remain low compared to those of engineered viral vectors. This reflects the currently poor understanding of transfection-related mechanisms at the molecular and self-assembled levels, including a lack of knowledge about interactions between membranes and double stranded NAs and between CL-NA complexes and cellular components. In this review we describe our recent efforts to improve the mechanistic understanding of transfection by CL-NA complexes, which will help to design optimal lipid-based carriers of DNA and siRNA for therapeutic gene delivery and gene silencing.

Ewert, K.K.; Zidovska, A.; Ahmad, A.; Bouxsein, N.F.; Evans, H.M.; McAllister, C.S.; Samuel, C.E.; Safinya, C.R.; /SLAC

2012-07-17T23:59:59.000Z

34

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

SciTech Connect (OSTI)

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

Hingerty, B.E.

1992-07-01T23:59:59.000Z

35

Calculation of the binding affinity of the anticancer drug daunomycin to DNA by a statistical mechanics approach  

Science Journals Connector (OSTI)

Equilibrium binding constants of the anticancer drug daunomycin, bound to several GC containing polymeric DNAs (G represent guanine and C cytosine), are calculated by means of a microscopic statistical mechanics approach and based on observed x-ray crystal structures. Our calculation shows base sequence specificity of daunomycin in agreement with the observations. We find the drug binding constant to be sensitive to the base composition of the host sequence. The binding stability decreases in the order of CGTACG, CGATCG, and CGGCCG, which is consistent with observations (T represents thymine and A adenine). This binding specificity arises from sequence specific hydrogen bond and nonbonded interactions between the drug and a host DNA. These interactions are affected by sequence specific structural features exhibited from x-ray crystallography. The agreement between our calculations and experiments shows that our method is of practical application in analyzing sequence specific binding stability of anticancer drugs.

Y. Z. Chen and Yong-Li Zhang

1997-06-01T23:59:59.000Z

36

CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL  

E-Print Network [OSTI]

CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL S. R. Bordet1 , B. Tanguy1 , S by warm pre-stress (WPS) on the cleavage fracture micromechanisms of a 18MND5 (A533B) reactor pressure vessel (RPV) steel. In this purpose, different WPS fracture test results obtained on compact tensile (CT

Boyer, Edmond

37

Exoproteolytic cleavage of N-terminal His tags QIAGEN Distributors  

E-Print Network [OSTI]

His tags using DAPase Enzyme 25 Buffer preparation 25 Desalting 25 Protocol 1. DAPase digestion (small-scale, and pGAPase Enzymes 30 Buffer preparation 30 Desalting 30 Protocol 4. DAPase ­ Qcyclase digestion (small-scale with TAGZyme cleavage His tags suitable for exoproteolytic cleavage by the TAGZyme system 50 Small-scale

Lebendiker, Mario

38

Pre-Steady-State Analysis of ATP Hydrolysis by Saccharomyces cereVisiae DNA Topoisomerase II. 2. Kinetic Mechanism for the Sequential Hydrolysis of Two  

E-Print Network [OSTI]

Pre-Steady-State Analysis of ATP Hydrolysis by Saccharomyces cereVisiae DNA Topoisomerase II. 2. Kinetic Mechanism for the Sequential Hydrolysis of Two ATP Timothy T. Harkins,,| Timothy J. Lewis two ATP and rapidly hydrolyzes at least one of them before encountering a slow step in the reaction

Lewis, Timothy

39

Detection of nucleic acid sequences by invader-directed cleavage  

DOE Patents [OSTI]

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

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

1999-01-01T23:59:59.000Z

40

The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography  

SciTech Connect (OSTI)

The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T = 16 icosahedron attached to a contractile tail via a head-tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid.

Fu, Xiaofeng [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)] [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Walter, Michael H. [Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 (United States)] [Department of Biology, University of Northern Iowa, Cedar Falls, IA 50614 (United States); Paredes, Angel [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)] [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States); Morais, Marc C., E-mail: mcmorais@utmb.edu [Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555 (United States); Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Liu, Jun, E-mail: Jun.Liu.1@uth.tmc.edu [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)] [Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030 (United States)

2011-12-20T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Surreptitious involvement of a metallacycle substituent in metal-mediated alkyne cleavage chemistry  

Science Journals Connector (OSTI)

Surreptitious involvement of a metallacycle substituent in metal-mediated alkyne cleavage chemistry ...

Joseph M. O'Connor; Lin Pu

1990-11-01T23:59:59.000Z

42

Reaction Pathways and Energetics of Etheric C?O Bond Cleavage Catalyzed by Lanthanide Triflates  

SciTech Connect (OSTI)

Efficient and selective cleavage of etheric C?O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C?O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C?O cleavage occurs via a C?H ? O?H proton transfer in concert with weakening of the C?O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C?O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.

2013-07-15T23:59:59.000Z

43

Designs of Autonomous Unidirectional Walking DNA Devices  

E-Print Network [OSTI]

a route programmably embedded in the under- lying nanostructure ­ existing synthetic DNA mechanical

Reif, John H.

44

Atomistic Details of the Associative Phosphodiester Cleavage...  

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

step the proton is shuttled to the O30 oxygen to generate the product state. During the reaction mechanism two Mg2+ ions support the formation of a stable associated in-line...

45

Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB  

Science Journals Connector (OSTI)

...1-methyladenine (m1A) ZZQQhy poly(dA), oligo(dA rich), ssand ds-DNA treated with [13 C]MeIa, [3 H]MNUb, DMSc, MMSd turnover = 0.02 ZZQQhy 0.2 min-1 HPLC/scintillatione, MALDI-TOFf, GC-MSg (1-4, 6, 8, 37) ZZQQhy poly...

Bomina Yu; John F. Hunt

2009-01-01T23:59:59.000Z

46

Imaging Adsorbate O-H Bond Cleavage: Methanol on TiO2(110). ...  

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

Adsorbate O-H Bond Cleavage: Methanol on TiO2(110). Imaging Adsorbate O-H Bond Cleavage: Methanol on TiO2(110). Abstract: We investigated methanol adsorption and dissociation on...

47

E-Print Network 3.0 - alkene group cleavage Sample Search Results  

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

cleavage Page: << < 1 2 3 4 5 > >> 1 Glaser, UMC, Chem210 Notes WS97, 1997 --1 --Chemistry 210 --Winter Semester 1997Chemistry 210 --Winter Semester 1997 Summary: Cleavage of...

48

Interdependent genotoxic mechanisms of monomethylarsonous acid: Role of ROS-induced DNA damage and poly(ADP-ribose) polymerase-1 inhibition in the malignant transformation of urothelial cells  

SciTech Connect (OSTI)

Exposure of human bladder urothelial cells (UROtsa) to 50 nM of the arsenic metabolite, monomethylarsonous acid (MMA{sup III}), for 12 weeks results in irreversible malignant transformation. The ability of continuous, low-level MMA{sup III} exposure to cause an increase in genotoxic potential by inhibiting repair processes necessary to maintain genomic stability is unknown. Following genomic insult within cellular systems poly(ADP-ribose) polymerase-1 (PARP-1), a zinc finger protein, is rapidly activated and recruited to sites of DNA strand breaks. When UROtsa cells are continuously exposed to 50 nM MMA{sup III}, PARP-1 activity does not increase despite the increase in MMA{sup III}-induced DNA single-strand breaks through 12 weeks of exposure. When UROtsa cells are removed from continuous MMA{sup III} exposure (2 weeks), PARP-1 activity increases coinciding with a subsequent decrease in DNA damage levels. Paradoxically, PARP-1 mRNA expression and protein levels are elevated in the presence of continuous MMA{sup III} indicating a possible mechanism to compensate for the inhibition of PARP-1 activity in the presence of MMA{sup III}. The zinc finger domains of PARP-1 contain vicinal sulfhydryl groups which may act as a potential site for MMA{sup III} to bind, displace zinc ion, and render PARP-1 inactive. Mass spectrometry analysis demonstrates the ability of MMA{sup III} to bind a synthetic peptide representing the zinc-finger domain of PARP-1, and displace zinc from the peptide in a dose-dependent manner. In the presence of continuous MMA{sup III} exposure, continuous 4-week zinc supplementation restored PARP-1 activity levels and reduced the genotoxicity associated with MMA{sup III}. Zinc supplementation did not produce an overall increase in PARP-1 protein levels, decrease the levels of MMA{sup III}-induced reactive oxygen species, or alter Cu-Zn superoxide dismutase levels. Overall, these results present two potential interdependent mechanisms in which MMA{sup III} may increase the susceptibility of UROtsa cells to genotoxic insult and/or malignant transformation: elevated levels of MMA{sup III}-induced DNA damage through the production of reactive oxygen species, and the direct MMA{sup III}-induced inhibition of PARP-1.

Wnek, Shawn M.; Kuhlman, Christopher L.; Camarillo, Jeannie M.; Medeiros, Matthew K. [Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States)] [Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States); Liu, Ke J. [Department of Pharmaceutical Sciences, College of Pharmacy, The University of New Mexico, Albuquerque, NM 87131 (United States)] [Department of Pharmaceutical Sciences, College of Pharmacy, The University of New Mexico, Albuquerque, NM 87131 (United States); Lau, Serrine S. [Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States) [Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States); Southwest Environmental Health Sciences Center, Department of Pharmacology and Toxicology, The University of Arizona Health Sciences Center, Tucson, AZ 85721 (United States); Gandolfi, A.J., E-mail: wnek@pharmacy.arizona.edu [Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States)

2011-11-15T23:59:59.000Z

49

Nanotechnology with DNA DNA Nanodevices  

E-Print Network [OSTI]

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

Ludwig-Maximilians-Universität, München

50

Brittle to ductile transition in cleavage fracture. Final techical report, April 1, 1987--June 30, 1991  

SciTech Connect (OSTI)

The problem of interpretation of fracture transition from brittle to ductile or vice versa is the subject of study. An instrumented tapered double cantilever beam (TDCB) has been developed as a definitive tool in the study of the intrinsic mechanism in single crystalline samples. In this experiment, the crack velocity is directly proportional to actuator velocity. In experiments performed on TDCB shaped Si single crystals, oriented for cleavage on either {l_brace}111{r_brace} or {l_brace}110{r_brace} planes, a number of troubling features of jerky carck extension were encountered. Evidence suggests that nucleation of dislocation loops from crack tip is easier than moving these dislocations away from crack tip. 14 refs, 1 fig.

Argon, A.S.; Berg, Q.

1992-09-30T23:59:59.000Z

51

Cleavage crack-tip deformation in single-crystal zinc  

Science Journals Connector (OSTI)

Dislocation distribution ahead of a cleavage crack tip in single crystal Zn is observed by using the etch pit technique. The results show that the distribution has the feature predicted by the DFZ models, and both X1, the distance from the crack tip to the first dislocation and N0, the total number of dislocations ahead of the crack tip, agree with Majumdar and Burns's DFZ theory. The problems of dislocation emission from the crack tip and dislocation shielding effects on the crack tip are also discussed based on the experimental results.

Fu Ran; Q Y Long; T Y Zhang; C W Lung

1989-01-01T23:59:59.000Z

52

Induction of NEIL1 and NEIL2 DNA glycosylases in aniline-induced splenic toxicity  

SciTech Connect (OSTI)

The mechanisms by which aniline exposure elicits splenotoxic response, especially the tumorigenic response, are not well-understood. Earlier, we have shown that aniline-induced oxidative stress is associated with increased oxidative DNA damage in rat spleen. The base excision repair (BER) pathway is the major mechanism for the repair of oxidative DNA base lesions, and we have shown an up-regulation of 8-oxoguanine glycosylase 1 (OGG1), a specific DNA glycosylase involved in the removal of 8-hydroxy-2'-deoxyguanosine (8-OHdG) adducts, following aniline exposure. Nei-like DNA glycosylases (NEIL1/2) belong to a family of BER proteins that are distinct from other DNA glycosylases, including OGG1. However, contribution of NEIL1/2 in the repair of aniline-induced oxidative DNA damage in the spleen is not known. This study was, therefore, focused on evaluating if NEILs also contribute to the repair of oxidative DNA lesions in the spleen following aniline exposure. To achieve that, male SD rats were subchronically exposed to aniline (0.5 mmol/kg/day via drinking water for 30 days), while controls received drinking water only. The BER activity of NEIL1/2 was assayed using a bubble structure substrate containing 5-OHU (preferred substrates for NEIL1 and NEIL2) and by quantitating the cleavage products. Aniline treatment led to a 1.25-fold increase in the NEIL1/2-associated BER activity in the nuclear extracts of spleen compared to the controls. Real-time PCR analysis for NEIL1 and NEIL2 mRNA expression in the spleen revealed 2.7- and 3.9-fold increases, respectively, in aniline-treated rats compared to controls. Likewise, Western blot analysis showed that protein expression of NEIL1 and NEIL2 in the nuclear extract of spleens from aniline-treated rats was 2.0- and 3.8-fold higher than controls, respectively. Aniline treatment also led to stronger immunoreactivity for NEIL1 and NEIL2 in the spleens, confined to the red pulp areas. These studies, thus, show that aniline-induced oxidative stress is associated with an induction of NEIL1/2. The increased NIEL-mediated BER activity is another indication of aniline-induced oxidative damage in the spleen and could constitute another important mechanism of removal of oxidative DNA lesions, especially in transcribed DNA following aniline insult.

Ma Huaxian; Wang Jianling [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Abdel-Rahman, Sherif Z. [Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Hazra, Tapas K. [Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Boor, Paul J. [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Khan, M. Firoze, E-mail: mfkhan@utmb.edu [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States)

2011-02-15T23:59:59.000Z

53

Efficient Nuclear DNA Cleavage in Human Cancer Cells by Synthetic Bleomycin Mimics  

Science Journals Connector (OSTI)

† Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands ... ‡ Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands ... We also thank the University of Groningen and the University Medical Center Groningen for financial support. ...

Qian Li; Monique G.P. van der Wijst; Hinke G. Kazemier; Marianne G. Rots; Gerard Roelfes

2014-02-14T23:59:59.000Z

54

Photoenhanced Oxidative DNA Cleavage with Non-Heme Iron(II) Complexes  

Science Journals Connector (OSTI)

Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands ... Financial support from the University of Groningen, and Netherlands Organization for Scientific Research (NWO) is gratefully acknowledged. ...

Qian Li; Wesley R. Browne; Gerard Roelfes

2010-11-08T23:59:59.000Z

55

The application of local approach to assess the influence of in-plane constraint on cleavage fracture  

SciTech Connect (OSTI)

The assessment of real or postulated flaws within critical components is conventionally carried out using methods based on single parameter fracture mechanics. For low constraint configurations (e.g. shallow cracks) such methods can provide highly conservative assessments. Two-parameter (J-T, J-Q) fracture mechanics has been developed to quantify the influence of crack-tip constraint on fracture and this development has been incorporated into a modified R6 framework to reduce the conservatisms associated with the assessment of low constraint configurations. This framework requires that the constraint of the structure is quantified (with respect to T or Q) and that the materials fracture response to constraint is measured by testing a number of cracked specimens which sample a range of constraint levels. An alternative method of assessment, which may be used in situations where fracture data are unavailable over the full range of constraint, is the so-called local approach to fracture. In this Paper, the local approach has been used alongside the modified R6 framework to assess the cleavage fracture behavior of a well characterized mild steel plate at {minus}50 C. The local approach method predicts: (i) an upswing in cleavage fracture toughness as a function of decreasing crack-tip constraint which is conservative with respect to the actual materials response, (ii) an increase in the scatter of cleavage fracture toughness as a function of decreasing crack-tip constraint. This is a direct consequence of framing the local approach model within two-parameter Weibull statistics. Finally it is shown that the local approach may be used successfully alongside the modified R6 framework to assess low constraint geometries: resultant failure assessment curves reduce the conservatism of the conventional Option 1 curve.

Sherry, A.H.; Sanderson, D.J.; Lidbury, D.P.G. [AEA Technology, Risley (United Kingdom); Ainsworth, R.A. [Nuclear Electric, Berkeley (United Kingdom); Kikuchi, K. [JAERI, Tokai, Ibaraki (Japan)

1995-11-01T23:59:59.000Z

56

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

E-Print Network [OSTI]

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

Gates, Kent. S.

57

DNA UPTAKE BY TRANSFORMABLE BACTERIA  

SciTech Connect (OSTI)

The various processes of DNA uptake by cells can be categorized as: viral DNA entry, conjugation, or transformation. Within each category, a variety of mechanisms have been found. However, considerable similarities occur among the different mechanisms of conjugation and, especially, transformation. All of these natural mechanisms of DNA transfer are quite elaborate and involve multiple protein components, as the case may be, of the virus, the donor cell, and the recipient cell. The mechanisms of viral infection and conjugation will be discussed mainly with respect to their relevance to transformation.

LACKS,S.A.

1999-09-07T23:59:59.000Z

58

Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism  

Science Journals Connector (OSTI)

...strain and its derivatives. Relative to input DNA, galactose-induction in the SRS2-13XMYC WT strain...performed as described in ref. 52. Input DNA was recovered before immunoprecipitation...Genetic screens and selections for cell and nuclear fusion mutants . Methods Enzymol 194 : 774...

Sidney D. Carter; Dana Vigašová; Jiang Chen; Miroslav Chovanec; Stefan U. Åström

2009-01-01T23:59:59.000Z

59

Preparation of TiO2(110)-(1x1) Surface via UHV Cleavage: An scanning...  

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

Preparation of TiO2(110)-(1x1) Surface via UHV Cleavage: An scanning tunneling microscopy study. Preparation of TiO2(110)-(1x1) Surface via UHV Cleavage: An scanning tunneling...

60

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

SciTech Connect (OSTI)

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.

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

2013-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

DNA Extraction  

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

DNA Extraction DNA Extraction Being able to extract deoxyribonucleic acid (DNA) is important for a number of reasons. By studying DNA, scientists can identify genetic disorders or diseases, and they can also possibly find cures for them by manipulating or experimenting with this DNA. At the Laboratory, researchers have studied DNA to detect biothreat agents in environmental and forensic samples. Scientists also are studying how human DNA may be destroyed by certain types of electromagnetic waves at certain frequencies. Classroom Activity: This activity is about the extraction of DNA from strawberries. Strawberries are a great fruit to use for this lesson because each student can work on his or her own. Strawberries are recommended because they yield more DNA than any other fruit. Strawberries are octoploid, which means that they have eight copies of each

62

Cellular responses to environmental DNA damage  

SciTech Connect (OSTI)

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

Not Available

1994-08-01T23:59:59.000Z

63

Structural mechanism of DNA recognition by the p202 HINa domain: insights into the inhibition of Aim2-mediated inflammatory signalling  

Science Journals Connector (OSTI)

Structural and biochemical data demonstrate that p202 recognizes foreign DNA in a distinct manner compared with AIM2/Aim2, leading to a new model for the negative regulation of Aim2-mediated inflammasome activation by p202.

Li, H.

2013-12-24T23:59:59.000Z

64

Controlling DNA Methylation  

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

Controlling DNA Methylation Though life on earth is composed of a diverse range of organisms, some with many different types of tissues and cells, all these are encoded by a molecule we call DNA. The information required to build a protein is stored in DNA within the cells. Not all the message in the DNA is used in each cell and not all the message is used all the time. During cell differentiation, the cells become dedicated for their specific function which involves selectively activating some genes and repressing others. Gene regulation is an important event in the developmental biology and the biology of various diseases, but a more complex process. Controlling DNA Methylation Though life on earth is composed of a diverse range of organisms, some with many different types of tissues and cells, all these are encoded by a molecule we call DNA. The information required to build a protein is stored in DNA within the cells. Not all the message in the DNA is used in each cell and not all the message is used all the time. During cell differentiation, the cells become dedicated for their specific function which involves selectively activating some genes and repressing others. Gene regulation is an important event in the developmental biology and the biology of various diseases, but a more complex process. In the bacteria there are distinct enzymes while one is capable of cleaving DNA, the other protects DNA by modification. The complementary function provided by the set of enzymes offers a defense mechanism against the phage infection and DNA invasion. The incoming DNA is cleaved sequence specifically by the class of enzymes called restriction endonuclease (REase). The host DNA is protected by the sequence specific action of matching set of enzymes called the DNA methyltransferase (MTase). The control of the relative activities of the REase and MTase is critical because a reduced ratio of MTase/REase activity would lead to cell death via autorestriction. However too high a ratio would fail to provide protection against invading viral DNA. In addition a separate group of proteins capable of controlling R-M proteins have been identified in various restriction-modification (R-M) systems which are called C proteins (Roberts et al., 2003).

65

Steps on CdSe (112¯0) and (101¯0) cleavage surfaces: Evidence for crack propagation in competing cleavage planes  

Science Journals Connector (OSTI)

We determined the structure and electronic properties of cleavage steps on CdSe (112¯0) and (101¯0) surfaces from atomically resolved scanning tunneling microscopy images. Steps occur in high concentrations and are always oriented parallel to the [0001] direction on both cleavage surfaces. The steps are electrically uncharged. Kinks are extremely rare and electrically charged. The edges of steps on (112¯0) surfaces consist of {101¯0} facets and steps on (101¯0) surfaces exhibit {112¯0} facets. Steps occur preferentially in pairs (one up and one down) on both surfaces. The step structure is explained by a crack propagation in neighboring cleavage planes favored by the creation of uncharged steps.

B. Siemens, C. Domke, Ph. Ebert, and K. Urban

1999-01-15T23:59:59.000Z

66

Studies of Enzymes in Mitochondrial DNA Precursor Synthesis  

E-Print Network [OSTI]

Studies of Enzymes in Mitochondrial DNA Precursor Synthesis Regulatory Mechanisms for Human;Studies of Enzymes in Mitochondrial DNA Precursor Synthesis - Regulatory Mechanisms for Human Thymidine Kinase 2 and Deoxyguanosine Kinase Abstract As important enzymes in mitochondrial nucleotide salvage

67

Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease  

SciTech Connect (OSTI)

The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg2+A, binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, Mg2+B is debated. Here, multiple independent molecular dynamics simulations suggest that Mg2+B is crucial for achieving a tightly bound protein DNA complex and stabilizing a conformation that allows cleavage. In the absence of Mg2+B in all simulations the protein DNA hydrogen bond network is significantly disrupted and the sharp kink at the central base pair step of the DNA, which is observed in the two-metal complex, is not present. Also, the active site residues rearrange in such a way that the formation of a nucleophile, required for DNA hydrolysis, is unlikely.

Zahran, Mai [ORNL; Berezniak, Tomasz [University of Heidelberg; Imhof, Petra [University of Heidelberg; Smith, Jeremy C [ORNL

2011-01-01T23:59:59.000Z

68

Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea  

E-Print Network [OSTI]

. In the AMP-PNP bound state observed in the HerA structure, the second trans-acting arginine, R381, forms a salt-bridge with E356 of the Walker-B motif. This interaction is deemed necessary for both stable interface formation and water activation prior... annular components would form a coaxial structure, able to thread the DNA substrate through the HerA motor and towards the NurA nuclease. We surmise that DNA would enter the HerA ring via the positively-charged face formed by the helix-bundle domains...

Rzechorzek, Neil J.; Blackwood, John K.; Bray, Sian M.; Maman, Joseph D.; Pellegrini, Luca; Robinson, Nicholas P.

2014-01-01T23:59:59.000Z

69

Radiation-induced electron migration along DNA  

SciTech Connect (OSTI)

Radiation-induced electron migration along DNA is a mechanism by which randomly produced stochastic energy deposition events can lead to nonrandom types of damage along DNA manifested distal to the sites of the initial energy deposition. Electron migration along DNA is significantly influenced by the DNA base sequence and DNA conformation. Migration along 7 base pairs in oligonucleotides containing guanine bases was observed for oligonucleotides irradiated in solution which compares to average migration distances of 6 to 10 bases for Escherichia coli DNA irradiated in solution and 5.5 base pairs for Escherichia coli DNA irradiated in cells. Evidence also suggests that electron migration can occur preferentially in the 5{prime} to 3{prime} direction along DNA. Our continued efforts will provide information regarding the contribution of electron transfer along DNA to formation of locally multiply damaged sites created in DNA by exposure to ionizing radiation.

Fuciarelli, A.F.; Sisk, E.C.; Miller, J.H. [Pacific Northwest Lab., Richland, WA (United States); Zimbrick, J.D. [National Research Council, Washington, DC (United States)

1994-04-01T23:59:59.000Z

70

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

DOE Patents [OSTI]

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.

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)

1995-01-01T23:59:59.000Z

71

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

DOE Patents [OSTI]

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.

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

1995-04-11T23:59:59.000Z

72

On the Mechanisms of OH Radical Induced DNA-Base Damage:? A Comparative Quantum Chemical and Car?Parrinello Molecular Dynamics Study  

Science Journals Connector (OSTI)

We present a detailed Car?Parrinello molecular dynamics study of DNA bases in explicit water interacting with an OH radical. ... Thus, we choose to compute the power spectrum of guanine in the gas phase and in the presence of 21 and 56 waters. ...

Yudong Wu; Christopher J. Mundy; Michael E. Colvin; Roberto Car

2004-02-25T23:59:59.000Z

73

Structure of the Full-Length Human RPA14/32 Complex Gives Insights Into the Mechanism of DNA Binding And Complex Formation  

SciTech Connect (OSTI)

Replication protein A (RPA) is the ubiquitous, eukaryotic single-stranded DNA (ssDNA) binding protein and is essential for DNA replication, recombination, and repair. Here, crystal structures of the soluble RPA heterodimer, composed of the RPA14 and RPA32 subunits, have been determined for the full-length protein in multiple crystal forms. In all crystals, the electron density for the N-terminal (residues 1--42) and C-terminal (residues 175--270) regions of RPA32 is weak and of poor quality indicating that these regions are disordered and/or assume multiple positions in the crystals. Hence, the RPA32 N terminus, that is hyperphosphorylated in a cell-cycle-dependent manner and in response to DNA damaging agents, appears to be inherently disordered in the unphosphorylated state. The C-terminal, winged helix-loop-helix, protein-protein interaction domain adopts several conformations perhaps to facilitate its interaction with various proteins. Although the ordered regions of RPA14/32 resemble the previously solved protease-resistant core crystal structure, the quaternary structures between the heterodimers are quite different. Thus, the four-helix bundle quaternary assembly noted in the original core structure is unlikely to be related to the quaternary structure of the intact heterotrimer. An organic ligand binding site between subunits RPA14 and RPA32 was identified to bind dioxane. Comparison of the ssDNA binding surfaces of RPA70 with RPA14/32 showed that the lower affinity of RPA14/32 can be attributed to a shallower binding crevice with reduced positive electrostatic charge.

Deng, X.; Habel, J.E.; Kabaleeswaran, V.; Snell, E.H.; Wold, M.S.; Borgstahl, G.E.O.

2009-06-03T23:59:59.000Z

74

Lycopene Attenuated Hepatic Tumorigenesis via Differential Mechanisms Depending on Carotenoid Cleavage Enzyme in Mice  

Science Journals Connector (OSTI)

...wild-type on HFD; KO, BCO2-KO on HFD), in which 45% of energy was fat derived, or the same HFD supplemented with lycopene...PCR (qRT-PCR) was performed using FastStart Universal SYBR Green Master (ROX; Roche). Relative gene expression was determined...

Blanche C. Ip; Chun Liu; Lynne M. Ausman; Johannes von Lintig; and Xiang-Dong Wang

2014-12-01T23:59:59.000Z

75

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

E-Print Network [OSTI]

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 ...

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

2009-01-01T23:59:59.000Z

76

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

E-Print Network [OSTI]

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 ...

Zhu, Ting, 1971-

2004-01-01T23:59:59.000Z

77

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

E-Print Network [OSTI]

adhesion mechanisms. Recently, supramolecular building blocks, such as synthetic DNA base- pair mimics link between supramolecular chemistry and adhesion science. In recent years, synthetic DNA base

Sottos, Nancy R.

78

Abstract LB-1: PKR promotes genetic instability and evolution of MDS to acute leukemia in mice by negatively regulating DDR and DNA repair in a novel mechanism  

Science Journals Connector (OSTI)

...As a means to understand the fundamental mechanisms of bleomycin cell...of BL-10 to bleomycin and does not increase the bleomycin...As a means to understand the fundamental mechanisms of bleomycin cell...of BL-10 to bleomycin and does not increase the bleomycin...

Xiaodong Cheng; Michael Byrne; Richard Lynn Bennett; and Stratford William May

2014-10-01T23:59:59.000Z

79

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

E-Print Network [OSTI]

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

Ritchie, Robert

80

Structural basis for activation of the complement system by component C4 cleavage  

Science Journals Connector (OSTI)

...component C4 cleavage 10.1073/pnas.1208031109 Rune T. Kidmose Nick S. Laursen Jozsef Dobo Troels R. Kjaer Sofia Sirotkina Laure...anomalous diffraction phases from the Ta6Br12 derivative (figure of merit, 0.33; phasing power, 2.5) calculated with CNS (8...

Rune T. Kidmose; Nick S. Laursen; József Dobó; Troels R. Kjaer; Sofia Sirotkina; Laure Yatime; Lars Sottrup-Jensen; Steffen Thiel; Péter Gál; Gregers R. Andersen

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds  

SciTech Connect (OSTI)

The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

John J. Kilbane II

2005-10-01T23:59:59.000Z

82

Pre-Steady-State Binding of Damaged DNA by XPC?hHR23B Reveals a Kinetic Mechanism for Damage Discrimination  

Science Journals Connector (OSTI)

9.?Sugasawa, K., Ng, J. M., Masutani, C., Maekawa, T., Uchida, A., van der Spek, P. J., Eker, A. P., Rademakers, S., Visser, C., Aboussekhra, A., Wood, R. D., Hanaoka, F., Bootsma, D., and Hoeijmakers, J. H. (1997) Two human homologs of Rad23 are functionally interchangeable in complex formation and stimulation of XPC repair activity, Mol. ... Sugasawa, Kaoru; Ng, Jessica M. Y.; Masutani, Chikahide; Maekawa, Takafumi; Uchida, Akio; van der Spek, Peter J.; Eker, Andre P. M.; Rademakers, Suzanne; Visser, Cecile; Aboussekhra, Abdelilah; Wood, Richard D.; Hanaoka, Fumio; Bootsma, Dirk; Hoeijmakers, Jan H. J. ... Rademakers, S., Volker, M., Hoogstraten, D., Nigg, A. L., Mone, M. J., van Zeeland, A. A., Hoeijmakers, J. H. J., Houtsmuller, A. B., and Vermeulen, W. (2003) Xeroderma pigmentosum group A protein loads as a separate factor onto DNA lesions, Mol. ...

Kelly S. Trego; John J. Turchi

2006-01-17T23:59:59.000Z

83

DNA Activity  

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

DNA Activity DNA Activity Name: Sara Location: N/A Country: N/A Date: N/A Question: Is DNA an anion or a cation? I thought since it was negatively charged it was an anion but mt teacher in class today said it was a cation because negatively charged molecules logically migrate to the positively charged plate of the cathode, ie molecules that migrate towards a cathode are cations. Where is the error in my logic or there error in my logic? Replies: DNA is negatively charged due to the phosphate ions present in the ribose-phosphate backbone. It moves towards the positive pole during electrophoresis. The definition kation/anion is confusing because: 1. a cation moves to the cathode 2. the cathode is negative, thus 3. a cation is positive DNA is an anion. The confusion is that a cathode is negative, but a cation is positively charged. For that reason these terms are not generally used in this context.

84

DNA adsorption on synthetic and natural allophanes  

Science Journals Connector (OSTI)

The adsorption of DNA on natural and synthetic samples of allophane, which is a primary clay mineral of andosols, was investigated with respect to the DNA concentration, pH, ionic strength in the sample solution, and competition between DNA molecules and phosphate ions for adsorption to understand the behavior of extracellular DNA molecules in andosols. The relationships between DNA adsorption and the final concentrations were significantly fitted to a simple linear Langmuir equation. DNA adsorption decreased considerably with increasing suspension pH in the range between 3 and 9. The adsorption was less affected by the ionic strength of the suspension from 0.1 to 0.5 mol L? 1. Under the same experimental conditions, DNA adsorption on allophanes was relatively higher than that on montmorillonite and silica but relatively lower than that on gibbsite and goethite. DNA adsorption on allophanes decreased on the addition of phosphate, indicating that there was a competition between DNA molecules and phosphate ions for adsorption on the minerals. These results suggested that DNA adsorption on allophanes occurred via two mechanisms: direct bonding of the phosphate group at the end of the DNA molecule to the OH groups of the Al-oxide layer on allophane, and the association of DNA molecules with the surface of negatively charged allophane via a bridging of inorganic cations.

Kazutoshi Saeki; Masao Sakai; Shin-Ichiro Wada

2010-01-01T23:59:59.000Z

85

ccsd00001150 Getting DNA twist rigidity from single molecule  

E-Print Network [OSTI]

ccsd­00001150 (version 1) : 17 Feb 2004 Getting DNA twist rigidity from single molecule experiments to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce single DNA molecules in order to test their mechanical properties. A #12;rst way to manipulate a single

86

DNA nanotechnology: understanding and optimisation through simulation  

E-Print Network [OSTI]

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 `overstepp...

Ouldridge, Thomas E

2014-01-01T23:59:59.000Z

87

Northwestern University Recombinant DNA  

E-Print Network [OSTI]

natural or synthetic DNA segments to DNA molecules that can replicate in a living cell · molecules that result from the replication of those described above Synthetic DNA segments which are likely to yield) are considered as equivalent to their natural DNA counterpart. If the synthetic DNA segment is not expressed

Shull, Kenneth R.

88

Single molecule studies of DNA mismatch repair  

Science Journals Connector (OSTI)

Abstract DNA mismatch repair, which involves is a widely conserved set of proteins, is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair.

Dorothy A. Erie; Keith R. Weninger

2014-01-01T23:59:59.000Z

89

Synthesis of DNA  

DOE Patents [OSTI]

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.

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

2008-11-18T23:59:59.000Z

90

Use of recombinant DNA (rDNA) and Biohazardous Materials  

E-Print Network [OSTI]

constructed outside living cells by joining natural or synthetic DNA segments to DNA molecules that can

Danforth, Bryan Nicholas

91

Asiakastyytyväisyystutkimus - DNA Kauppa Lappeenranta.  

E-Print Network [OSTI]

??Opinnäytetyön aiheena oli DNA Kauppa Lappeenrannan asiakastyytyväisyyden tutkiminen. Tutkimuksen ensisijaisena tavoitteena oli selvittää, kuinka tyytyväisiä asiakkaat olivat olleet DNA Kauppa Lappeenrannan ja asiakkaan väliseen kontaktipintaan… (more)

Pitkänen, Jesse

2013-01-01T23:59:59.000Z

92

Effect of phosphorus on cleavage fracture in -carbide N. I. Medvedeva,1,2 R. A. Howell,2 D. C. Van Aken,2 and J. E. Medvedeva2  

E-Print Network [OSTI]

Effect of phosphorus on cleavage fracture in -carbide N. I. Medvedeva,1,2 R. A. Howell,2 D. C. Van of the phosphorus effect on ideal cleavage energy and critical stress in -carbide, Fe3AlC, a precipitate the cleavage characteristics of -carbide. We show that strong anisotropy of the Fe-P bonds in Fe3 Al,P C under

Medvedeva, Julia E.

93

JGI - Why Sequence Sea Squirt cDNA?  

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

Sea Squirt cDNA? Sea Squirt cDNA? Ascidians are invertebrate chordates, which diverged from the vertebrate lineage near the root of the chordate phylogenetic tree. Their larvae have a tadpole structure that closely resembles lower vertebrate larvae. They are, however, composed of a very small number of cells (2600 for Ciona intestinalis), have a stereotyped development due to invariant cleavage patterns, and are therefore simpler to study than vertebrate embryos. This, combined with the recent establishment of powerful functional genomics tools in the wake of the sequencing of the Ciona intestinalis genome, has led to the re-emergence of ascidians as a chordate model organism of great evolutionary and developmental significance. Ciona studies have provided crucial insights into chordate evolution and the function of families of

94

Roles of the Major, Small, Acid-Soluble Spore Proteins and Spore-Specific and Universal DNA Repair Mechanisms in Resistance of Bacillus subtilis Spores to Ionizing Radiation from X Rays and High-Energy Charged-Particle Bombardment  

Science Journals Connector (OSTI)

...mutagenic effects induced by ionizing radiation are thought to be the result...of DNA damage caused by given doses of ionizing radiation for different bacteria are very similar, although the range of ionizing-radiation resistance...

Ralf Moeller; Peter Setlow; Gerda Horneck; Thomas Berger; Günther Reitz; Petra Rettberg; Aidan J. Doherty; Ryuichi Okayasu; Wayne L. Nicholson

2007-11-30T23:59:59.000Z

95

Imaging individual dopant atoms on cleavage surfaces of wurtzite-structure compound semiconductors  

Science Journals Connector (OSTI)

We report the identification of bulk-dopant atoms in (112¯0) and (101¯0) cleavage surfaces of wurtzite CdSe in atomically resolved scanning tunneling microscopy images. The In dopant atoms give rise to elevations (hillocks) of up to 5 nm in diameter in the empty- and occupied-state images. This contrast is simulated and it shows that the dopant atoms are positively charged. Hillocks with different symmetries with respect to the underlying lattice are correlated with different subsurface locations of the In-dopant atoms. Dopant atoms can be observed up to a depth below the surface of 3 to 5 layers. A quantitative analysis of the concentration of dopant atoms in the bulk yield the same values for both surfaces and agrees well with the In content of the crystal. Similar features in CdS(101¯0) surfaces are also attributed to In-dopant atoms.

B. Siemens, C. Domke, M. Heinrich, Ph. Ebert, and K. Urban

1999-01-15T23:59:59.000Z

96

Electronic structure of wurtzite II-VI compound semiconductor cleavage surfaces studied by scanning tunneling microscopy  

Science Journals Connector (OSTI)

We report atomically resolved scanning tunneling microscopy (STM) images of cleavage surfaces of wurtzite II-VI compound semiconductors. CdSe(112¯0), CdSe(101¯0), and CdS(101¯0) were investigated. The STM images confirm a 1×1 reconstruction for all surfaces. At negative and positive sample voltages the occupied and empty dangling-bond states above anions and cations, respectively, dominate the contrast of the STM images. No states in the band gap were found. The electronic structure of the surface permits the observation of dopant atoms in subsurface layers and thus also cross-sectional scanning tunneling microscopy studies of point defects and heterostructures.

B. Siemens, C. Domke, Ph. Ebert, and K. Urban

1997-11-15T23:59:59.000Z

97

Physical process Mechanical mechanisms  

E-Print Network [OSTI]

1 Physical process Generation · Mechanical mechanisms F = m·a · Electric/Magnetic mechanisms F ­ Quadrupoles......shear stress fluctuations ­ High order poles...... phys. interpretation difficult Governing

Berlin,Technische Universität

98

Cleavage of the 1,6-anhydro bridge in the levoglucosenone adduct with isoprene and its derivatives  

Science Journals Connector (OSTI)

Methods of opening of the 1,6-anhydro bridge in levoglucosenone (ZnCl2-Ac2O), its adducts with isoprene (ZnCl2-Ac2O, HCl-MeOH), and hydroxy derivatives (H3PO4-Ac2 O...) were studied. Cleavage of t...

B. T. Sharipov; O. Yu. Krasnoslobodtseva…

2010-01-01T23:59:59.000Z

99

DNA Nanotechnology- Architechtures Designed with DNA.  

E-Print Network [OSTI]

??As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such… (more)

Han, Dongran

2012-01-01T23:59:59.000Z

100

Mechanistic Examination of C?–C? Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations  

SciTech Connect (OSTI)

In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The C?–C? bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan ?-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against C?–C? bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The C?–C? bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote C?–C? bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

2013-02-14T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

Capstan friction model for DNA ejection from bacteriophages  

E-Print Network [OSTI]

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.

Sandip Ghosal

2013-01-09T23:59:59.000Z

102

Automating DNA processing  

E-Print Network [OSTI]

Center are exploring the potential of sequencing by hybridization (3). They are developing electronically addressable fixtures to contain immobilized synthetic DNA probes that can bind to target DNA samples. They call these microfabricated devices... Center are exploring the potential of sequencing by hybridization (3). They are developing electronically addressable fixtures to contain immobilized synthetic DNA probes that can bind to target DNA samples. They call these microfabricated devices...

Wienen, Michael Jan

2012-06-07T23:59:59.000Z

103

Covalently Linked DNA Nanotubes  

Science Journals Connector (OSTI)

SEM analyses of the nanotubes generated according to Scheme 2 further support the suggested folding of the 2D cross-linked DNA array into the nanotube structure. ... Here, we report a modular approach to DNA nanotube synthesis that provides access to geometrically well-defined triangular and square-shaped DNA nanotubes. ... and assembly of carbon nanotubes, and in nanotube-based DNA sensing and sepns. ...

Ofer I. Wilner; Anja Henning; Bella Shlyahovsky; Itamar Willner

2010-03-17T23:59:59.000Z

104

DNA nanotechnology: a future perspective  

Science Journals Connector (OSTI)

The rise of DNA-based nanobiotechnology has led to an increase in demand for synthetic DNA. DNA can be synthesized from nucleotides into ... technology has been the significant error rate of synthetic DNA sequenc...

Muniza Zahid; Byeonghoon Kim; Rafaqat Hussain; Rashid Amin…

2013-03-01T23:59:59.000Z

105

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

Protein Bridges DNA Base and Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

106

Natural DNA sequencing by synthesis  

E-Print Network [OSTI]

labeling of a synthetic DNA template. By combining the bestpolyadenylation of a 100-base synthetic DNA template (nSBST)

Roller, Eric E.

2011-01-01T23:59:59.000Z

107

DNA Sequencing apparatus  

DOE Patents [OSTI]

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.

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

1992-01-01T23:59:59.000Z

108

An unusual carbon?carbon bond cleavage reaction during phosphinothricin biosynthesis  

SciTech Connect (OSTI)

Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp{sup 3})-C(sp{sup 3}) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(II)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.

Cicchillo, Robert M.; Zhang, Houjin; Blodgett, Joshua A.V.; Whitteck, John T.; Li, Gongyong; Nair, Satish K.; van derDonk, Wilfred A.; Metcalf, William W.; (UIUC)

2010-01-12T23:59:59.000Z

109

Meta-DNA: synthetic biology via DNA nanostructures and  

E-Print Network [OSTI]

Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 strands and may be modified to allow for mutations. Keywords: DNA self-assembly; synthetic biology; DNA nanostructures 1. INTRODUCTION 1.1. Synthetic biology using DNA nanosystems A major goal of synthetic biology

Reif, John H.

110

DNA nanotechnology: understanding and optimisation through simulation  

E-Print Network [OSTI]

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.

Thomas E. Ouldridge

2014-11-07T23:59:59.000Z

111

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

112

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

113

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

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

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development.

114

Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad  

SciTech Connect (OSTI)

Meta-cleavage product (MCP) hydrolases are members of the {alpha}/{beta}-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 {angstrom} resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of {sup 18}O into the benzoate produced during hydrolysis in H{sub 2}{sup 18}O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES{sup red}, previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.

Ruzzini, Antonio C.; Ghosh, Subhangi; Horsman, Geoff P.; Foster, Leonard J.; Bolin, Jeffrey T.; Eltis, Lindsay D. (Purdue); (UBC)

2014-10-02T23:59:59.000Z

115

DNA's Role with Proteins  

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

DNA's Role with Proteins DNA's Role with Proteins Name: Hans Location: N/A Country: N/A Date: N/A Question: Is it sure that the most important information of living cells is stored in the DNA? DNA seems to be nothing more than an inventory of useful proteins and a tool to create those proteins. Could it be that more important operational know how of how these proteins interact to build a living organism is actually located in the rest of the cell? So that the rest of the cell is the most important inheritance, whereas DNA merely takes care of the genetic variation? Replies: DNA is the entire library of protein information for an organism. All seven types of protein. It is true that in developmental stages of an organism that the presence and absences of certain proteins and other chemicals generated by proteins will influence what the DNA in a "particular" cell will express. Hence, you can start out with one cell and end up with a complex organism. You may have heard some of this information with the cloning activities that have been going on lately. All the inheritance comes from the DNA, but what parts of the DNA expression may be dictated by the cells special characteristics developed upon specializing. In that way the liver cells will only do "liver" things and the kidney cells will only do "kidney" things, BUT they use the same DNA information to operate, just a different portion of the same DNA that pertains to their particular "job". If you can convince a cell that it does not have a special job anymore, then you can develop the entire organism from this cell with the right signals; this is what cloning techniques have done!

116

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)

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.

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

2009-05-11T23:59:59.000Z

117

DNA | Open Energy Information  

Open Energy Info (EERE)

DNA DNA Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home NEPA Casual Use Determination of NEPA Adequacy Categorical Exclusion Environmental Assessment Environmental Impact Statements Print PDF NEPA-Related Analysis: Determination of NEPA Adequacy (DNA) General Document Collections (28) Documents Regulatory Roadmap NEPA-Related Analysis: Determination of NEPA Adequacy and Land Use Plan Conformance (DNA) placeholder. This query has been included to allow you to use the black arrows in the table header cells to sort the table data. Document # Serial Number Applicant Lead Agency District Office Field Office Development Phase(s) Techniques DOI-BLM-NM-L000-2012-0020-DNA Lightning Dock Geothermal Inc BLM BLM Las Cruces District Office BLM Geothermal/Exploration

118

Supramolecular DNA nanotechnology : discrete nanoparticle organization, three-dimensional DNA construction, and molecule templated DNA assembly.  

E-Print Network [OSTI]

??The field of structural DNA nanotechnology utilizes DNA's powerful base-pairing molecular recognition criteria to help solve real challenges facing researchers in material science and nanotechnology,… (more)

Aldaye, Faisal A., 1979-

2008-01-01T23:59:59.000Z

119

Alkali Metal Control over N–N Cleavage in Iron Complexes  

Science Journals Connector (OSTI)

We propose that the reaction of 1-Na with benzene is slower because the mechanism is different; after all, there are not enough Fe sites to accept the six electrons from two N3– to reform N2 in the mechanism followed by 1-K and 1-Rb. ... Therefore, extreme care must be taken when synthesizing and handling these alkali graphite reductants! ... This work was supported by the National Institutes of Health (GM065313) and Yale University. ...

Katarzyna Grubel; William W. Brennessel; Brandon Q. Mercado; Patrick L. Holland

2014-11-20T23:59:59.000Z

120

AMEAerospace & Mechanical  

E-Print Network [OSTI]

AMEAerospace & Mechanical Engineering #12;Aerospace and Mechanical Engineers design complex mechanical, thermal, fluidic, acousti- cal, optical, and electronic systems, with char- acteristic sizes space. Aerospace and Mechanical Engineering (AME) students conduct basic and applied research within

Wang, Hai

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Synthetic utility of sydnones: synthesis of pyrazolines derivatized with 1,2,4-triazoles as antihyperglymic, antioxidant agents and their DNA cleavage study  

Science Journals Connector (OSTI)

Ring transformation of sydnone (1a–i) to 1,3,4-oxadiazoline-2-one (2a–i) was carried out using bromine in acetic anhydride. The compounds (2a–i) on heating with hydrazine hydrate gave 1,2,4-triazole (3a–i) in goo...

Tasneem Taj; Ravindra R. Kamble; Pramod P. Kattimani…

2012-11-01T23:59:59.000Z

122

High-Throughput Genotyping of Green Algal Mutants Reveals Random Distribution of Mutagenic Insertion Sites and Endonucleolytic Cleavage of Transforming DNA  

Science Journals Connector (OSTI)

...false discovery rate-adjusted P values 0.00001, Kruskal-Wallis test) are responsible for 15% of the reads, and...observed cassette fragments. We used the nonparametric Kruskal-Wallis test to determine whether the read counts for each...

Ru Zhang; Weronika Patena; Ute Armbruster; Spencer S. Gang; Sean R. Blum; Martin C. Jonikas

2014-04-04T23:59:59.000Z

123

Induction of Endonucleolytic DNA Cleavage in Human Acute Myelogenous Leukemia Cells by Etoposide, Camptothecin, and Other Cytotoxic Anticancer Drugs: A Cautionary Note  

Science Journals Connector (OSTI)

...assess the possibility that an energy-requiring step might be needed...undertaken to assess whether the energy-requiring step(s) suggested...27. Compton, M. M., Car n, L-A. M., and Cidlowski...and Shaper, J. H. An alternative approach to the quantitation...

Scott H. Kaufmann

1989-11-01T23:59:59.000Z

124

Automated Image Processing for the Analysis of DNA Repair Dynamics  

E-Print Network [OSTI]

The efficient repair of cellular DNA is essential for the maintenance and inheritance of genomic information. In order to cope with the high frequency of spontaneous and induced DNA damage, a multitude of repair mechanisms have evolved. These are enabled by a wide range of protein factors specifically recognizing different types of lesions and finally restoring the normal DNA sequence. This work focuses on the repair factor XPC (xeroderma pigmentosum complementation group C), which identifies bulky DNA lesions and initiates their removal via the nucleotide excision repair pathway. The binding of XPC to damaged DNA can be visualized in living cells by following the accumulation of a fluorescent XPC fusion at lesions induced by laser microirradiation in a fluorescence microscope. In this work, an automated image processing pipeline is presented which allows to identify and quantify the accumulation reaction without any user interaction. The image processing pipeline comprises a preprocessing stage where the ima...

Riess, Thorsten; Tomas, Martin; Ferrando-May, Elisa; Merhof, Dorit

2011-01-01T23:59:59.000Z

125

Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures  

E-Print Network [OSTI]

-Assembled DNA Nanostructures: · use synthetic DNA to self-assemble into DNA nanostructure devices. Goals

Reif, John H.

126

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

E-Print Network [OSTI]

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 induced by naked CpG DNA or DNA/cationic liposome complex (lipoplex) CpG motif recognition by Toll-like receptor 9 (TLR9) Significance of the immune response to DNA Apoptotic ornecrotic cells...

Yoshida, Hiroyuki

2006-10-27T23:59:59.000Z

127

Chromium reduces the in vitro activity and fidelity of DNA replication mediated by the human cell DNA synthesome  

SciTech Connect (OSTI)

Hexavalent chromium Cr(VI) is known to be a carcinogenic metal ion, with a complicated mechanism of action. It can be found within our environment in soil and water contaminated by manufacturing processes. Cr(VI) ion is readily taken up by cells, and is recognized to be both genotoxic and cytotoxic; following its reduction to the stable trivalent form of the ion, chromium(Cr(III)), within cells. This form of the ion is known to impede the activity of cellular DNA polymerase and polymerase-mediated DNA replication. Here, we report the effects of chromium on the activity and fidelity of the DNA replication process mediated by the human cell DNA synthesome. The DNA synthesome is a functional multiprotein complex that is fully competent to carry-out each phase of the DNA replication process. The IC{sub 50} of Cr(III) toward the activity of DNA synthesome-associated DNA polymerases {alpha}, {delta} and {epsilon} is 15, 45 and 125 {mu}M, respectively. Cr(III) inhibits synthesome-mediated DNA synthesis (IC{sub 50} = 88 {mu}M), and significantly reduces the fidelity of synthesome-mediated DNA replication. The mutation frequency induced by the different concentrations of Cr(III) ion used in our assays ranges from 2-13 fold higher than that which occurs spontaneously, and the types of mutations include single nucleotide substitutions, insertions, and deletions. Single nucleotide substitutions are the predominant type of mutation, and they occur primarily at GC base-pairs. Cr(III) ion produces a lower number of transition and a higher number of transversion mutations than occur spontaneously. Unlike Cr(III), Cr(VI) ion has little effect on the in vitro DNA synthetic activity and fidelity of the DNA synthesome, but does significantly inhibit DNA synthesis in intact cells. Cell growth and proliferation is also arrested by increasing concentrations of Cr(VI) ion. Our studies provide evidence indicating that the chromium ion induced decrease in the fidelity and activity of synthesome mediated DNA replication correlates with the genotoxic and cytotoxic effects of this metal ion; and promotes cell killing via inhibition of the DNA polymerase activity mediating the DNA replication and repair processes utilized by human cells.

Dai Heqiao; Liu Jianying; Malkas, Linda H.; Catalano, Jennifer; Alagharu, Srilakshmi [Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202 (United States); Hickey, Robert J. [Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indiana University Cancer Research Institute, 1044 W. Walnut Street R4-170 Indianapolis, IN 46202 (United States)], E-mail: rohickey@iupui.edu

2009-04-15T23:59:59.000Z

128

DNA repair: Dynamic defenders against cancer and aging  

SciTech Connect (OSTI)

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.

Fuss, Jill O.; Cooper, Priscilla K.

2006-04-01T23:59:59.000Z

129

Direct femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO to 2CH3 CO: Resolving  

E-Print Network [OSTI]

devoted to answer such a question, and the issue in different reactions pericyclic, SN2, elimination, etcDirect femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO, California 91125 Received 17 April 1995; accepted 2 May 1995 When a reaction involving two equivalent bonds

Kim, Sang Kyu

130

Review Paper. Ancient DNA  

Science Journals Connector (OSTI)

...poorly char- acterized (Gilbert et al. 2003a,b...research has been done in microbiology departments where the...unlikely to preserve DNA (Gilbert et al. 2005a). This...Smith, B. D., Gilbert, M. T. P., Cooper...the tenacity of life. Microbiology 140, 25132529. Kim...

2005-01-01T23:59:59.000Z

131

Recognition of DNA by Synthetic Antibodies  

Science Journals Connector (OSTI)

Recognition of DNA by Synthetic Antibodies ... The recombinant anti-ssDNA Fab, DNA-1, and 16 heavy chain complementarity determining region 3 (HCDR3) mutant variants were selected for thermodynamic characterization of ssDNA binding. ...

Shana M. Barbas; Peter Ghazal; Carlos F. Barbas III; Dennis R. Burton

1994-03-01T23:59:59.000Z

132

Nuclear DNA Amounts in Angiosperms  

Science Journals Connector (OSTI)

27 May 1976 research-article Nuclear DNA Amounts in Angiosperms M. D. Bennett...number of angiosperm species for which nuclear DNA amount estimates have been made has...is overdue. This paper lists absolute nuclear DNA amounts for 753 angiosperm species...

1976-01-01T23:59:59.000Z

133

DNA Structural Nanotechnology Duke University  

E-Print Network [OSTI]

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

Reif, John H.

134

Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly  

Science Journals Connector (OSTI)

Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly ... In concert with entirely de novo synthesis, a swathe of alternative DNA assembly methods are being introduced(4-6) that concatenate parts from hundreds of base pairs in length, through gene fusions, to synthetic biological devices built from catalogued parts, up to megabase fragments and entire chromosomes. ... De novo synthesis relies on synthetic oligos that are inherently error prone, and therefore, reusing existing error-free DNA in constructing new DNA provides an inherent advantage. ...

Jonathan Blakes; Ofir Raz; Uriel Feige; Jaume Bacardit; Pawe? Widera; Tuval Ben-Yehezkel; Ehud Shapiro; Natalio Krasnogor

2014-02-20T23:59:59.000Z

135

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations  

Science Journals Connector (OSTI)

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations ... To form the hydrated intermediate, a water molecule (WAT) must attack the carbonyl carbon of SUB15,17,18,21,31 (chemical step 1). ... This result, surprising at first, can be rationalized by realizing that a fundamental ingredient of HIV-1 PR catalytic power is the low polarity of the cleavage site environment15 that destabilizes the negatively charged Asp dyad. ...

Stefano Piana; Denis Bucher; Paolo Carloni; Ursula Rothlisberger

2004-06-25T23:59:59.000Z

136

Molecular Recognition of DNA Damage Sites by Apurinic/Apyrimidinic Endonucleases  

SciTech Connect (OSTI)

The DNA repair/redox factor AP endonuclease 1 (APE1) is a multifunctional protein which is known to to be essential for DNA repair activity in human cells. Structural/functional analyses of the APE activity is thus been an important research field to assess cellular defense mechanisms against ionizing radiation.

Braun, W. A.

2005-07-28T23:59:59.000Z

137

Dimension Augmentation and Combinatorial Criteria for Efficient Error-resistant DNA Self-assembly  

E-Print Network [OSTI]

Dimension Augmentation and Combinatorial Criteria for Efficient Error-resistant DNA Self-assembly Abstract DNA self-assembly has emerged as a rich and promising primitive for nano-technology. Experimental-correction mech- anisms have been proposed for the tile model of self- assembly. These error-correction mechanisms

Goel, Ashish

138

Fleet DNA (Presentation)  

SciTech Connect (OSTI)

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.

Walkokwicz, K.; Duran, A.

2014-06-01T23:59:59.000Z

139

Chiral Mesophases of DNA  

E-Print Network [OSTI]

In the hexagonal columnar phase of chiral polymers a bias towards cholesteric twist competes with braiding along an average direction. When the chirality is strong, topological defects proliferate, leading to either a tilt grain boundary phase or a new ``moire state'' with twisted bond order. This moire phase can melt leading to a new phase: the chiral hexatic. I will discuss some recent experimental results from the NIH on DNA liquid crystals in the context of these theories.

Randall D. Kamien

1998-12-08T23:59:59.000Z

140

Radiation and viral DNA  

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

Radiation and viral DNA Radiation and viral DNA Name: Loretta L Lamb Age: N/A Location: N/A Country: N/A Date: N/A Question: Can viral DNA be changed through exposure to radiation? If so, what type of radiation will do this? Can these irradiated viruses cause changes in the genome of any human cells they may infect? Can these (or any) viruses actually cause cancer, or do they merely act as triggering devices for cancer? Replies: In theory, any nucleic acid (viral or otherwise) can be changed by exposure to many kinds of radiation. Depending on the type of virus, these may then change the human cells that they infect. Although there are many different things that are being implicated in causing cancers, it looks like a fairly common model involves the sequential "knockout" of several human genes. Viruses may be one cause of such gene changes, radiation and other environmental causes may also contribute. Some of these changes may be inherited through families, so it becomes more likely that the environmental factors may happen to "hit" the right places in cells to cause cancers in these families. If you ask something more specific, perhaps I can focus my response a bit more

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Transcription Inhibition by Platinum DNA Cross-links in Live Mammalian Cells  

E-Print Network [OSTI]

We have investigated the processing of site-specific Pt?DNA cross-links in live mammalian cells to enhance our understanding of the mechanism of action of platinum-based anticancer drugs. The activity of platinum drugs ...

Ang, Wee Han

142

Unscheduled DNA synthesis and mitochondrial DNA synthetic rate following injury of the facial nerve  

Science Journals Connector (OSTI)

Unscheduled DNA synthesis (UDS) of nuclear DNA and mitochondrial (mt) DNA synthetic rates were determined autoradiographically in different cell ... nerve transection. In addition to an increased synthetic rate ...

H. Korr; V. Philippi; C. Helg; J. Schiefer; M. B. Graeber…

1997-11-01T23:59:59.000Z

143

The Cleavage and Polyadenylation Specificity Factor in Xenopus laevis Oocytes Is a Cytoplasmic Factor Involved in Regulated Polyadenylation  

Science Journals Connector (OSTI)

...removed from oocytes under mineral oil as described in reference 7...described by the manufacturer (Marathon cDNA Amplification kit; Clontech...manually dissected under mineral oil to reduce nuclear leakage...manually dissected under mineral oil to reduce nuclear leakage...

Kirsten S. Dickson; Andrea Bilger; Scott Ballantyne; Marvin P. Wickens

1999-08-01T23:59:59.000Z

144

Fusion function of the Semliki Forest virus spike is activated by proteolytic cleavage of the envelope glycoprotein precursor p62.  

Science Journals Connector (OSTI)

...similar, if not identical, to those in wing that the cleav- virus-infected cells...cDNA microinjected into the nucleus of baby hamster kidney cells. Proc. Natl. Acad...tein-protein interactions in plasma membrane of baby hamster kidney cells infected with Sindbis...

M Lobigs; H Garoff

1990-03-01T23:59:59.000Z

145

Structural Characterization of the Major Adducts Obtained after Reaction of an Ultimate Carcinogen Aflatoxin B1-Dichloride with Calf Thymus DNA in Vitro  

Science Journals Connector (OSTI)

...by the adducts derived from reaction of AFBi-epoxide and DNA...guanine bases in DNA by an SN1 reaction pathway. If so, then both...with DNA. If this is so, then reaction must take place by an SN2 mechanism, so that the product...

Michael L. Wood; J. R. Lindsay Smith; and R. Colin Garner

1988-10-01T23:59:59.000Z

146

Identification and Characterization of a Small Inhibitory Peptide That Can Target DNA-PKcs Autophosphorylation and Increase Tumor Radiosensitivity  

SciTech Connect (OSTI)

Purpose: The DNA protein kinase catalytic subunit (DNA-PKcs) is one of the critical elements involved in the DNA damage repair process. Inhibition of DNA-PKcs results in hypersensitivity to ionizing radiation (IR); therefore, this approach has been explored to develop molecular targeted radiosensitizers. Here, we aimed to develop small inhibitory peptides that could specifically target DNA-PKcs autophosphorylation, a critical step for the enzymatic activation of the kinase in response to IR. Methods and Materials: We generated several small fusion peptides consisting of 2 functional domains, 1 an internalization domain and the other a DNA-PKcs autophosphorylation inhibitory domain. We characterized the internalization, toxicity, and radiosensitization activities of the fusion peptides. Furthermore, we studied the mechanisms of the inhibitory peptides on DNA-PKcs autophosphorylation and DNA repair. Results: We found that among several peptides, the biotin-labeled peptide 3 (BTW3) peptide, which targets DNA-PKcs threonine 2647 autophosphorylation, can abrogate IR-induced DNA-PKcs activation and cause prolonged {gamma}-H2AX focus formation. We demonstrated that BTW3 exposure led to hypersensitivity to IR in DNA-PKcs-proficient cells but not in DNA-PKcs-deficient cells. Conclusions: The small inhibitory peptide BTW3 can specifically target DNA-PKcs autophosphorylation and enhance radiosensitivity; therefore, it can be further developed as a novel class of radiosensitizer.

Sun Xiaonan [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China)] [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China); Yang Chunying [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States)] [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Liu Hai; Wang Qi [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China)] [Department of Radiation Oncology, Sir Run Run Shaw Hospital, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, Hangzhou (China); Wu Shixiu [Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou (China)] [Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou (China); Li Xia; Xie Tian [Research Center of Biomedicine and Health, Hangzhou Normal University, Hangzhou (China)] [Research Center of Biomedicine and Health, Hangzhou Normal University, Hangzhou (China); Brinkman, Kathryn L.; Teh, Bin S.; Butler, E. Brian [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States)] [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Xu Bo, E-mail: bxu@tmhs.org [Department of Radiation Oncology, Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX (United States); Zheng, Shu, E-mail: zhengshu@zju.edu.cn [Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China)] [Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China)

2012-12-01T23:59:59.000Z

147

DNA attachment to support structures  

SciTech Connect (OSTI)

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

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

2002-01-01T23:59:59.000Z

148

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

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

A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples...

149

A Model for Structure and Thermodynamics of ssDNA and dsDNA Near...  

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

Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse Grained Approach. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse...

150

Design of a New Fluorescent Cofactor for DNA Methyltransferases and Sequence-Specific Labeling of DNA  

Science Journals Connector (OSTI)

Sequence-specific labeling of DNA is of immense interest for analytical and functional studies of DNA. We present a novel approach for sequence-specific labeling of DNA using a newly designed fluorescent cofactor for the DNA methyltransferase from ...

Goran Pljevaljcic; Marc Pignot; Elmar Weinhold

2003-02-26T23:59:59.000Z

151

Structural investigations of platinum anticancer drugs with DNA  

SciTech Connect (OSTI)

The antitumor agent cis-diamminedichloroplatinum (II) (cis-DDP) can successfully treat testicular and ovarian cancers, presumably by binding to DNA and preventing replication. cis-DDP is less successful in treating lung and breast cancers and the trans isomer is inactive. It has been suggested that cellular recognition and repair processes may be responsible for the difference in activity between cis- and trans-DDP, the differential effectiveness against different types of cancers, as well as acquired resistance. The author reviews structural methods used to characterize several site-specific adducts. Structure-function relations that emerge may help clarify the mechanism of action. The extent of DNA bending caused by several site-specific DNA adducts formed by cis- and trans-DDP has been determined using a gel electrophoresis assay. The adducts cis-GG, cis-AG, cis-GTG, and trans-GTG were incorporated into synthetic DNA oligonucleotides of varying lengths with two bp cohesive ends. Subtle DNA distortions were amplified by polymerizing these monomers and quantitated using polyacrylamide gel electrophoresis. The three adducts cis-GG, cis-AG, and cis-GTG were all found to bend the helix in a directed fashion by about 32-35[degrees]. The trans-GTG adduct gave a degree of flexibility to the double helix, allowing bending in more than one direction. The DNA unwinding caused by the platinum binding was measured by systematically varying the interplatinum distance in a series of synthetic DNA oligonucleotides. The cis-GG and cis-AG adducts both unwind the double helix by 13[degrees]C, while the cis-GTG adduct unwinds by 23[degrees]. To determine the complete structure of platinated duplex DNA< single crystals of a platinated 12 base pair duplex oligonucletide were obtained. Despite extreme temperature and radiation sensitivity problems, a complete set of data was collected. Several different approaches to solve the structure were attempted.

Bellon, S.F.

1992-01-01T23:59:59.000Z

152

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

SciTech Connect (OSTI)

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).

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

2012-09-17T23:59:59.000Z

153

DNA Meta-Molecules: Synthe4c Biology via DNA Nanostructures &  

E-Print Network [OSTI]

reaction - DNA walkers - Activatable tiles and assemblies (4) DNA-based synthetic biology (slides 107-122) - Synthetic biology - DNA-based meta molecules and their use in synthetic biology - Meta DNA #12;SelfDNA Meta-Molecules: Synthe4c Biology via DNA Nanostructures & Hybridiza4on Reac

Reif, John H.

154

Conserved and Unconventional Responses to DNA Damage in Tetrahymena  

E-Print Network [OSTI]

in the transition G1/S phase to promote the loading of DNA polymerases. Additionally CDK prevent any further activation of pre-RC. CDK also induce phosphorylation of Sld2, Sld3 and Mcm5 that promotes the initiation of DNA synthesis. Diagram modified from Sclafani... and Holzen (2007). Cdc45 Sld2-3 S-CDK Initiation G1 phase G1/S transition S phase 21 21 mechanism to restrict pre-RC formation to only once per cell cycle (Lutzmann et al., 2006). Cdc6 in budding yeast stimulates the Abf1 binding activity...

Sandoval Oporto, Pamela

2012-07-16T23:59:59.000Z

155

Integrated Microfluidic Electrochemical DNA Sensor  

E-Print Network [OSTI]

of small scale fluid flow Laminar flow Easy to predict the flow patterns Very little diffusion This can make mixing difficult Small volumes Don't need to waste expensive reagents Easy fluid control;DNA Purification The DNA will be extracted using Invitrogen Charge Switch beads. Cellular Lysis

Fygenson, Deborah Kuchnir

156

Single Molecule Studies of Telomere DNA  

E-Print Network [OSTI]

2009) G-quadruplex DNA bound by a synthetic ligand is highly2009) G-quadruplex DNA bound by a synthetic ligand is highly2009) G-quadruplex DNA bound by a synthetic ligand is highly

Long, Xi

2014-01-01T23:59:59.000Z

157

DNA Origami: A History and Current Perspective  

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

DNA origami' has emerged as one of the most promising assembly techniques in DNA nanotechnology with a broad range of applications. In the past two years alone, DNA origami has...

158

Mechanical memory  

DOE Patents [OSTI]

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.

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)

2006-05-16T23:59:59.000Z

159

Mechanical memory  

DOE Patents [OSTI]

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.

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)

2006-08-15T23:59:59.000Z

160

Challenges and opportunities for structural DNA nanotechnology  

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

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

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Nanotechnology Applications in Self-Assembly and DNA Computing  

E-Print Network [OSTI]

Covalent attachment of synthetic DNA to self-assembledof synthetic oligodeoxyribonucleotides to phi chi 174 DNA:

Akin, Hayri Engin

2011-01-01T23:59:59.000Z

162

Sequence independent amplification of DNA  

DOE Patents [OSTI]

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.

Bohlander, S.K.

1998-03-24T23:59:59.000Z

163

Sequence independent amplification of DNA  

DOE Patents [OSTI]

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.

Bohlander, Stefan K. (Chicago, IL)

1998-01-01T23:59:59.000Z

164

Unnatural nucleotides for DNA sequencing  

E-Print Network [OSTI]

'-dT4XT5 (below). . . 65 4. 4 Attempted incorporation of dXTP by A) Sequenase~ Version 2. 0, B) Klenow, Exonuclease-free and C) DNA Polymerase, Klenow Fragment. . . . . . . , . . . . . . . . . . . . . . . . . . , . . . . . . 68 4. 5 Attempted... detection of small amounts of DNA present in DNA sequencing gels. Second, tMferent fluorophores are used for each of the base specific reactions. Fluorophores (Figure 1. 4) are covalently attached to the 5' end CHs CHs 0 0 0 HsC CHs 0 ~NH 0 I NH CHs...

Jacutin, Swanee E

2012-06-07T23:59:59.000Z

165

Normalized cDNA libraries  

DOE Patents [OSTI]

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.

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

1997-01-01T23:59:59.000Z

166

Normalized cDNA libraries  

DOE Patents [OSTI]

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.

Soares, M.B.; Efstratiadis, A.

1997-06-10T23:59:59.000Z

167

Computational mechanics  

SciTech Connect (OSTI)

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

Goudreau, G.L.

1993-03-01T23:59:59.000Z

168

Single molecule techniques in DNA repair: A primer  

Science Journals Connector (OSTI)

Abstract A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit – searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.

Craig D. Hughes; Michelle Simons; Cassidy E. Mackenzie; Bennett Van Houten; Neil M. Kad

2014-01-01T23:59:59.000Z

169

Modeling DNA Shuffling Fengzhu Sun  

E-Print Network [OSTI]

Modeling DNA Shuffling Fengzhu Sun 1Department of Genetics Emory University School of Medicine property are selected. Irvine et al. (1991) and Sun et al. (1996) studied in vitro evolution not involving

Sun, Fengzhu - Sun, Fengzhu

170

Nanoscale Molecular Transport by Synthetic DNA Machines  

E-Print Network [OSTI]

Nanoscale Molecular Transport by Synthetic DNA Machines Jong-Shik Shin1 and Niles A. Pierce1,2 1 a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. On a periodic DNA track

Pierce, Niles A.

171

Ancient DNA: the first three decades  

Science Journals Connector (OSTI)

...Romanov family by DNA analysis. Nat. Genet. 6...Tyler-Smith, C. 1998 Reliability of DNA-based sex tests...W. 2000 Molecular analysis of Neanderthal DNA from...and mitochondrial DNA analysis of a 2000-year-old...high-density picolitre reactors. Nature 437, 376-380...

2015-01-01T23:59:59.000Z

172

Molecular Computing with DNA Self-Assembly  

E-Print Network [OSTI]

Molecular Computing with DNA Self-Assembly Urmi Majumder #12;Self-Assembly in Nature #12;Key to DNA for Molecular Computing with DNA Self-Assembly Compact: Small library of assembly primitives Complex: Capable in Tiling Assembly: vitroation tural DNA self-assembly has powerful echanisms for error correction

Reif, John H.

173

Covalent Structure of the DNA-DNA Interstrand Cross-Link Formed by Reductively Activated FR66979 in Synthetic DNA Duplexes  

Science Journals Connector (OSTI)

Covalent Structure of the DNA-DNA Interstrand Cross-Link Formed by Reductively Activated FR66979 in Synthetic DNA Duplexes ...

Huifang Huang; Tom K. Pratum; Paul B. Hopkins

1994-04-01T23:59:59.000Z

174

Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions  

Science Journals Connector (OSTI)

...articles 1004 181 131 18 Meta-DNA: synthetic biology via DNA nanostructures...protocols for its manipulation. Synthetic DNA is also cheaply and readily available...specific to mDNA and also occurs in synthetic DNA synthesis. One of the key technological...

2012-01-01T23:59:59.000Z

175

SELF-ASSEMBLED DNA NANOSTRUCTURES AND DNA-TEMPLATED SILVER NANOWIRES  

E-Print Network [OSTI]

helix bundles, and the cross-tiles as well as synthetic double-stranded DNA moleculesSELF-ASSEMBLED DNA NANOSTRUCTURES AND DNA-TEMPLATED SILVER NANOWIRES by Sung Ha Park Department;ABSTRACT SELF-ASSEMBLED DNA NANOSTRUCTURES AND DNA-TEMPLATED SILVER NANOWIRES by Sung Ha Park Department

Reif, John H.

176

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database  

E-Print Network [OSTI]

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database Wellcome Trust response on the important topic of the forensic use of DNA and the National DNA Database (NDNAD). Given the Trust Assembly; "Forensic DNA Databasing: A European perspective" - a biomedical ethics grant to Professor Robin

Rambaut, Andrew

177

Mechanical Vibration  

Science Journals Connector (OSTI)

... THE suppression and control of mechanical vibration have assumed great importance in engineering. One consequence of this is that the number ... degree of emphasis is placed on transient oscillation (in addition to steady-State and free vibration). The treatment of this topic is based mainly on phase-plane constructions and it ...

R. E. D. BISHOP

1958-12-06T23:59:59.000Z

178

Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo  

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

Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo Quantitative, non-invasive imaging of radiation-induced DNA double strand breaks in vivo Wenrong Li 1, , Fang Li 1 , Qian Huang 1 , Jingping Shen 1 , Frank Wolf 1 , Yujun He 1 , Xinjian Liu 1 , Y. Angela Hu 1 , Joel. S. Bedford 5 , and Chuan-Yuan Li 1,2,* Departments of 1 Radiation Oncology, 2 Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA; 3 Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA DNA double strand breaks are a major form of DNA damage and a key mechanism through which radiotherapy and some chemotherapeutic agents kill cancer cells. Despite its importance, measuring DNA double strand breaks is still a tedious task that is normally carried out by gel electrophoresis or immunofluorescence staining. Here we report a novel approach to image and

179

Quantum Confinement in Hydrogen Bond of DNA and RNA  

E-Print Network [OSTI]

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.

Santos, da Silva dos; Ricotta, Regina Maria

2015-01-01T23:59:59.000Z

180

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]

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 A Thesis by NESTOR ENRIQUE ACEVEDO-PABON Submitted to the Office... of Graduate Studies of Texas A&M University in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE December 1988 Major Subject: Veterinary Anatomy IN VIVO AND IN VITRO EFFECTS OF ETHANOL ON THE INCORPORATION AND CLEAVAGE OF S IALI...

Acevedo-Pabon, Nestor Enrique

2012-06-07T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

Mass Spectrometric Study of Genetic and Epigenetic DNA Modifications  

E-Print Network [OSTI]

of cytosine in synthetic duplex DNA. Moreover, the level ofmethylation in synthetic duplex DNA. The underlined “C”of cytosine in synthetic duplex DNA. Moreover, the global

Wang, Hongxia

2010-01-01T23:59:59.000Z

182

C-terminal region of DNA ligase IV drives XRCC4/DNA ligase IV complex to chromatin  

SciTech Connect (OSTI)

Highlights: •Chromatin binding of XRCC4 is dependent on the presence of DNA ligase IV. •C-terminal region of DNA ligase IV alone can recruit itself and XRCC4 to chromatin. •Two BRCT domains of DNA ligase IV are essential for the chromatin binding of XRCC4. -- Abstract: DNA ligase IV (LIG4) and XRCC4 form a complex to ligate two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). It is not fully understood how these proteins are recruited to DSBs. We recently demonstrated radiation-induced chromatin binding of XRCC4 by biochemical fractionation using detergent Nonidet P-40. In the present study, we examined the role of LIG4 in the recruitment of XRCC4/LIG4 complex to chromatin. The chromatin binding of XRCC4 was dependent on the presence of LIG4. The mutations in two BRCT domains (W725R and W893R, respectively) of LIG4 reduced the chromatin binding of LIG4 and XRCC4. The C-terminal fragment of LIG4 (LIG4-CT) without N-terminal catalytic domains could bind to chromatin with XRCC4. LIG4-CT with W725R or W893R mutation could bind to chromatin but could not support the chromatin binding of XRCC4. The ability of C-terminal region of LIG4 to interact with chromatin might provide us with an insight into the mechanisms of DSB repair through NHEJ.

Liu, Sicheng; Liu, Xunyue; Kamdar, Radhika Pankaj; Wanotayan, Rujira; Sharma, Mukesh Kumar [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)] [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Adachi, Noritaka [Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027 (Japan)] [Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027 (Japan); Matsumoto, Yoshihisa, E-mail: yoshim@nr.titech.ac.jp [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)] [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)

2013-09-20T23:59:59.000Z

183

DNA chips --Integrated Chemical Circuits for DNADiagnosis and DNA computers  

E-Print Network [OSTI]

. Their needs are i nc reasing with the rapid progress of the genome projects. DNA chips will also provide basic about 6,000 genes. In 2002­2005, sequencing of the whole human genome w i l l be finished. There are about 100,000 genes in the human genome. These efforts are about to open a new age where everything

Hagiya, Masami

184

DNA damage and repair in human skin in situ  

SciTech Connect (OSTI)

Understanding the molecular and cellular origins of sunlight-induced skin cancers in man requires knowledge of the damages inflicted on human skin during sunlight exposure, as well as the ability of cells in skin to repair or circumvent such damage. Although repair has been studied extensively in procaryotic and eucaryotic cells - including human cells in culture - there are important differences between repair by human skin cells in culture and human skin in situ: quantitative differences in rates of repair, as well as qualitative differences, including the presence or absence of repair mechanisms. Quantitation of DNA damage and repair in human skin required the development of new approaches for measuring damage at low levels in nanogram quantities of non-radioactive DNA. The method allows for analysis of multiple samples and the resulting data should be related to behavior of the DNA molecules by analytic expressions. Furthermore, it should be possible to assay a variety of lesions using the same methodology. The development of new analysis methods, new technology, and new biochemical probes for the study of DNA damage and repair are described. 28 refs., 4 figs.

Sutherland, B.M.; Gange, R.W.; Freeman, S.E.; Sutherland, J.C.

1987-01-01T23:59:59.000Z

185

The assessment of DNA-synthetic activity  

Science Journals Connector (OSTI)

A method is described by which a numerical value can be assigned to the amount of DNA-synthesis shown graphically by population-histograms obtained ... index appeared to give a reasonable measure of DNA-synthetic

L. A. Coulton; B. Henderson; J. Chayen

1981-01-01T23:59:59.000Z

186

Fralin Life Science Institute DNA Biotechnology Kit  

E-Print Network [OSTI]

Fralin Life Science Institute DNA Biotechnology Kit INFORMATION MANUAL Kristi DeCourcy & Erin Dolan ..................................................................................................... 3 DNA Biotechnology Kit contents), in partnership with the Virginia Biotechnology Association (VaBIO) and the Virginia Manufacturers Association

Virginia Tech

187

A DNA tweezer-actuated enzyme nanoreactor  

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

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

188

DNA Concentration By UV Spectrophotometry Measure Absorption  

E-Print Network [OSTI]

DNA Concentration By UV Spectrophotometry Measure Absorption: 1. Dilute DNA to 0.5 to 50 µg 2. Measure absorption at 260 nm (A260). Start by zeroing instrument with TE buffer or dH2O alone

Aris, John P.

189

Towards Privacy Preserving of Forensic DNA Databases  

E-Print Network [OSTI]

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...

Liu, Sanmin

2012-02-14T23:59:59.000Z

190

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

191

Chromosome specific repetitive DNA sequences  

DOE Patents [OSTI]

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).

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

1991-01-01T23:59:59.000Z

192

International Standards in Forensic DNA  

E-Print Network [OSTI]

International Standards in Forensic DNA John M. Butler, Ph.D. National Institute of Standards and Technology NIST Fellow & Special Assistant to the Director for Forensic Science Vice-Chair, National Commission on Forensic Science World Forensics Festival Seoul, Korea October 15, 2014 #12;Definition

193

DNA Hybridization Catalysts and Catalyst Circuits  

E-Print Network [OSTI]

blocks for a synthetic DNA-based circuit. While ri- bozymes are the best known example of nucleic acids

Winfree, Erik

194

Amplification of chromosomal DNA in situ  

DOE Patents [OSTI]

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

Christian, Allen T. (Tracy, CA); Coleman, Matthew A. (Livermore, CA); Tucker, James D. (Livermore, CA)

2002-01-01T23:59:59.000Z

195

Mutations & DNA Repair I. What are Mutations?  

E-Print Network [OSTI]

­ one strand loops out and becomes displaced during replication ­ DNA pol stuttering ­ Occurs frequently

Dever, Jennifer A.

196

DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems  

Science Journals Connector (OSTI)

Simply put, the DNA assembly challenge is to take a set of double-stranded DNA fragments, and physically (as well as ... to yield a single, potentially circular, assembled DNA sequence. These DNA sequence fragmen...

Nathan J. Hillson

2011-01-01T23:59:59.000Z

197

Meta-DNA: A DNA-Based Approach to Synthetic Harish Chandran1  

E-Print Network [OSTI]

Meta-DNA: A DNA-Based Approach to Synthetic Biology Harish Chandran1 harish@cs.duke.edu Nikhil Gopalkrishnan, Bernard Yurke, John Reif, Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization@cs.duke.edu Abstract The goal of synthetic biology is to design and assemble synthetic systems that mimic bio- logical

Reif, John H.

198

Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins  

Science Journals Connector (OSTI)

......transcription factor MEF-2C for synthetic DNA (Meierhans et al ., 1997; Meierhans...Savinkova et al ., 1998) Synthetic DNA start 20 affinity yTBP/DNA X1...Bendall and Molloy, 1994) Synthetic DNA start X1 X2 10; 13 10; 18 depth......

MP Ponomarenko; JV Ponomarenko; AS Frolov; NL Podkolodny; LK Savinkova; NA Kolchanov; GC Overton

1999-07-01T23:59:59.000Z

199

DNA nanotubes and helical nanotapes via self-assembly of ssDNA-amphiphiles  

E-Print Network [OSTI]

DNA nanotubes and helical nanotapes via self- assembly of ssDNA-amphiphiles Timothy R. Pearcea and Efrosini Kokkoli*b DNA nanotubes were created using molecular self-assembly of single-stranded DNA (ss. The nanotube structures were formed by bilayers of amphiphiles, with the hydrophobic components forming

Kokkoli, Efie

200

Supplementary Information for: Integrating DNA Strand Displacement Circuitry with DNA Tile Self-assembly  

E-Print Network [OSTI]

Supplementary Information for: Integrating DNA Strand Displacement Circuitry with DNA Tile Self-assembly of Contents: · Supplementary Figures 1. Native polyacrylamide gel electrophoresis of DNA tile self-assembly 2. UV absorbance annealing and melting curves of DNA tile self-assembly 3. Characterization

Zhang, David Yu

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

Electromechanical Unzipping of Individual DNA Molecules Using  

E-Print Network [OSTI]

Electromechanical Unzipping of Individual DNA Molecules Using Synthetic Sub-2 nm Pores Ben Mc synthetic pores can be used to electrome- chanically unzip DNA duplexes.13 However, direct measure- ment time that the unzipping kinetics of individual DNA duplexes can be probed by analyzing the dwell

202

DNA Nanotechnology and its Biological Applications1  

E-Print Network [OSTI]

1 DNA Nanotechnology and its Biological Applications1 Chapter 13 of Book: Bio-inspired and Nano, amplified sensing, and molecular transport. 13.1 Introduction 13.1.1 DNA Nanotechnology and its use conventional top-down manufacturing techniques. Other surveys of DNA nanotechnology and devices have been given

Reif, John H.

203

Self-assembled DNA Structures for Nanoconstruction  

E-Print Network [OSTI]

Self-assembled DNA Structures for Nanoconstruction Hao Yan, Peng Yin, Sung Ha Park, Hanying Li methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano

Yin, Peng

204

HELICASE DEPENDENT AMPLICATION transfer the DNA  

E-Print Network [OSTI]

STEP 1 STEP 2 STEP 3 HELICASE DEPENDENT AMPLICATION HELICASE DNA POLYMERASE transfer the DNA instrumentation. MOLECULAR BIOMARKERS MADE UP DNA or RNA STRANDS ARE A POWERFUL WEAPON IN DETECTING DISEASE. USING for sample preparation at the point to care using only hand generated power.... #12;

205

Self-Assembled DNA Crystals: The Impact on Resolution of 5?-Phosphates and the DNA Source  

Science Journals Connector (OSTI)

Self-assembled 3D DNA crystals; crystal resolution; phosphorylated DNA; natural and synthetic DNA; X-ray diffraction; designed crystals ... During the last two decades, we have found two instances where synthetic DNA did not produce the results expected from it, when used as an enzymatic substrate; by contrast, DNA generated by the polymerase chain reaction (PCR) was an effective substrate. ... One example was the low level at which a synthetic DNA molecule was transcribed by T7 RNA polymerase to produce an RNA knot;(6, 7) the other instance was the incomplete restriction of a DNA graph assembled from synthetic branched junctions. ...

Ruojie Sha; Jens J. Birktoft; Nam Nguyen; Arun Richard Chandrasekaran; Jianping Zheng; Xinshuai Zhao; Chengde Mao; Nadrian C. Seeman

2013-01-16T23:59:59.000Z

206

DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting  

Science Journals Connector (OSTI)

...cholesteric liquid crystals. This interaction...polymers confined in a spherical cavity produces, on the...term that disfavors bent-chain configurations...the surface of the spherical capsid (45 nm diameter...cholesteric liquid crystals of DNA . Eur Phys...cholesteric liquid crystals. This interaction...

Davide Marenduzzo; Enzo Orlandini; Andrzej Stasiak; De Witt Sumners; Luca Tubiana; Cristian Micheletti

2009-01-01T23:59:59.000Z

207

Translationally Controlled Tumor Protein Protects against DNA Damage in Low  

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

Translationally Controlled Tumor Protein Protects against DNA Damage in Low Translationally Controlled Tumor Protein Protects against DNA Damage in Low Dose γ-Irradiated Cells Edouard Azzam New Jersey Medical School Cancer Center Abstract We have previously shown that exposure to low dose/low dose rate γ-rays can protect normal human and rodent cells against oxidative/clastogenic damages induced spontaneously or by a subsequent challenge dose of ionizing radiation. To gain insight into the mechanisms underlying these effects, we used amine-specific isobaric tags for relative and absolute quantitation (iTRAQ)-based approach to identify induced proteolytic events. Intriguingly, the Translationally Controlled Tumor Protein (TCTP) was significantly up-regulated after 10cGy (0.2cGy/h) but not after 4 Gy (1 Gy/min) in several strains of normal human fibroblasts maintained in 2- or

208

Regulation of chloroplast number and DNA synthesis in higher plants. Final report  

SciTech Connect (OSTI)

The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailing description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

Mullet, J.E.

1995-11-10T23:59:59.000Z

209

Regulation of chloroplast number and DNA synthesis in higher plants. Final report  

SciTech Connect (OSTI)

The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.

Mullet, J.E.

1995-11-10T23:59:59.000Z

210

Microfluidic DNA sample preparation method and device  

DOE Patents [OSTI]

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.

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)

2002-01-01T23:59:59.000Z

211

Human Genome Research: Decoding DNA  

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

Human Genome Research: Decoding DNA Human Genome Research: Decoding DNA Resources with Additional Information Charles DeLisi As head of DOE's Office of Health and Environmental Research, Charles DeLisi played a pivotal role in proposing and initiating the Human Genome Program in 1986. The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the government's Human Genome Project. At DOE's Office of Science, Dr. Patrinos is the Associate Director for Biological and Environmental Research. He has been a researcher at the department's Oak Ridge National Laboratory and Brookhaven National Laboratory.

212

Electromagnetic Signals from Bacterial DNA  

E-Print Network [OSTI]

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.

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

2012-02-09T23:59:59.000Z

213

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

214

Mechanical Engineer Company Description  

E-Print Network [OSTI]

Mechanical Engineer Company Description Control Solutions Inc. is a small, dynamic, and rapidly. Position Description The Mechanical Engineer is responsible for all aspects associated with the mechanical enclosures, brackets, cabling assemblies among others. Systems include mechanisms, sensors, hydraulics, among

Kostic, Milivoje M.

215

MECHANICAL ENGINEERING Ross Schlueter  

E-Print Network [OSTI]

MECHANICAL ENGINEERING Ross Schlueter Engineering Deputy For Mechanical Engineering Russ Wells Mechanical Engineering Department Deputy ELECTRONICS, SOFTWARE & INSTRUMENTATION ENGINEERING Henrik von Der Sen Mechanical Admin. Assist. Joan Wolter Electronics Admin. Assist. Marilyn Wong Division Admin

216

Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction  

SciTech Connect (OSTI)

Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H • • • H distance of 1.489(10) Å between the protic N-H?+ and hydridic Fe-H?-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 °C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Liu, Tianbiao L.; Wang, Xiaoping; Hoffmann, Christina; DuBois, Daniel L.; Bullock, R. Morris

2014-05-19T23:59:59.000Z

217

INFLUENCE OF CORIOLIS FORCE ON DNA MOLECULE MIGRATION AND HYBRIDIZATION IN COMPACT DISK (CD)  

E-Print Network [OSTI]

) MICROFLUIDICS PLATFORMS _______________ A Thesis Presented to the Faculty of San Diego State University in Compact Disk (CD) Microfluidics Platforms by Nithesh Paramesh Master of Science in Mechanical Engineering and hybridization of DNA molecules in CD microfluidics platform where centrifugal force is used as the driving force

Kassegne, Samuel Kinde

218

EGFR Nuclear Translocation Modulates DNA Repair following Cisplatin and Ionizing Radiation Treatment  

Science Journals Connector (OSTI)

...results suggest that nuclear expression of EGFR plays...the mechanisms by which nuclear expression modulates...C2259/A9994). The costs of publication of this...DNA-PK kinase assay. The graph shows the percentage...radiation-induced EGFR nuclear import by C225 (cetuximab...

Gianmaria Liccardi; John A. Hartley; and Daniel Hochhauser

2011-02-01T23:59:59.000Z

219

PcrA Helicase Dismantles RecA Filaments by Reeling in DNA in Uniform Steps  

E-Print Network [OSTI]

. Static disorder limited previous ensemble studies of a PcrA stepping mechanism. Here, highly repetitive Translocation of helicase-like proteins on nucleic acids underlies key cellular functions. However, it is still unclear how translocation can drive removal of DNA-bound proteins, and basic properties like

Lohman, Timothy M.

220

Enhancing the DNA Patent Database  

SciTech Connect (OSTI)

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.

Walters, LeRoy B.

2008-02-18T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Si–H and Si–C Bond Cleavage Reactions of Silane and Phenylsilanes with Mo(PMe3)6: Silyl, Hypervalent Silyl, Silane, and Disilane Complexes  

Science Journals Connector (OSTI)

Si–H and Si–C Bond Cleavage Reactions of Silane and Phenylsilanes with Mo(PMe3)6: Silyl, Hypervalent Silyl, Silane, and Disilane Complexes ... Mo(PMe3)6 cleaves the Si–H bonds of SiH4, PhSiH3, and Ph2SiH2 to afford a variety of novel silyl, hypervalent silyl, silane, and disilane complexes, as respectively illustrated by Mo(PMe3)4(SiH3)2H2, Mo(PMe3)4(?2-H2-H2SiPh2H)H, Mo(PMe3)3(?-HSiHPh2)H4, and Mo(PMe3)3(?2-H2-H2Si2Ph4)H2. ... Mo(PMe3)4(?2-H2-H2SiPh2H)H and Mo(PMe3)3(?2-H2-H2Si2Ph4)H2 are respectively the first examples of complexes that feature a hypervalent ?2-H2-H2SiPh2H silyl ligand and a chelating disilane ligand, and both compounds convert to the diphenylsilane adduct, Mo(PMe3)3(?-HSiHPh2)H4, in the presence of H2. ...

Ashley A. Zuzek; Gerard Parkin

2014-05-30T23:59:59.000Z

222

Self-Assembly of Metal-DNA Triangles and DNA Nanotubes with Synthetic Junctions  

Science Journals Connector (OSTI)

While DNA represents one of nature’s most predictable ... catalytic properties that are not observed naturally for DNA. Conceptually, this brings the toolbox of ... a diverse array of structures and functions usi...

Hua Yang; Pik Kwan Lo; Christopher K. McLaughlin; Graham D. Hamblin…

2011-01-01T23:59:59.000Z

223

A Synthetic DNA Walker for Molecular Transport  

Science Journals Connector (OSTI)

A Synthetic DNA Walker for Molecular Transport ... The authors report the incrementally staged design, synthesis, characterization, and operation of a mol. ...

Jong-Shik Shin; Niles A. Pierce

2004-08-17T23:59:59.000Z

224

IT for synthetic biology and DNA nanotechnology  

Science Journals Connector (OSTI)

Somewhere between the studies of information technology and organic chemistry, researchers are trying to make tiny robots out of DNA molecules.

Masami Hagiya; Fumiaki Tanaka; Ibuki Kawamata

2010-09-01T23:59:59.000Z

225

j5 DNA Assembly Design Automation Software  

Science Journals Connector (OSTI)

j5 DNA Assembly Design Automation Software ... Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. ... The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. ...

Nathan J. Hillson; Rafael D. Rosengarten; Jay D. Keasling

2011-12-07T23:59:59.000Z

226

Local elasticity of strained DNA studied by all-atom simulations  

Science Journals Connector (OSTI)

Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

Alexey K. Mazur

2011-08-03T23:59:59.000Z

227

ENGINEERING MECHANICS SEMINARSENGINEERING MECHANICS SEMINARS THINK COMPOSITE  

E-Print Network [OSTI]

ENGINEERING MECHANICS SEMINARSENGINEERING MECHANICS SEMINARS THINK COMPOSITE "THINK outside the box" for more competitive structural COMPOSITES Dr. Melih Papila Visiting Professor, Aero/Astro Department, Stanford University. Adv. Composites and Polymer Processing Lab., Sabanci University, Istanbul. mpapila

Ponce, V. Miguel

228

Voyage of RepA protein from plasmid DNA replication through amyloid aggregation towards synthetic biology  

Science Journals Connector (OSTI)

Summary DNA replication of plasmids in Gram-negative bacteria has been an object of study at CIB-CSIC for nearly 30 years. We have been focused on the enterobacterial antibiotic resistance factor R1 (1981–1992) and the pPS10 replicon from the phytopathogen Pseudomonas savastanoi (since 1984). Our group has used multidisciplinary (genetic, biochemical and biophysical-structural) approaches to unravel the molecular mechanism for the activation of RepA. Rep-type plasmidic proteins are either transcriptional repressors or replication initiators/inhibitors, depending on their association state (dimers vs. monomers) and targeting of alternative (operator or iteron) DNA sites. We discovered that allosteric DNA-binding remodels the structure of RepA N-terminal domain (WH1), transforming ?-helical portions into ?-strands. This precisely tunes the distances between the DNA reading heads in WH1 and the C-terminal domain (WH2), to match the target operator or iteron sequences. We have recently moved into engineering such structural transformation in RepA-WH1 to build-up synthetic protein devices that allow for customized ligand (DNA)-promoted amyloidogenesis. Our basic studies on plasmid DNA replication are relevant for settling the bases of a minimalist bacterial model to tackle transmissible amyloid proteinopathies and are a valuable tool for bottom-up synthetic biology.

Rafael Giraldo; María Elena Fernández-Tresguerres

2010-01-01T23:59:59.000Z

229

Codeword design and information encoding in DNA ensembles  

Science Journals Connector (OSTI)

Encoding of information in DNA-, RNA- and other biomolecules is an important area of research in fields such as DNA computing, bioinformatics, and, conceivably, microbiology and genetics. This survey focuses on two fundamental problems, the codeword ... Keywords: h-distance, DNA space dimension, DNA-based computing, Gibbs energy, codeword design, information encoding in DNA, partition function, template method, tensor product

Max H. Garzon; Russell J. Deaton

2004-08-01T23:59:59.000Z

230

Comparison of genomic, plasmid, synthetic, and combined DNA probes for detecting Plasmodium falciparum DNA.  

Science Journals Connector (OSTI)

...pRepHind, and a 21-base-long synthetic DNA probe (PFR1), the sequence...second brief hybridization with synthetic DNA to amplify signals from samples...pRepHind, and a 21-base-long synthetic DNA probe (PFR1), the sequence...

G L McLaughlin; W E Collins; G H Campbell

1987-05-01T23:59:59.000Z

231

DNA barcoding of stranded marine mammals 5 The use of DNA barcoding to monitor the marine  

E-Print Network [OSTI]

barcoding to monitor the marine mammal biodiversity along the French Atlantic coast. In: Nagy ZT, Backeljau of the monitoring of marine mammal biodiversity. Keywords DNA barcoding, COI, control region, marine mammalsDNA barcoding of stranded marine mammals 5 The use of DNA barcoding to monitor the marine mammal

Paris-Sud XI, Université de

232

Selective cleavage in the avian retroviral long terminal repeat sequence by the endonuclease associated with the alpha beta form of avian reverse transcriptase  

Science Journals Connector (OSTI)

...Research Center, Nutley, NJ 07110 Communicated by John J. Burns, July 20, 1983 ABSTRACT M13 recombinant DNA clones containing...Goulson, A. R., Barrell, B. G., Smith, A. S. E. & Roe, B. A. (1980)J. Mol. Biol. 143, 161-172. 10. Ehrlich...

G Duyk; J Leis; M Longiaru; A M Skalka

1983-01-01T23:59:59.000Z

233

Mechanical & Biomedical Engineering  

E-Print Network [OSTI]

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

Barrash, Warren

234

Magnetic study of the electronic states in B-DNA and M-DNA doped with metal ions Kenji Mizoguchi,  

E-Print Network [OSTI]

- tivity of synthetic DNA (poly(G)-poly(C)) with a length of 10 nm to find a semiconducting behaviorMagnetic study of the electronic states in B-DNA and M-DNA doped with metal ions Kenji Mizoguchi. Purified salmon DNA gives intrinsically no EPR signal, which is consistent with DNA being a semiconductor

Mizoguchi, Kenji

235

Property:NEPA DNA Worksheet | Open Energy Information  

Open Energy Info (EERE)

DNA Worksheet DNA Worksheet Jump to: navigation, search Property Name NEPA DNA Worksheet Property Type Page Description DNA Worksheet files for NEPA Docs. This is a property of type Page. It links to pages that use the form NEPA_Doc. Pages using the property "NEPA DNA Worksheet" Showing 19 pages using this property. D DOI-BLM-NV-C010-2011-0517-DNA + DOI-BLM-NV-C010-2011-0517-DNA.pdf + DOI-BLM-NV-C010-2012--044-DNA + DOI-BLM-NV-C010-2012-0044-DNA.pdf + DOI-BLM-NV-C010-2012-0005-DNA + DOI-BLM-NV-C010-2012-0005-DNA.pdf + DOI-BLM-NV-C010-2012-0016-DNA + DOI-BLM-NV-C010-2012-0016-DNA.pdf + DOI-BLM-NV-C010-2012-0019-DNA + DOI-BLM-NV-C010-2012-0019-DNA.pdf + DOI-BLM-NV-C010-2012-0020-DNA + DOI-BLM-NV-C010-2012-0020-DNA.pdf + DOI-BLM-NV-C010-2012-0028-DNA + DOI-BLM-NV-C010-2012-0028-DNA.pdf +

236

Mechanical Engineering Graduate Student  

E-Print Network [OSTI]

......................................................................................9 Engineering Career Services ................................................................9 McMechanical Engineering Graduate Student Handbook January 2014 Department of Mechanical Engineering University of Wisconsin-Madison #12;Mechanical Engineering Web Page: http://www.engr.wisc.edu/me Graduate

Wisconsin at Madison, University of

237

Mechanical & Industrial Engineering  

E-Print Network [OSTI]

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

Mountziaris, T. J.

238

MECHANICAL ENGINEERING UNDERGRADUATE MAJOR  

E-Print Network [OSTI]

HANDBOOK FOR MECHANICAL ENGINEERING UNDERGRADUATE MAJOR Old Dominion University Department of Mechanical Engineering Batten College of Engineering and Technology Norfolk, Virginia 23529-0247 #12;TABLE OF CONTENTS MECHANICAL ENGINEERING HANDBOOK

239

Mechanical engineering Department Seminar  

E-Print Network [OSTI]

Mechanical engineering Department Seminar Katia Bertoldi Harvard University Soft materials in response to diverse stimuli. While the mechanical attributes - such as energy absorption, stiffness and switchable functionalities. Katia Bertoldi is an Assistant Professor of Applied Mechanics at Harvard

240

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

E-Print Network [OSTI]

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 ...

Fedele?, Bogdan I

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

The Initiation of Bacterial DNA Replication  

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

The Initiation of Bacterial DNA The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

242

Mass Spectrometry and Density Functional Theory Characterizations of DNA Modifications  

E-Print Network [OSTI]

to fully characterize synthetic DNA bearing cisplatin cross-in the hydrolysis of synthetic DNA as part of the MS-basedlink yield from synthetic DNA harboring 5-X-pyrimidines,

Williams, Renee Therese

2012-01-01T23:59:59.000Z

243

Stabilizing synthetic data in the DNA of living organisms  

Science Journals Connector (OSTI)

Data-encoding synthetic DNA, inserted into the genome of a living ... generations, one of the merits of using DNA material is long-term data storage within ... broken by mutation, deletion, and insertion of DNA, ...

Nozomu Yachie; Yoshiaki Ohashi; Masaru Tomita

2008-06-01T23:59:59.000Z

244

Single-molecule studies of DNA dynamics and intermolecular forces  

E-Print Network [OSTI]

in relating DNA solutions to synthetic polymer melts. In any?x or ?y. DNA and numerous synthetic polymer solutions havethe other hand, DNA differs from many synthetic polymers in

Robertson, Rae Marie

2007-01-01T23:59:59.000Z

245

Mass Spectrometry and Density Functional Theory Characterizations of DNA Modifications  

E-Print Network [OSTI]

link yield from synthetic DNA harboring 5-X-pyrimidines,dU- and Br dC-containing synthetic DNA were reported, it wasthe phosphoramidites into synthetic DNA at a 5’-CpG-3’ site;

Williams, Renee Therese

2012-01-01T23:59:59.000Z

246

Electric DNA chips for determination of pathogenic microorganisms  

E-Print Network [OSTI]

Electric DNA chips for determination of pathogenic microorganisms Yanling Liu Doctoral thesis Liu (2008): Electric DNA chips for determination of pathogenic microorganisms. School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden Abstract Silicon-based electric DNA chip arrays

Enfors, Sven-Olof

247

Single molecule analysis of DNA electrophoresis in microdevices  

E-Print Network [OSTI]

Given that current electrophoresis technology is inadequate for mapping large O[100 kilobasepair] DNA, several promising lab-on-chip designs for DNA mapping have been recently proposed that require either 1) a DNA molecule ...

Randall, Greg C

2006-01-01T23:59:59.000Z

248

Mitochondrial DNA phylogenetic analysis of Myrmecolacidae (Insecta: Strepsiptera) va  

E-Print Network [OSTI]

Guinea are determined. Methods were developed for extraction, amplification, and sequencing of mitochondrial DNA (mtDNA) from Strepsiptera. High-resolution mtDNA sequences obtained by these methods were used in the phylogenetic analysis of Myrmecolacidae...

Halbert, Natalie Rose

2013-02-22T23:59:59.000Z

249

The Molecular Mechanism of Stretch Activation in Insect Muscle | Advanced  

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

A Newly Discovered DNA Repair Mechanism A Newly Discovered DNA Repair Mechanism Assessing the Risk of Arsenic Ingestion An Electronic Dance of Spins and Orbits How a Virus Prepares to Infect Cells Magnetic Switching under Pressure Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed The Molecular Mechanism of Stretch Activation in Insect Muscle DECEMBER 21, 2010 Bookmark and Share Main image: X-ray pattern from contracting flight muscle; top: match-mismatch of crossbridge origins with actin target zones; bottom: thick filament twisting bring myosin crossbridges closer to actin binding sites ("target zones"). Pink = target zones; red = myosin heads. Intruder at bottom: Lethocerus indicus.

250

Allosteric Modulation of DNA by Small Molecules  

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

Allosteric Modulation of DNA by Small Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell permeable small molecules that can be programmed to disrupt transcription factor-DNA interfaces could silence aberrant gene expression pathways. Pyrrole-imidazole polyamides are DNA minor groove binding small molecules that are programmable for a large repertoire of DNA motifs.

251

Monroe Thomas, Mechanical Technician  

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

Monroe Thomas, Mechanical Technician Print The weekend before the ALS was scheduled to start up again after the most recent shutdown, mechanical technician Monroe Thomas kept...

252

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

SciTech Connect (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

253

Catalytic Hydrolytic Cleavage and Oxy-Cleavage of Lignin Linkages  

SciTech Connect (OSTI)

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.

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

2014-07-26T23:59:59.000Z

254

Constraint of DNA on Functionalized Graphene Improves Its Biostability...  

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

Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity. Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity....

255

Minor Groove Deformability of DNA: A Molecular Dynamics Free...  

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

Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Abstract:...

256

Electrochemical Branched-DNA Assay for Polymerase Chain Reaction...  

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

Branched-DNA Assay for Polymerase Chain Reaction-Free Detection and Quantification of Oncogenes in Messenger RNA Electrochemical Branched-DNA Assay for Polymerase Chain...

257

Isolation of Discrete Nanoparticle-DNA Conjugates for Plasmonic Applications  

E-Print Network [OSTI]

Isolation of Discrete Nanoparticle-DNA Conjugates forABSTRACT. Discrete DNA-gold nanoparticle conjugates with DNABG_Keywords”). GOLD, NANOPARTICLE, NANOCRYSTAL, PLASMON,

Claridge, Shelley

2008-01-01T23:59:59.000Z

258

Unidirectional Scaffold-Strand Arrangement in DNA Origami  

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

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

259

Single molecule studies of DNA packaging by bacteriophages  

E-Print Network [OSTI]

for the study of single molecule protein- DNA interactions.Physics Studies in Single Molecule Biophysics ProfessorOF THE DISSERTATION Single Molecule Studies of DNA Packaging

Fuller, Derek Nathan

2008-01-01T23:59:59.000Z

260

Mechanical & Industrial Engineering  

E-Print Network [OSTI]

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

Mountziaris, T. J.

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Career Map: Mechanical Engineer  

Broader source: Energy.gov [DOE]

The Wind Program's Career Map provides job description information for Mechanical Engineer positions.

262

Mechanical Engineering Undergraduate  

E-Print Network [OSTI]

Mechanical Engineering Department Undergraduate Advising Manual for Bachelor of Science Degrees in Mechanical Engineering and Engineering Mechanics 2011-2012 - Updated April 15, 2012 #12;Johns Hopkins University ­ Department of Mechanical Engineering 2011-2012 Undergraduate Student Advising Manual Page 2

Ghosh, Somnath

263

Mechanical engineering Department Seminar  

E-Print Network [OSTI]

Mechanical engineering Department Seminar James Bird Department of Mechanical Engineering Boston ­ are discussed. James Bird is an Assistant Professor in the Mechanical Engineering Department at Boston completed post-doctoral research at MIT. His research interests include experimental fluid mechanics

264

Mechanical Engineering Undergraduate  

E-Print Network [OSTI]

Mechanical Engineering Department Undergraduate Advising Manual for Bachelor of Science Degrees in Mechanical Engineering and Engineering Mechanics 2012-2013 - Updated July 14, 2013 #12;Johns Hopkins University ­ Department of Mechanical Engineering 2012-2013 Undergraduate Student Advising Manual Page 2

Ghosh, Somnath

265

Mechanical Engineering & Thermal Group  

E-Print Network [OSTI]

Mechanical 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 evolved with the complexity of instrument design demands, LASP mechanical engineers develop advanced

Mojzsis, Stephen J.

266

Combined Quantum Mechanical and Molecular Mechanics Studies of...  

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

Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Combined Quantum Mechanical and Molecular Mechanics Studies of the...

267

The Initiation of Bacterial DNA Replication  

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

The Initiation of Bacterial DNA Replication Print The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

268

DNA hydration studied by neutron fiber diffraction  

SciTech Connect (OSTI)

The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix.

Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others

1994-12-31T23:59:59.000Z

269

DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.  

SciTech Connect (OSTI)

Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNA populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.

SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

2004-03-24T23:59:59.000Z

270

The Initiation of Bacterial DNA Replication  

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

The Initiation of Bacterial DNA Replication Print The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya.

271

Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting  

SciTech Connect (OSTI)

Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

1997-03-01T23:59:59.000Z

272

DNA fragment sizing and sorting by laser-induced fluorescence  

DOE Patents [OSTI]

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

Hammond, Mark L. (Angier, NC); Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Marrone, Babetta L. (Los Alamos, NM); Martin, John C. (Los Alamos, NM)

1996-01-01T23:59:59.000Z

273

Photo-mechanical patterning with light activated polymers.  

SciTech Connect (OSTI)

Light activated polymers, which are capable of mechanically responding to light, promise to offer exciting, innovative, and unique material capabilities. Such materials include: photo-radical mediated cleavage and reformation of the polymer backbone in cross-linked elastomers that results in local stress relaxation; photo-switching cross-links in shape memory polymers; and photo-isomerization of azobenzene groups contained in liquid crystal elastomers. In this paper, using our recent material model that couples multiphysical processes involved in light-activated polymers, we demonstrate that a variety of patterns can be created on light activated polymer thin films when coupling mechanical deformation with light irradiation. Here, the polymer thin film is first stretched uniaxially or biaxially. Light is then irradiated on the surface of the thin film. After light irradiation, removal external load partially recovers the initial stretching of the polymer thin film and induces patterns. The variation of the geometry of the patterns can be controlled by a variety of parameters such as initial stretching, light intensity, etc. Photo-patterning with light activated polymer therefore offers a novel way to create surface patterns.

Long, Kevin N.; Qi, H. Jerry (University of Colorado, Boulder, CO); Dunn, Martin L. (University of Colorado, Boulder, CO)

2010-11-01T23:59:59.000Z

274

Sandia National Laboratories: Mechanical Testing  

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

EnergyNuclear Energy Systems Laboratory (NESL) Brayton LabMechanical Testing Mechanical Testing Mechanical Testing Overview Mechanical 1-2 (2008). Standard Test Methods for...

275

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

DOE Patents [OSTI]

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

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

2013-06-25T23:59:59.000Z

276

Free energy landscape and characteristic forces for the initiation of DNA unzipping  

E-Print Network [OSTI]

DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives from a free energy basin that is distinct from the basins of subsequent base pairs because of entropic contributions and we highlight the microscopic origin of the peak. Our results suggest a new window of exploration for single molecule experiments.

Ahmet Mentes; Ana Maria Florescu; Elizabeth Brunk; Jeff Wereszczynski; Marc Joyeux; Ioan Andricioaei

2015-01-27T23:59:59.000Z

277

Highly specific electronic signal transduction mediated by DNA/metal self-assembly.  

SciTech Connect (OSTI)

Highly specific interactions between DNA could potentially be amplified if the DNA interactions were utilized to assemble large scale parts. Fluidic assembly of microsystem parts has the potential for rapid and accurate placement of otherwise difficult to handle pieces. Ideally, each part would have a different chemical interaction that allowed it to interact with the substrate only in specific areas. One easy way to obtain a multiple chemical permutations is to use synthetic DNA oligomers. Si parts were prepared using silicon-on-insulator technology microfabrication techniques. Several surface chemistry protocols were developed to react commercial oligonucleotides to the parts. However, no obvious assembly was achieved. It was thought that small defects on the surface did not allow the microparts to be in close enough proximity for DNA hybridization, and this was. in part, confirmed by interferometry. To assist in the hybridization, plastic, pliable parts were manufactured and a new chemistry was developed. However, assembly was still absent even with the application of force. It is presently thought that one of three mechanisms is preventing the assembly. The surfaces of the two solid substrates can not get in close enough proximity, the surface chemistry lacks sufficient density to keep the parts from separating, or DNA interactions in close proximity on solid substrates are forbidden. These possibilities are discussed in detail.

Dentinger, Paul M.; Pathak, Srikant

2003-11-01T23:59:59.000Z

278

Free energy landscape and characteristic forces for the initiation of DNA unzipping  

E-Print Network [OSTI]

DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives...

Mentes, Ahmet; Brunk, Elizabeth; Wereszczynski, Jeff; Joyeux, Marc; Andricioaei, Ioan

2015-01-01T23:59:59.000Z

279

NSLS Mechanical Tech  

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

Mechanical Tech Mechanical Tech The Mechanical Technician group is supervised by Robert Scheuerer and consists of Mechanical Technicians with fabrication/machining, assembly, installation, and alignment/surveying skills. This group also serves as an interface to Central Fabrication Services when more complex or larger fabrication efforts are needed. The Mechanical Tech group is responsible for fabricating, installing, aligning, and troubleshooting the mechanical hardware used on NSLS and SDL accelerators, front ends, and User beamlines, often starting solely from Mechanical Design group drawings or CAD files. The Mechanical Tech Group is responsible for the fabrication, assembly and installation of components at the NSLS. These components include all mechanical assemblies and RF cavities. Another part of their job is to

280

DNA interaction with synthetic polymers in solution  

Science Journals Connector (OSTI)

The complexes in which a DNA molecule is compact and protected from the ... lipids, inactivated viral particles, polymeric micelles and synthetic polycations are used [12–23...]. The latter have important advanta...

Nina Kasyanenko; Daria Afanasieva; Boris Dribinsky; Dmitry Mukhin…

2007-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Interconnecting gold islands with DNA origami  

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

to integrate the bottom-up self-assembly of DNA origami with the top-down lithographic methods used to generate surface patterning. In this report we demonstrate that fixed length...

282

DNA Assembly Line for Nano-Construction  

ScienceCinema (OSTI)

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

Oleg Gang

2010-01-08T23:59:59.000Z

283

Linear Thermodynamics of Rodlike DNA Filtration  

E-Print Network [OSTI]

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 ...

Li, Zirui

284

The beauty of DNA architecture : the design and applications in DNA nanotechnology.  

E-Print Network [OSTI]

??The mainframe of this thesis is about DNA nanotechnology in the perspectives of materials science and molecular architecture. My first project was to develop a… (more)

Wei, Diming

2009-01-01T23:59:59.000Z

285

DNA-incorporating nanomaterials in biotechnological applications  

SciTech Connect (OSTI)

The recently developed ability to controllably connect biological and inorganic objects on a molecular scale opens a new page in biomimetic methods with potential applications in biodetection, tissue engineering, targeted therapeutics and drug/gene delivery. Particularly in the biodetection arena, a rapid development of new platforms has largely been stimulated by a spectrum of novel nanomaterials with physical properties that offer efficient, sensitive and inexpensive molecular sensing. Recently, DNA-functionalized nano-objects have emerged as a new class of nanomaterials that can be controllably assembled in predesigned structures. Such DNA-based nanoscale structures might provide a new detection paradigm due to their regulated optical, electrical and magnetic responses, chemical heterogeneity and high local biomolecular concentration. The specific biorecognition DNA and its physical-chemical characteristics allows for an exploitation of DNA-functionalized nanomaterials for sensing of nucleic acids, while a broad tunability of DNA interactions permits extending their use for detection of proteins, small molecules and ions. We discuss the progress that was achieved in the last decade in the exploration of new detection methods based on DNA-incorporating nanomaterials as well as their applications to gene delivery. The comparison between various detection platforms, their sensitivity and selectivity, and specific applications are reviewed.

Stadler, A.; van der Lelie, D.; Chi, C.; Gang, O.

2010-02-01T23:59:59.000Z

286

Oligonucleotide and Long Polymeric DNA Encoding  

SciTech Connect (OSTI)

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

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

2003-11-24T23:59:59.000Z

287

When DNA Needs to Stand Up and Be Counted  

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

When DNA Needs to Stand Up and Be Counted Print When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

288

When DNA Needs to Stand Up and Be Counted  

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

When DNA Needs to Stand Up and Be Counted Print When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

289

Disorder in DNA-Linked Gold Nanoparticle Assemblies  

Science Journals Connector (OSTI)

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a nonmonotonic “zigzag” pattern in the melting temperature as a function of DNA linker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.

Nolan C. Harris and Ching-Hwa Kiang

2005-07-21T23:59:59.000Z

290

Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment  

SciTech Connect (OSTI)

The complete nucleotide sequence of the Bacillus subtilis dnaB gene and its flanking regions was determined. The dnaB gene is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110. It has been known that there are two different classes (dnaBI and dnaBII) in the dnaB mutants; dnaBI is essential for both chromosome and pUB110 replication, whereas dnaBII is necessary only for chromosome replication. The nucleotide sequence revealed that dnaBI and dnaBII are two functional domains in the single dnaB gene. The mutation sites of two mutants, belonging to dnaBI and dnaBII, respectively, were also determined as substitutions of amino acids. The putative DnaB protein deduced from nucleotide sequence consists of 472 amino acids (55 kDa) with no cysteine residue. A 55-kDa polypeptide produced in an in vitro transcription-translation system was labeled with (/sup 35/S)methionine but not with (/sup 35/S)cysteine. The DnaB protein has a highly hydrophobic sequence of 20 amino acids in its N-terminal region, a possible DNA binding site, and two possible ATP binding sites. The dnaBI domain is between the DNA binding site and one of the ATP binding sites; the dnaBII domain is close to the other ATP binding site. Comparison of the amino acid sequence between the dnaB protein and those of other dna genes of Escherichia coli showed no homology, suggesting that the dnaB gene of B, subtilis may be analogous to a hitherto undiscovered gene in E. coli.

Hoshino, T.; McKenzie, T.; Schmidt, S.; Tanaka, T.; Sueoka, N.

1987-02-01T23:59:59.000Z

291

Self-assembled DNA Nanostructures and DNA Devices John Reif Harish Chandran Nikhil Gopalkrishnan Thomas LaBean  

E-Print Network [OSTI]

and current state of the emerging research area in the field of nanoscience that make use of synthetic DNA. They are constructed primarily of synthetic DNA. 1.2 Use of bottom-up self-assembly Construction of molecularSelf-assembled DNA Nanostructures and DNA Devices John Reif Harish Chandran Nikhil Gopalkrishnan

Reif, John H.

292

Baseline Cellular HIV DNA Load Predicts HIV DNA Decline and Residual HIV Plasma Levels during Effective Antiretroviral Therapy  

Science Journals Connector (OSTI)

...significant predictive power, but published data on its correlation...correlated with HIV DNA load decrease until...cellular HIV DNA load predicts HIV DNA...significant predictive power, but published data on its correlation...correlated with HIV DNA load decrease until...

Saverio Giuseppe Parisi; Samantha Andreis; Carlo Mengoli; Renzo Scaggiante; Roberto Ferretto; Vinicio Manfrin; Mario Cruciani; Mario Giobbia; Caterina Boldrin; Monica Basso; Massimo Andreoni; Giorgio Palù; Loredana Sarmati

2011-11-30T23:59:59.000Z

293

The Relationship between Polyamine Accumulation and DNA Replication in Synchronized Chinese Hamster Ovary Cells after Heat Shock  

Science Journals Connector (OSTI)

...polyamine biosyn thesis after heat shock because of previous...understand the mechanisms of heat shock-induced loss of cellular proliferative...A and B, shows DNA distributions from untreated cultures...cultures exposed to 43 heat in mig-G1 phase at...

Eugene W. Gerner and Diane Haddock Russell

1977-02-01T23:59:59.000Z

294

Compliant mechanism learning toolkit  

E-Print Network [OSTI]

This thesis concerns a toolkit designed to assist in learning the behavior of complaint mechanisms. In the design of complaint mechanisms, increasingly complicated designs behave in ways that are harder to intuitively ...

Allard, Nicholas (Nicholas A.)

2006-01-01T23:59:59.000Z

295

Programmable Mechanical Metamaterials  

E-Print Network [OSTI]

We create mechanical metamaterials whose response to uniaxial compression can be programmed by lateral confinement, allowing monotonic, non-monotonic and hysteretic behavior. These functionalities arise from a broken rotational symmetry which causes highly nonlinear coupling of deformations along the two primary axes of these metamaterials. We introduce a soft mechanism model which captures the programmable mechanics, and outline a general design strategy for confined mechanical metamaterials. Finally, we show how inhomogeneous confinement can be explored to create multi stability and giant hysteresis.

Bastiaan Florijn; Corentin Coulais; Martin van Hecke

2014-07-17T23:59:59.000Z

296

Mechanical & Industrial Engineering  

E-Print Network [OSTI]

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

Mountziaris, T. J.

297

Mechanical engineering Department Seminar  

E-Print Network [OSTI]

Mechanical engineering Department Seminar Shuodao Wang Postdoctoral Fellow University of Illinois, Urbana-Champaign Mechanical Design and Fabrication Techniques for Bio-Electronic Systems 11:00 AM Friday that bridge this gap in mechanics and form will create new opportunities in bio-inspired and bio

Lin, Xi

298

Mechanical and Aerospace Engineering  

E-Print Network [OSTI]

Mechanical and Aerospace Engineering Abstract Solid materials used in energy conversion and storage that couples the mechanical and chemical (or electrochemical) fields in solids via the use of stress-chemo- mechanical theory, two examples of practical interest will be discussed, namely, solid oxide fuel cells

299

Mechanical engineering Department Seminar  

E-Print Network [OSTI]

Mechanical engineering Department Seminar Maureen Lynch Postdoctoral Fellow Cornell University Mechanical Loading Decreases Osteolysis and Tumor Formation via Effects on Bone Remodeling 11:00 AM Friday to mechanical stimuli in the skeleton, yet the role of biomechanical loading remains poorly characterized

Lin, Xi

300

Victor Yakhot Mechanical Engineering  

E-Print Network [OSTI]

to flows of strongly non-linear fluids relevant for mechanical engineering, polymers and bio-fluid dynamicsVictor Yakhot Mechanical Engineering UniversalReynoldsNumberofTransition,Renormalizationand Mechanical Engineering 11 AM Friday, October 31st Room 245, 110 Cummington Mall Refreshments served at 10

Lin, Xi

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301

Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain  

SciTech Connect (OSTI)

Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent interaction of the 13.5-kDa DNA binding domain of PU.1 (PU.1-DBD) with specific double-stranded DNA (dsDNA) target molecules. Mixtures of PU.1-DBD protein and wildtype target DNA sequence yielded ESI-MS spectra showing only protein-dsDNA complex ions of 1:1 stoichiometry and free dsDNA. When PU.1-DBD protein, wild type target DNA, and a mutant target DNA lacking the consensus sequence were mixed, only the 1:1 complex with the wild-type DNA was observed, consistent with gel electrophoresis mobility shift assay results, demonstrating the observation of sequence-specific protein-dsDNA complexes using ESI-MS. 22 refs., 5 figs., 1 tab.

Cheng, Xueheng; Harms, A.C.; Bruce, J.E. [Pacific Northwest National Lab., Richland, WA (United States)] [and others] [Pacific Northwest National Lab., Richland, WA (United States); and others

1996-07-15T23:59:59.000Z

302

Theory of Nucleosome Corkscrew Sliding in the Presence of Synthetic DNA Ligands  

E-Print Network [OSTI]

Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong through one-basepair twist defects and through ten-basepair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study we give a quantitative theory for nucleosome repositioning in the presence of such ligands. We show that the experimentally observed octamer mobilities are consistent with the picture of bound ligands blocking the passage of twist defects through the nucleosome. This strongly supports the model of twist defects inducing a corkscrew motion of the nucleosome as the underlying mechanism of nucleosome sliding. We provide a theoretical estimate of the nucleosomal mobility without adjustable parameters, as a function of ligand concentration, binding affinity, binding site orientiation, temperature and DNA anisotropy. Having this mobility at hand we speculate about the interaction between a nucleosome and a transcribing RNA polymerase and suggest a novel mechanism that might account for polymerase induced nucleosome repositioning.

Farshid Mohammad-Rafiee; Igor M. Kulic; H. Schiessel

2004-06-16T23:59:59.000Z

303

R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences  

Science Journals Connector (OSTI)

R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences ... As the cost of whole gene synthesis is decreasing, whole genome synthesis at the other end of the spectrum has expanded our horizons to the prospect of fully engineered synthetic cells. ...

Arturo Casini; Georgia Christodoulou; Paul S. Freemont; Geoff S. Baldwin; Tom Ellis; James T. MacDonald

2014-01-31T23:59:59.000Z

304

Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions  

E-Print Network [OSTI]

Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions Harish Chandran University, Durham NC email: reif@cs.duke.edu Abstract The goal of synthetic biology is to design and assemble synthetic systems that mimic bio- logical systems. One of the most fundamental challenge

Reif, John H.

305

Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA  

Science Journals Connector (OSTI)

...synthetic polydeoxyribonucleotides Activity DNA DNA Substrate MeTase I MeTase II Poly(dG-dC) 2.1 2.4 Poly(dG-dC,dmSC)* 70.1 105.4 Poly(dC) 0.003 0.001 Poly(dC,dA) 0.003 0.001 A...

T H Bestor; V M Ingram

1983-01-01T23:59:59.000Z

306

Role of CYP1B1 in PAH-DNA Adduct Formation and Breast Cancer Risk  

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

Role of CYP1B1 in PAH-DNA Adduct Formation and Breast Cancer Risk Role of CYP1B1 in PAH-DNA Adduct Formation and Breast Cancer Risk Title Role of CYP1B1 in PAH-DNA Adduct Formation and Breast Cancer Risk Publication Type Report Year of Publication 2010 Authors Goth-Goldstein, Regine, Marion L. Russell, Donghui Li, Ana P. Müller, Maira Caleffi, Joao Eschiletti, Marcia Graudenz, and Michael D. Sohn Date Published 04/2010 Publisher Lawrence Berkeley National Laboratory City Berkeley Abstract This study investigated the hypothesis that increased exposure to polycyclic aromatic hydrocarbons (PAHs) increases breast cancer risk. PAHs are products of incomplete burning of organic matter and are present in cigarette smoke, ambient air, drinking water, and diet. PAHs require metabolic transformation to bind to DNA, causing DNA adducts, which can lead to mutations and are thought to be an important pre-cancer marker. In breast tissue, PAHs appear to be metabolized to their cancer-causing form primarily by the cytochrome P450 enzyme CYP1B1. Because the genotoxic impact of PAH depends on their metabolism, we hypothesized that high CYP1B1 enzyme levels result in increased formation of PAH-DNA adducts in breast tissue, leading to increased development of breast cancer. We have investigated molecular mechanisms of the relationship between PAH exposure, CYP1B1 expression and breast cancer risk in a clinic-based case-control study. We collected histologically normal breast tissue from 56 women (43 cases and 13 controls) undergoing breast surgery and analyzed these specimens for CYP1B1 genotype, PAH-DNA adducts and CYP1B1 gene expression. We did not detect any difference in aromatic DNA adduct levels of cases and controls, only between smokers and non-smokers. CYP1B1 transcript levels were slightly lower in controls than cases, but the difference was not statistically significant. We found no correlation between the levels of CYP1B1 expression and DNA adducts. If CYP1B1 has any role in breast cancer etiology it might be through its metabolism of estrogen rather than its metabolism of PAHs. However, due to the lack of statistical power these results should be interpreted with caution

307

Oxidative DNA damage and its repair in rat spleen following subchronic exposure to aniline  

SciTech Connect (OSTI)

The mechanisms by which aniline exposure elicits splenotoxic response, especially the tumorigenic response, are not well-understood. Splenotoxicity of aniline is associated with iron overload and generation of reactive oxygen species (ROS) which can cause oxidative damage to DNA, proteins and lipids (oxidative stress). 8-Hydroxy-2'-deoxyguanosine (8-OHdG) is one of the most abundant oxidative DNA lesions resulting from ROS, and 8-oxoguanine glycosylase 1 (OGG1), a specific DNA glycosylase/lyase enzyme, plays a key role in the removal of 8-OHdG adducts. This study focused on examining DNA damage (8-OHdG) and repair (OGG1) in the spleen in an experimental condition preceding a tumorigenic response. To achieve that, male Sprague-Dawley rats were subchronically exposed to aniline (0.5 mmol/kg/day via drinking water for 30 days), while controls received drinking water only. Aniline treatment led to a significant increase in splenic oxidative DNA damage, manifested as a 2.8-fold increase in 8-OHdG levels. DNA repair activity, measured as OGG1 base excision repair (BER) activity, increased by {approx} 1.3 fold in the nuclear protein extracts (NE) and {approx} 1.2 fold in the mitochondrial protein extracts (ME) of spleens from aniline-treated rats as compared to the controls. Real-time PCR analysis for OGG1 mRNA expression in the spleen revealed a 2-fold increase in expression in aniline-treated rats than the controls. Likewise, OGG1 protein expression in the NEs of spleens from aniline-treated rats was {approx} 1.5 fold higher, whereas in the MEs it was {approx} 1.3 fold higher than the controls. Aniline treatment also led to stronger immunostaining for both 8-OHdG and OGG1 in the spleens, confined to the red pulp areas. It is thus evident from our studies that aniline-induced oxidative stress is associated with increased oxidative DNA damage. The BER pathway was also activated, but not enough to prevent the accumulation of oxidative DNA damage (8-OHdG). Accumulation of mutagenic oxidative DNA lesions in the spleen following exposure to aniline could play a critical role in the tumorigenic process.

Ma Huaxian; Wang Jianling [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Abdel-Rahman, Sherif Z. [Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX 77555 (United States); Boor, Paul J. [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States); Khan, M. Firoze [Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 (United States)], E-mail: mfkhan@utmb.edu

2008-12-01T23:59:59.000Z

308

Mechanical seal assembly  

DOE Patents [OSTI]

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.

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

2001-01-01T23:59:59.000Z

309

Mechanical seal assembly  

DOE Patents [OSTI]

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.

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

2002-01-01T23:59:59.000Z

310

Optical selection and collection of DNA fragments  

DOE Patents [OSTI]

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

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

1998-01-01T23:59:59.000Z

311

Reactivity studies of a pseudo three-coordinate vanadium(II) complex: Synthesis of terminal oxo and sulfido complexes of vanadium(IV) and S?S and Se?Se reductive bond cleavage reactions  

SciTech Connect (OSTI)

Terminal oxo and sulfido complexes in the form of (nacnac)V=E(Ntol{sub 2}) (nacnac = [ArNC(CH{sub 3})]{sub 2}CH{sup -}, Ar = 2,6-(CHMe{sub 2}){sub 2}C{sub 6}H{sub 3}, Ntol{sub 2} = {sup -}N(C{sub 6}H{sub 4}-4-Me), E = O (1), S (2)) were isolated from treatment of the masked three-coordinate vanadium(II) complex, (nacnac)V(Ntol{sub 2}), with C{sub 5}H{sub 5}NO and S{sub 8}, respectively. Both vanadium(IV) species, 1 and 2, have been characterized by room temperature X-band EPR spectroscopic studies, and in the case of complex 1, a single crystal molecular structure confirmed the presence of a terminal oxo moiety. Moreover, reaction of (nacnac)V(Ntol{sub 2}) with diphenyl-disulfide and diphenyl-diselenide results in the reductive cleavage of these compounds to produce the vanadium(III) complexes (nacnac)V(XPh)(Ntol{sub 2}) (X = S, (3), Se (4)). A molecular structure of the phenylsulfide complex, 3, confirmed formation of the d{sup 2} complex resulting from reductive cleavage of the S-S bond.

Tran, Ba L.; Chen, Chun-Hsing; Mindiola, Daniel J. (Indiana)

2012-02-07T23:59:59.000Z

312

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

SciTech Connect (OSTI)

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.

Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Shahverdi, Ahmad Reza [Department of Pharmaceutical Biotechnology and Biotechnology Research Centre, Faculty of Pharmacy, TUMS, Tehran (Iran, Islamic Republic of)] [Department of Pharmaceutical Biotechnology and Biotechnology Research Centre, Faculty of Pharmacy, TUMS, Tehran (Iran, Islamic Republic of); Ahmadi, Abbas [Department of Histology and Embryology, Faculty of Veterinary Medicine, Urmia University, Urmia (Iran, Islamic Republic of)] [Department of Histology and Embryology, Faculty of Veterinary Medicine, Urmia University, Urmia (Iran, Islamic Republic of); Baeeri, Maryam; Mohammadirad, Azadeh [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Abdollahi, Mohammad, E-mail: mohammad.abdollahi@utoronto.ca [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)

2013-02-01T23:59:59.000Z

313

Examining the regulation of DNA end-processing at telomeres and double-strand breaks  

E-Print Network [OSTI]

do not exhibit synthetic growth or DNA damage responsedo not exhibit synthetic growth or DNA damage responsedo not exhibit synthetic growth or DNA damage response

Ballew, Bari Jane

2011-01-01T23:59:59.000Z

314

Computationally Optimised DNA Assembly of synthetic genes  

Science Journals Connector (OSTI)

Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes.

Liza S.Z. Larsen; Christopher D. Wassman; G. Wesley Hatfield; Richard H. Lathrop

2008-01-01T23:59:59.000Z

315

Mechanical Properties of Nanocrystal Supercrystals  

E-Print Network [OSTI]

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

Tam, Enrico

2010-01-01T23:59:59.000Z

316

Mechanics of Funding matrix  

Broader source: Energy.gov (indexed) [DOE]

FUNDING MECHANISMS FUNDING MECHANISMS Funding Mechanism Advantages Disadvantages Comments 1. From Doe to regional organizations * * Facilitates a broad, regional approach to planning and implementation that enhances consistency and uniformity * * Especially beneficial for new programs where early planning is needed * * Simplifies communication for DOE to have only one point of contact for information and discussion * * Cooperative agreement mechanism has proven relatively simple to administer * * Approach would require modification for Tribes * * Would also require that funding be provided to individual States to enable them to participate in the process, since planning authority and responsibility rests with the individual State * * Differs from OCRWM approach to 180(c) funding * * Introduces another layer of

317

Technology Partnering Mechanisms  

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

expand a business with INL technologies, or require business support our Technology Transfer team is available to discuss the following contractual mechanisms: Cooperative...

318

The self-assembly of particles with isotropic interactions: Using DNA coated colloids to create designer nanomaterials  

SciTech Connect (OSTI)

Self-consistent field theory equations are presented that are suitable for use as a coarse-grained model for DNA coated colloids, polymer-grafted nanoparticles and other systems with approximately isotropic interactions. The equations are generalized for arbitrary numbers of chemically distinct colloids. The advantages and limitations of such a coarse-grained approach for DNA coated colloids are discussed, as are similarities with block copolymer self-assembly. In particular, preliminary results for three species self-assembly are presented that parallel results from a two dimensional ABC triblock copolymer phase. The possibility of incorporating crystallization, dynamics, inverse statistical mechanics and multiscale modelling techniques are discussed.

Thompson, R. B.; Dion, S.; Konigslow, K. von [Department of Physics and Astronomy and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada)

2014-03-31T23:59:59.000Z

319

Molecular Mechanisms of Anthrax Toxin Assembly and Transport  

E-Print Network [OSTI]

LF N ?1/?1-replacement synthetic DNA fragments were ligatedDNA fragment. These synthetic DNA fragments were ligated via

Feld, Geoffrey Keith

2012-01-01T23:59:59.000Z

320

Therapeutic plasmid DNA versus siRNA delivery: Common and different tasks for synthetic carriers  

Science Journals Connector (OSTI)

Gene therapy offers great opportunities for the treatment of severe diseases including cancer. In recent years the design of synthetic carriers for nucleic acid delivery has become a research field of increasing interest. Studies on the delivery of plasmid DNA (pDNA) have brought up a variety of gene delivery vehicles. The more recently emerged gene silencing strategy by the intracellular delivery of small interfering RNA (siRNA) takes benefit from existing expertise in pDNA transfer. Despite common properties however, delivery of siRNA also faces distinct challenges due to apparent differences in size, stability of the formed nucleic acid complexes, the location and mechanism of action. This review emphasizes the common aspects and main differences between pDNA and siRNA delivery, taking into consideration a wide spectrum of polymer-based, lipidic and peptide carriers. Challenges and opportunities which result from these differences as well as the recent progress made in the optimization of carrier design are presented.

Claudia Scholz; Ernst Wagner

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Boston University Department of Mechanical Engineering ME 303 Fluid Mechanics  

E-Print Network [OSTI]

Boston University Department of Mechanical Engineering ME 303 ­ Fluid Mechanics Fall 2011 Class: EK301 Engineering Mechanics Course Textbook: Fundamentals of Fluid Mechanics, 6th ed., Munson B. Reference Texts: Fluid Mechanics, Landau and Lifshitz, Vol. 6 Fluid Mechanics, Y. Cengel and J. Cimbala

322

DNA Duplication Revealed in New Beginnings | Department of Energy  

Broader source: Energy.gov (indexed) [DOE]

DNA Duplication Revealed in New Beginnings DNA Duplication Revealed in New Beginnings DNA Duplication Revealed in New Beginnings April 3, 2012 - 9:36am Addthis The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is proposed to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete and ready to load another protein onto the DNA. This last protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab. The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is

323

Nucleic Acid Library Construction Using Synthetic DNA Constructs  

Science Journals Connector (OSTI)

The synthesis of a high-diversity double-stranded DNA pool can require hundreds of milliliters of...3,10...). Large volumes are required because the maximum concentration of single-stranded synthetic DNA template...

Hani S. Zaher; Peter J. Unrau

2005-01-01T23:59:59.000Z

324

Aromatic Interactions in Proteins, DNA and Synthetic Receptors  

Science Journals Connector (OSTI)

...research-article Aromatic Interactions in Proteins, DNA and Synthetic Receptors C. A. Hunter Non-covalent interactions between...and three-dimensional structure in double-helical DNA. The - interaction model has been used to calculate the...

1993-01-01T23:59:59.000Z

325

Sequence Specific Recognition of Double Helical DNA. A Synthetic Approach  

Science Journals Connector (OSTI)

The design of synthetic sequence-specific DNA-binding molecules has advanced in recent years ... rapid and precise analyses of hundreds of potential DNA-binding sites to nucleotide resolution on sequencing ... bi...

P. B. Dervan

1988-01-01T23:59:59.000Z

326

Facile Dimer Synthesis for DNA-Binding Polyamide Ligands  

Science Journals Connector (OSTI)

Pyrrole-imidazole polyamide ligands are highly sequence specific synthetic DNA-binding ligands that bind with high affinity. ... Regulation of gene expression by synthetic DNA-binding ligands ...

Modi Wetzler; David E. Wemmer

2010-07-13T23:59:59.000Z

327

International congress on DNA damage and repair: Book of abstracts  

SciTech Connect (OSTI)

This document contains the abstracts of 105 papers presented at the Congress. Topics covered include the Escherichia coli nucleotide excision repair system, DNA repair in malignant transformations, defective DNA repair, and gene regulation. (TEM)

Not Available

1987-01-01T23:59:59.000Z

328

Scaling down DNA circuits with competitive neural networks  

Science Journals Connector (OSTI)

...only. It is straightforward to enforce competition in synthetic DNA circuits, because strands with common domains can easily...have presented two implementations of the WTA effect in synthetic DNA systems. While they both use autocatalysis and competition...

2013-01-01T23:59:59.000Z

329

De Novo DNA Synthesis Using Single-Molecule PCR  

Science Journals Connector (OSTI)

The broad availability of synthetic DNA oligonucleotides enabled the development of many powerful applications in biotechnology. Longer synthetic DNA molecules and libraries (generated from assembly of...1–7). Th...

Tuval Ben Yehezkel; Gregory Linshiz; Ehud Shapiro

2012-01-01T23:59:59.000Z

330

Nuclear DNA content in the genus Helianthus L. (sunflower)  

E-Print Network [OSTI]

. 1974. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12: 257-269. Geber, G. and G. Hasibeder. 1980. Cytophotometrische Bestimmung von DNA-Nengen: Vergleich einer neuen DAPI-Fluoreszenz Method mit...

Sims, Lynne Eileen

2012-06-07T23:59:59.000Z

331

DNA Origami with Complex Curvatures in Three-Dimensional Space  

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

DNA Origami with Complex Curvatures in Three-Dimensional Space Authors: Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. Title: DNA Origami with Complex Curvatures...

332

A DNA damage checkpoint response in telomere-initiated senescence  

Science Journals Connector (OSTI)

... array) or triplicate (tiling path) onto 3D-link activated slides (Motorola) using a MicroGrid II arrayer (BioRobotics). DNA labelling, hybridization and analysisDNA labelling and hybridization were essentially ...

Fabrizio d'Adda di Fagagna; Philip M. Reaper; Lorena Clay-Farrace; Heike Fiegler; Philippa Carr; Thomas von Zglinicki; Gabriele Saretzki; Nigel P. Carter; Stephen P. Jackson

2003-11-05T23:59:59.000Z

333

DNA-Directed Artificial Light-Harvesting Antenna  

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

DNA-Directed Artificial Light-Harvesting Antenna Authors: Dutta, P. K., Varghese, R., Nangreave, J., Lin, S., Yan, H., and Liu, Y. Title: DNA-Directed Artificial Light-Harvesting...

334

A Golden Ruler Used to Measure DNA Structure in Solution  

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

8 A Golden Ruler Used to Measure DNA Structure in Solution The first crystal structures of DNA double helices appeared in 1979 and directly confirmed the atomic model of...

335

DNA Damage and Repair in Translational Oncology: An Overview  

Science Journals Connector (OSTI)

...is a molecular sensor of DNA breaks that facilitates DNA repair and controls genomic stability and apoptosis. PARP inhibitors...PARP-1 inhibitor NSC 737664 entered the NCI clinical development pipeline, we initiated a program to model pharmacodynamic responses...

Eddie Reed

2010-09-15T23:59:59.000Z

336

Single cell trapping and DNA damage analysis using microwell arrays  

E-Print Network [OSTI]

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 ...

Wood, David

337

Improved Stool DNA Integrity Method for Early Colorectal Cancer Diagnosis  

Science Journals Connector (OSTI)

...semiautomatic extraction systems and analyzed using FL-DNA tests by CE and RT assays. The RT FL-DNA approach showed...be classified into three broad categories: stool tests [fecal occult blood test (FOBT)], endoscopic examinations (flexible sigmoidoscopy...

Claudia Rengucci; Giulia De Maio; Maura Menghi; Emanuela Scarpi; Simona Guglielmo; Pietro Fusaroli; Giancarlo Caletti; Luca Saragoni; Andrea Casadei Gardini; Wainer Zoli; Fabio Falcini; Dino Amadori; Daniele Calistri

2014-11-01T23:59:59.000Z

338

Responses of E. coli to DNA Damage and Stress  

Science Journals Connector (OSTI)

Exposure of Escherichia coli to agents that damage DNA or interfere with DNA replication results in the induction of the SOS response. A number of chromosomal genes that are repressed by the LexA protein are tran...

Toshihiro Ohta; John R. Battista…

1992-01-01T23:59:59.000Z

339

Contributing Data to the Fleet DNA Project (Brochure), NREL ...  

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

Photo from iStock9420677 Contributing Data to the Fleet DNA Project Sponsored by the U.S. Department of Energy, the Fleet DNA project aims to accelerate the evolution of advanced...

340

Defining functional DNA elements in the human genome  

E-Print Network [OSTI]

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 ...

Kellis, Manolis

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Mechanical & Aerospace Engineering  

E-Print Network [OSTI]

, and nuclear energy. She is a member of the American Society of Mechanical Engineers (ASME), Fluids EngineeringMechanical & Aerospace Engineering Interfacial flows are multi-material flows comprised of two of the interface between the fluids and the interface physics (like surface tension) needs to be predicted as part

342

MECHANICAL ENGINEERING Program of Study  

E-Print Network [OSTI]

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

Thomas, Andrew

343

Integrated Mechanical & Electrical Engineering (IMEE)  

E-Print Network [OSTI]

Integrated Mechanical & Electrical Engineering (IMEE) Department of Electronic & Electrical Engineering and Department of Mechanical Engineering #12;Graduates able to work in both mechanical of Mechanical Engineers (IMechE) n Develop essential engineering skills through extensive project work n Enhance

Burton, Geoffrey R.

344

DNA-Based Optomechanical Molecular Motor  

Science Journals Connector (OSTI)

A particularly rich and promising use of this force spectroscopy setup is for constructing molecular motors. ... The resulting structure?function insights are important for future DNA motor design. ... The quantum yield of the trans to cis isomerization using 365 nm (5.5 × 10?19 J) photons is ?0.1, and hence, 10 of these photons are required per cycle. ...

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

2011-02-22T23:59:59.000Z

345

Machine Methods for Identifying DNA Binding Sites  

E-Print Network [OSTI]

of biological and DNA sequence information. Large numbers of genomic and proteomic projects are ongoing transcription of genetic information)? Act as a break point during genetic recombination? These are very High transformation oftranslation #12;Identification of transcription promoter motifs mRNA tRNA protein.� � Human: µ

Kon, Mark

346

Determination of nucleotide sequences in DNA  

Science Journals Connector (OSTI)

...nu-cleotides long, which codes for ten genes. The most unexpected finding from this work was the presence of 3' 5' 5' 3' sExo l 5' W3e_3 5' Fig. 5. Degradation of double-stranded DNA with exonuclease III. Restriction Galactosidase enzyme site...

F Sanger

1981-12-11T23:59:59.000Z

347

PML nuclear bodies: dynamic sensors of DNA  

E-Print Network [OSTI]

-a (RAR-a).(8­10) Nuclear domains containing PML are disrupted or dispersed in the lymphocytes of APLPML nuclear bodies: dynamic sensors of DNA damage and cellular stress Graham Dellaire and David P. Bazett-Jones* Summary Promyelocytic leukaemia nuclear bodies (PML NBs) are generally present in all

Dellaire, Graham

348

Mechanical code comparator  

DOE Patents [OSTI]

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.

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

2002-01-01T23:59:59.000Z

349

A DNA Nanostructure Platform for Directed Assembly of Synthetic Vaccines  

Science Journals Connector (OSTI)

A DNA Nanostructure Platform for Directed Assembly of Synthetic Vaccines ... Here we report the design and synthesis of a 1,669-nucleotide, single-stranded DNA mol. ... These DL-DNAs induced greater amts. of tumor necrosis factor-? and interleukin-6 from RAW264.7 macrophage-like cells than did a mixt. of Y-DNA with the same sequences as the corresponding DL-DNA. ...

Xiaowei Liu; Yang Xu; Tao Yu; Craig Clifford; Yan Liu; Hao Yan; Yung Chang

2012-07-03T23:59:59.000Z

350

Regulation of Gene Expression by Synthetic DNA-Binding Ligands  

E-Print Network [OSTI]

Regulation of Gene Expression by Synthetic DNA-Binding Ligands Peter B. Dervan ( ) · Adam T. Poulin

Dervan, Peter B.

351

Control of DNA Strand Displacement Kinetics Using Toehold Exchange  

E-Print Network [OSTI]

static structures that self-assemble from synthetic DNA oligonucleotides of defined sequence.1-4 Fur

Zhang, David Yu

352

DNA Nanorobotics Harish Chandran, Nikhil Gopalkrishnan, and John Reif  

E-Print Network [OSTI]

of synthetic DNA to self-assemble operational molecular-scale devices. Recently there have been a series

Reif, John H.

353

String Tile Models for DNA Computing by SelfAssembly  

E-Print Network [OSTI]

­based computation. These suggestions were predicated on the #12; 2 complex synthetic DNA structures invented

Winfree, Erik

354

Conformational flexibility facilitates self-assembly of complex DNA nanostructures  

E-Print Network [OSTI]

to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range

Jiang, Wen

355

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

E-Print Network [OSTI]

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

Bernstein, Bradley E.

356

Evolutionary theory, web-search technology combine for DNA analysis  

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

Sequedex: bioinformatics breakthrough Evolutionary theory, web-search technology combine for DNA analysis Sequedex: bioinformatics breakthrough with clinical & environmental...

357

Rate of DNA replication in the DNA synthetic period of the barley chromosomes  

Science Journals Connector (OSTI)

The rate of DNA replication, as judged by H3-thymidine incorporation, at the specific time of the S-period in chromosomes of barley (Hakata No. 2) is studied by means of autoradiography.

Akio Kusanagi

358

Chromosomes and DNA of Mus: Terminal DNA synthetic sequences in three species  

Science Journals Connector (OSTI)

The DNA replication patterns of the terminal S phase of three species of Mus were analyzed by tritiated thymidine autoradiography. The centromeric heterochromatin of M. fulvidiventris is the latest component to f...

T. C. Hsu; Amara Markvong

359

Predictive evaluation for the preparation of a synthetic Y-shaped DNA nanostructure  

Science Journals Connector (OSTI)

With the advent of deoxyribonucleic acid (DNA) nanotechnology, the Y-shaped DNA nanostructure (Y-DNA) as a basic block was first created ... to their characteristic selectivity and specificity, Y-DNA-based materi...

Kyung Soo Park; Seung Won Shin; Jin-Ha Choi…

2014-03-01T23:59:59.000Z

360

Polyomavirus and simian virus 40 large T antigens bind to common DNA sequences.  

Science Journals Connector (OSTI)

...polyomavirus and SV40 DNA and to synthetic DNA substrates which did or did not...large T antigen only bound to synthetic DNA substrates which contained repeats of the pentameric sequence. This synthetic DNA also competed effectively with...

B J Pomerantz; J A Hassell

1984-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

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

SciTech Connect (OSTI)

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.

Giri, Anupam; Goswami, Nirmal [Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India)] [Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India); Lemmens, Peter [Institute for Condensed Matter Physics, Technical University of Braunschweig, Mendelssohnstr. 3, 38106 Braunschweig (Germany)] [Institute for Condensed Matter Physics, Technical University of Braunschweig, Mendelssohnstr. 3, 38106 Braunschweig (Germany); Pal, Samir Kumar, E-mail: skpal@bose.res.in [Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India)

2012-08-15T23:59:59.000Z

362

A Unidirectional DNA Walker Moving Autonomously Along a Track  

E-Print Network [OSTI]

. Cross Lab) Kinesin Synthetic unidirectional DNA walker that moves autonomously along a linear route over this challenge. However, existing nanoscale synthetic DNA devices are unsuitable for the above purpose: they onlyA Unidirectional DNA Walker Moving Autonomously Along a Track Peng Yin*, Hao Yan*, Xiaoju G

Reif, John H.

363

Autonomous Programmable DNA Nanorobotic Devices Using John H. Reif  

E-Print Network [OSTI]

- ior can be modified without complete redesign of the device). DNA-based synthetic molecular devices-based synthetic molecular device. We present the design of a class of DNA-based molecular de- vices using DNAzyme complex devices at the molecular scale using synthetic materials such as DNA has gone from theoretical

Reif, John H.

364

DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis  

E-Print Network [OSTI]

scatter plots. Materials and Methods Nucleic Acid Preparations. Synthetic DNA oligonucleotides were purchased from different commercial suppliers. DNA prepared by PCR was amplified with synthetic primers fromDNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis Hui Wang*, James

365

DNA Damage Induced by 193-nm Radiation in Mammalian Cells  

Science Journals Connector (OSTI)

...States Department of Energy. Irene E. Kochevar...and, therefore, the nuclear DNA in tissue will be...and, therefore, the nuclear DNA in tissue will be...States Depart ment of Energy. 2To whom requests for...nm (14). In cells, nuclear DNA will be partially...

Irene E. Kochevar; Agnes A. Walsh; Howard A. Green; Margaret Sherwood; Alice G. Shih; and Betsy M. Sutherland

1991-01-01T23:59:59.000Z

366

DNA Nanotechnology DOI: 10.1002/anie.201203716  

E-Print Network [OSTI]

DNA Nanotechnology DOI: 10.1002/anie.201203716 Discovery of the DNA "Genetic Code" for Abiological on nanotechnology, because of the wide range of applications for nanomaterials with various shapes and structures in catalysis, sensing, imaging, electronics, and medicine.[4] Recently, we reported that DNA could adsorb onto

Lawson, Catherine L.

367

A new pathway in the generation of defective retrovirus DNA.  

Science Journals Connector (OSTI)

...pathway in the generation of defective retrovirus DNA. J C Olsen...suggest that in the formation of defective circular DNA, the U5 domain...II I I I I , I I Il I I 1. DEFECTIVE RETROVIRUS DNA 783 deletions...Nucleotide sequence analysis was car- ried out on the relevant...

J C Olsen; R Swanstrom

1985-12-01T23:59:59.000Z

368

Self-assembling DNA templates for programmed artificial biomineralization  

E-Print Network [OSTI]

Self-assembling DNA templates for programmed artificial biomineralization Enrique C. Samano created via engineered DNA self-assembly represent an important new class of soft matter. These assemblies nanostructures Our current ability to create complex DNA nanostructures via designed self- assembly owes much

Finkelstein, Gleb

369

NMR Studies of DNA Oligomerers and Their Interactions with Minor Groove Binding Ligands  

E-Print Network [OSTI]

the minor groove of A-T synthetic DNA polymers by volume anda linearized plasmid and synthetic DNA oligomers (Sigurdsson

Fagan, P.A.

2010-01-01T23:59:59.000Z

370

E-Print Network 3.0 - anonymous dna sequences Sample Search Results  

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

Duke University Collection: Computer Technologies and Information Sciences 37 Resuspension of DNA Sequencing Reaction Summary: Resuspension of DNA Sequencing Reaction...

371

Rotary mechanical latch  

DOE Patents [OSTI]

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.

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

2012-11-13T23:59:59.000Z

372

Molecular Mechanisms of Anthrax Toxin Assembly and Transport  

E-Print Network [OSTI]

LF N ?1/?1-replacement synthetic DNA fragments were ligatedDNA fragment. These synthetic DNA fragments were ligated viaµM each) to make the synthetic double-stranded DNA fragment.

Feld, Geoffrey Keith

2012-01-01T23:59:59.000Z

373

Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold  

E-Print Network [OSTI]

Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold in the electron micro- scope by histone-depleting chromosomes; the resulting micro- graphs show 40-kb DNA loops chromosomes and was essentially a fibrous network of nonhistone proteins (3), which could be isolated

Poirier, Michael

374

Optimized fabrication and electrical analysis of silver nanowires templated on DNA molecules  

E-Print Network [OSTI]

. In this letter, we present the base sequence design of synthetic double-stranded DNA dsDNA and fabrication of metallic silver nanowires templated on both synthetic dsDNA and bacteriophage -DNA molecules. We also as programmable interconnects in bio- electronic devices. The DNA base sequence of the synthetic unit dsDNA tile

Finkelstein, Gleb

375

T4 DNA condensation in water-alcohol media  

E-Print Network [OSTI]

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.

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

2011-07-21T23:59:59.000Z

376

Counter Current Multiplier Mechanism  

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

Counter Current Multiplier Mechanism Counter Current Multiplier Mechanism Name: Stephen Location: N/A Country: N/A Date: N/A Question: Can you please explain to me the counter-current multiplier mechanism. I understand that cholride and sodium ions are filtered out of the ascending loop of Henle into the interstial fluid, however, I'm not sure exactly what happens from there and how this effects osmotic pressure gradients in the nephron. Any help would be greatly appriciated. Replies: This mechanism is very complex when it comes to writing a response. You have to have a strong background in osmotic pressure understanding and the anatomy of the kidney. It involves the cortex, outer and inner medula in relationship to the vasa recta, interstitial fluids at two points, the loop of Henle and the collecting duct. The size of the tubes and the position in relations to the cortex and medulla is an essential part. I can suggest some references.

377

Contaminant-Generation Mechanisms  

Science Journals Connector (OSTI)

In the last chapter, the areas where contaminants are generated were discussed. Knowing the location of contaminant generation is helpful in controlling that contamination, but understanding the mechanisms is ...

Alvin Lieberman

1992-01-01T23:59:59.000Z

378

Mechanical & Aerospace Engineering  

E-Print Network [OSTI]

Mechanical & Aerospace Engineering This presentation will address the development and transition of advanced structural health management (SHM) technologies from the perspective of understanding and the importance of understanding this role to increase the likelihood for transition of new technologies

379

Mechanical engineering Department Seminar  

E-Print Network [OSTI]

people trained from both perspectives can result in innovative solutions. At Fraunhofer CMI ­ coMechanical engineering Department Seminar Alexis Sauer-Budge Senior Research Scientist, Fraunhofer CMI Adjunct Research Assistant Professor, BME, Boston University Innovations at the intersection

380

Syngas Oxidation Mechanism  

Science Journals Connector (OSTI)

A comprehensive analysis of synthesis gas (syngas) oxidation kinetics in wide ranges of temperature ... on the basis of the reaction mechanism of syngas ignition and combustion in air. A vast set of experimental ...

A. M. Starik; N. S. Titova; A. S. Sharipov…

2010-09-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Mechanical Compression Heat Pumps  

E-Print Network [OSTI]

MECHANICAL COMPRESSION HEAT PUMPS Thomas-L. Apaloo and K. Kawamura Mycom Corporation, Los Angeles, California J. Matsuda, Mayekawa Mfg. Co., Tokyo, Japan ABSTRACT Mechanical compression heat pumping is not new in industrial applications.... In fact, industry history suggests that the theoretical concept was developed before 1825. Heat pump manufacturers gained the support of consultants and end-users when the energy crisis hit this country in 1973. That interest, today, has been...

Apaloo, T. L.; Kawamura, K.; Matsuda, J.

382

Mechanical Engineering Is Mechanical Engineering right for me?  

E-Print Network [OSTI]

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

Harman, Neal.A.

383

Protein Activity that Protects Our DNA - Research Highlights | ORNL Neutron  

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

Neutrons help shed light on critical protein activity that protects our DNA Neutrons help shed light on critical protein activity that protects our DNA "New study provides a framework for understanding how protein works and how it stimulates the DNA processing machines" Research Contact: Walter Chazin Illustration of the change in architecture of the essential eukaryotic ssDNA binding protein RPA as it engages progressively longer segments of ssDNA. Small-angle x-ray scattering data are displayed in the background for the DNA binding core of RPA in its DNA-free state (green) and when engaged on 10 (yellow), 20 (red, and 30 (blue) nucleotide ssDNA substrates. Overlaid molecular surfaces and ribbon representations of the three distinct architectural states of RPA are shown, one for the DNA-free protein and the two others for the initial and fully ssDNA-engaged modes, revealing the progressive compaction of the protein as it binds to the substrate. The RPA70 subunit is colored in blue, RPA32 in green, and RPA14 in red, with ssDNA displayed as a yellow ribbon.

384

When DNA Needs to Stand Up and Be Counted  

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

When DNA Needs to Stand Up and When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA chips are parallel, accurate, fast, and small. These advantages, however, can only be realized if the fragile biomolecules survive the attachment process intact. Furthermore, biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment and orientation of DNA on gold surfaces was the goal of recent experiments performed at ALS Beamline 8.0.1 by an international collaboration of scientists.

385

Low Dose Radiation Research Program: Assessing Biological Function of DNA  

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

Assessing Biological Function of DNA Damage Response Genes Assessing Biological Function of DNA Damage Response Genes Larry H. Thompson Lawrence Livermore National Laboratory Why This Project To understand the relative importance of individual DNA repair and DNA-damage response pathways to the recovery of mammalian cells after exposure to low doses of ionizing radiation (IR). This understanding may lead to better ways of setting limits on human exposure to IR. In spite of the discovery of many mammalian DNA repair genes, our current knowledge of how many of these genes contribute to cellular recovery from IR exposure is quite limited. Project Goals Measure cellular responses at doses in the 5-100 cGy range, which generally cause changes too small to detect in normal, repair-proficient cells Focus on DNA double-strand breaks (DSBs) and DNA oxidative base

386

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

SciTech Connect (OSTI)

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

Tang, Song; Cai, Qingsong [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States); Chibli, Hicham [Department of Biomedical Engineering, McGill University, Montréal, QC H3A 2B4 (Canada); Allagadda, Vinay [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States); Nadeau, Jay L. [Department of Biomedical Engineering, McGill University, Montréal, QC H3A 2B4 (Canada); Mayer, Gregory D., E-mail: greg.mayer@ttu.edu [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States)

2013-10-15T23:59:59.000Z

387

Patterning quantum dot arrays using DNA replication principles.  

SciTech Connect (OSTI)

The convergence of nanoscience and biotechnology has opened the door to the integration of a wide range of biological molecules and processes with synthetic materials and devices. A primary biomolecule of interest has been DNA based upon its role as information storage in living systems, as well as its ability to withstand a wide range of environmental conditions. DNA also offers unique chemistries and interacts with a range of biomolecules, making it an ideal component in biological sensor applications. The primary goal of this project was to develop methods that utilize in vitro DNA synthesis to provide spatial localization of nanocrystal quantum dots (nQDs). To accomplish this goal, three specific technical objectives were addressed: (1) attachment of nQDs to DNA nucleotides, (2) demonstrating the synthesis of nQD-DNA strands in bulk solution, and (3) optimizing the ratio of unlabeled to nQD-labeled nucleotides. DNA nucleotides were successfully attached to nQDs using the biotin-streptavidin linkage. Synthesis of 450-nm long, nQD-coated DNA strands was demonstrated using a DNA template and the polymerase chain reaction (PCR)-based method of DNA amplification. Modifications in the synthesis process and conditions were subsequently used to synthesize 2-{micro}m long linear nQD-DNA assemblies. In the case of the 2-{micro}m structures, both the ratio of streptavidin-coated nQDs to biotinylated dCTP, and streptavidin-coated nQD-dCTPs to unlabeled dCTPs affected the ability to synthesize the nQD-DNA assemblies. Overall, these proof-of-principles experiments demonstrated the successful synthesis of nQD-DNA using DNA templates and in vitro replication technologies. Continued development of this technology may enable rapid, spatial patterning of semiconductor nanoparticles with Angstrom-level resolution, as well as optically active probes for DNA and other biomolecular analyses.

Crown, Kevin K.; Bachand, George David

2004-11-01T23:59:59.000Z

388

Low Dose Radiation Research Program: Genetic Mechanisms of Induced  

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

Mechanisms of Induced Chromosomal Instability and their Mechanisms of Induced Chromosomal Instability and their Relationships with Radiation Tumorigenesis Robert Ullrich Colorado State University Why This Project A combination of epidemiological, experimental, animal, and cellular molecular data is used in the estimation of tumor risk after low doses of low-LET radiation. Uncertainties are recognized in the interpretation of all these data sets, and recent findings concerning genomic instability in irradiated cells challenge the conventional view that induced DNA damage is expressed during the immediate post-irradiation cell cycle. These data on genomic instability are based largely upon studies of cell cultures the mechanisms involved and implications for tumor formation in living organisms remain unclear. Nevertheless, if induced genomic instability were

389

Thiol-Modulated Mechanisms of the Cytotoxicity of Thimerosal and Inhibition of DNA Topoisomerase II?  

Science Journals Connector (OSTI)

Thimerosal is an organic mercury compound that is widely used as a preservative in vaccines and other solution formulations. The use of thimerosal has caused concern about its ability to cause neurological abnormalities due to mercury accumulation during ...

Xing Wu; Hong Liang; Kimberley A. O’Hara; Jack C. Yalowich; Brian B. Hasinoff

2008-01-16T23:59:59.000Z

390

Insight into the Catalytic Mechanism of DNA Polymerase : Structures of Intermediate Complexes,  

E-Print Network [OSTI]

enhance nucleo- tide incorporation fidelity, we have used Cr(III) ions to experimentally distinguish by the Department of Energy, Office of Basic Energy Sciences. The X4A beamline at the National Synchrotron Light Source, a Department of Energy facility, is supported by the Howard Hughes Medical Institute

Tsai, Ming-Daw

391

DNA Repair Mechanisms and Their Biological Roles in the Malaria Parasite Plasmodium falciparum  

Science Journals Connector (OSTI)

...Fabre, and M Kupiec. 2013. Effect of nuclear architecture on the efficiency of double-strand...2013. Gene copy-number alterations: a cost-benefit analysis. Cell 152 :394-405...pnas.93.3.1130 . 140. Crabb, BS , and AF Cowman. 1996. Characterization...

Andrew H. Lee; Lorraine S. Symington; David A. Fidock

2014-09-01T23:59:59.000Z

392

Transcription-coupled repair of oxidative DNA damage in human cells: Mechanisms and consequences  

E-Print Network [OSTI]

10518. Citterio E. , Rademakers S. , Van Der Horst G.T. ,A.J. , Citterio E. , Rademakers S. , Van Os R. , VermeulenE. , Auriol J. , Rademakers S. , Frit P. , Appeldoorn E. ,

Tsutakawa, Susan; Cooper, Priscilla K.

2001-01-01T23:59:59.000Z

393

Determining orientation and direction of DNA sequences  

DOE Patents [OSTI]

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.

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

2000-01-01T23:59:59.000Z

394

Chromium Cross-Links Histone Deacetylase 1-DNA Methyltransferase 1 Complexes to Chromatin, Inhibiting Histone-Remodeling Marks Critical for Transcriptional Activation  

Science Journals Connector (OSTI)

...at the proximal promoter. Whether a looping or a simpler sliding mechanism is correct...10 Dipple, A. 1995. DNA adducts of chemical carcinogens. Carcinogenesis 16: 437-441...Lung cancer among workers in chromium chemical production. Am. J. Ind. Med. 38...

Michael Schnekenburger; Glenn Talaska; Alvaro Puga

2007-08-06T23:59:59.000Z

395

Repair of Site-Specific DNA Double-Strand Breaks in Barley Occurs via Diverse Pathways Primarily Involving the Sister Chromatid  

Science Journals Connector (OSTI)

...research-article RESEARCH ARTICLES Repair of Site-Specific DNA Double-Strand...various double-strand break repair pathways in the monocot plant...0.307_win32 with UPARSE pipeline (Edgar, 2013). The three...polymorphisms indicative of distinct repair mechanisms. SCE and Mitotic...

Giang T.H. Vu; Hieu X. Cao; Koichi Watanabe; Goetz Hensel; Frank R. Blattner; Jochen Kumlehn; Ingo Schubert

2014-05-29T23:59:59.000Z

396

The Novel Poly(ADP-Ribose) Polymerase Inhibitor, AG14361, Sensitizes Cells to Topoisomerase I Poisons by Increasing the Persistence of DNA Strand Breaks  

Science Journals Connector (OSTI)

...topoisomerase I as a resistance mechanism to camptothecin in tumour cells. Cancer Res 2001;61:5926-32. 46 El-Khamisy SF, Saifi GM, Weinfeld M, et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy. Nature...

Lisa M. Smith; Elaine Willmore; Caroline A. Austin; Nicola J. Curtin

2005-12-01T23:59:59.000Z

397

MECHANICAL ENGINEERING UNDERGRADUATE HONORS THESIS  

E-Print Network [OSTI]

, when two bound copies are to be submitted to the Mechanical Engineering Services Office #12;PLEASE Mechanical Engineering Student Services: ¨ Application Approved ¨ Application Denied Signature of UGMECHANICAL ENGINEERING UNDERGRADUATE HONORS THESIS The Department of Mechanical Engineering

Prinz, Friedrich B.

398

STANFORD UNIVERSITY MECHANICAL ENGINEERING DEPARTMENT  

E-Print Network [OSTI]

20062007 Mechanical Engineering Student Services Building 530, Room 125 (650) 7257695 FAX (650) 7234882STANFORD UNIVERSITY MECHANICAL ENGINEERING DEPARTMENT GRADUATE STUDENT HANDBOOK Academic Year Revised 9/06 #12;MECHANICAL ENGINEERING GRADUATE STUDENT HANDBOOK 20062007 TABLE OF CONTENTS (Clickable

Prinz, Friedrich B.

399

Molecular mechanisms controlling complex traits in yeast  

E-Print Network [OSTI]

A fundamental goal in biology is to understand how the information stored in DNA results in a cellular function. However, it is insufficient to study one variant of a particular DNA sequence because most people do not share ...

Chin, Brian L. (Brian Leland)

2012-01-01T23:59:59.000Z

400

Insight into the Mechanism of Inhibition of Recombinant Adeno-Associated Virus by the Mre11/Rad50/Nbs1 Complex  

Science Journals Connector (OSTI)

...this factor. Currently, the mechanism through which MRN inhibits AAV and other viruses is poorly understood. Our results reform the predominant model that inhibition of rAAV by MRN is due to limiting second-strand DNA synthesis. Instead, a novel mechanism...

Thomas B. Lentz; R. Jude Samulski

2014-10-15T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

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...

402

A Novel Activation Mechanism of Avian Influenza Virus H9N2 by Furin  

Science Journals Connector (OSTI)

...by fluorescence resonance energy transfer-based peptide assays...directly proportional to the efficiency of HA cleavage, with implications...and the relative cleavage efficiencies were calculated by using the...to determine the knockdown efficiency. Quantitative reverse-transcribed...

Longping V. Tse; Alice M. Hamilton; Tamar Friling; Gary R. Whittaker

2013-11-20T23:59:59.000Z

403

Acoustic hemostasis: Underlying mechanisms  

Science Journals Connector (OSTI)

Cessation of hemorrhage using extrinsic interventional methods is possible with delivery of energy to bleeding tissues i.e. cauterization. High intensity focused ultrasound (HIFU) is one such method with significant advantages of delivering high levels of energy to well?defined regions of deep?seated tissues even during profuse bleeding. The physical mechanisms involved in this process include thermal and mechanical effects of HIFU leading to various biological effects. Our results using HIFU devices of 1–5 MHz and focal derated intensities of 1 000–10 000 W/cm2 in solid organs such as liver spleen and kidneys and major and minor blood vessels show that temperature of targeted tissues reaches 70–100°C within seconds with formation of microbubbles approximately 5??200 ? in size and concentration of 100 bubbles/mm3. It appears that boiling of interstitial fluids and blood and acoustic cavitation are both involved. The biological effects include coagulative necrosis mechanical disruption of tissue structure potentially leading to release of tissue factors enhancing the coagulation coagulum and thrombus formation at a wound site tissue fusion via collagen and elastin remodeling and fibrin plug formation with minimal damage of the surrounding tissues. These mechanisms appear to provide an effective and safe method of hemorrhage control. [Work supported by NIH DoD NSBRI.

Shahram Vaezy; Lawrence Crum; Steve Carter; Grant O’Keefe; Vesna Zderic; Roy Martin; Riyad Karmy?Jones

2007-01-01T23:59:59.000Z

404

Thermodynamics and statistical mechanics  

Science Journals Connector (OSTI)

... IN this book, Professor Landsberg brings together thermodynamics and statistical mechanics to provide a coherent account of these interrelated branches of physical theory ... side usually result in the essential structures of both becoming obscured. The value of classical thermodynamics lies in what it can do without invoking microscopic models and it is best learnt ...

C.J. Adkins

1979-12-20T23:59:59.000Z

405

Residential Mechanical Precooling  

SciTech Connect (OSTI)

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.

German, A.; Hoeschele, M.

2014-12-01T23:59:59.000Z

406

Department of Mechanical Engineering "From Compliant Mechanisms to  

E-Print Network [OSTI]

such as 3D printing with materials specialized in electro- mechanical sensing and actuation in addition

Militzer, Burkhard

407

Program Transformation Mechanics A Classification of Mechanisms for Program Transformation  

E-Print Network [OSTI]

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

Utrecht, Universiteit

408

MECHANICAL ENGINEERING 121 Department of Mechanical Engineering (MEE)  

E-Print Network [OSTI]

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

Kostic, Milivoje M.

409

Mechanical engineering Mechanical engineering is about solving problems, designing processes,  

E-Print Network [OSTI]

Mechanical engineering Mechanical engineering is about solving problems, designing processes, and making products to improve the quality of human life and shape the economy. Mechanical engineers apply the principles of physics, mathematics, computing and practical skills to design mechanical systems and artefacts

Waikato, University of

410

114 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE)  

E-Print Network [OSTI]

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

Kostic, Milivoje M.

411

Persistent DNA damage foci, cellular senescence and low dose radiation  

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

Persistent DNA damage foci, cellular senescence and low dose radiation Persistent DNA damage foci, cellular senescence and low dose radiation Denise Munoz 1 , Albert Davalos 1 , Francis Rodier 1 , Misako Kawahara 1 , Judith Campisi 1,2 and Steven Yannone 1,3 1 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley CA 94720; 2 Buck Institute for Age Research, 8001 Redwood Boulevard, Novato CA 94945; 3 Corresponding author Ionizing radiation (IR) induced DNA double-strand breaks (DSBs) are cytologically detectable as large nuclear foci that contain phosphorylated histone H2AX (γH2AX), the adaptor protein 53BP1, and several other proteins that participate in the sensing and processing of DNA damage (DNA damage foci). In normal human cells, moderately high IR (0.5-1 Gy) doses cause the rapid appearance of these foci (acute DNA damage foci), which gradually disappear

412

How effective is graphene nanopore geometry on DNA sequencing?  

E-Print Network [OSTI]

In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.

Satarifard, Vahid; Ejtehadi, Mohammad Reza

2015-01-01T23:59:59.000Z

413

Chapter Ten - DNA Assembler: A Synthetic Biology Tool for Characterizing and Engineering Natural Product Gene Clusters  

Science Journals Connector (OSTI)

Abstract The majority of existing antibacterial and anticancer drugs are natural products or their derivatives. However, the characterization and engineering of these compounds are often hampered by limited ability to manipulate the corresponding biosynthetic pathways. Recently, we developed a genomics-driven, synthetic biology-based method, DNA assembler, for discovery, characterization, and engineering of natural product biosynthetic pathways (Shao, Luo, & Zhao, 2011). By taking advantage of the highly efficient yeast in vivo homologous recombination mechanism, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication in individual hosts in a single-step manner. In this chapter, we describe the general guidelines for construct design. By using two distinct biosynthetic pathways, we demonstrate that DNA assembler can perform multiple tasks, including heterologous expression, introduction of single or multiple point mutations, scar-less gene deletion, generation of product derivatives, and creation of artificial gene clusters. As such, this method offers unprecedented flexibility and versatility in pathway manipulations.

Zengyi Shao; Huimin Zhao

2012-01-01T23:59:59.000Z

414

Design of a combinatorial dna microarray for protein-dnainteraction studies  

SciTech Connect (OSTI)

Background: Discovery of precise specificity oftranscription factors is an important step on the way to understandingthe complex mechanisms of gene regulation in eukaryotes. Recently,doublestranded protein-binding microarrays were developed as apotentially scalable approach to tackle transcription factor binding siteidentification. Results: Here we present an algorithmic approach toexperimental design of a microarray that allows for testing fullspecificity of a transcription factor binding to all possible DNA bindingsites of a given length, with optimally efficient use of the array. Thisdesign is universal, works for any factor that binds a sequence motif andis not species-specific. Furthermore, simulation results show that dataproduced with the designed arrays is easier to analyze and would resultin more precise identification of binding sites. Conclusion: In thisstudy, we present a design of a double stranded DNA microarray forprotein-DNA interaction studies and show that our algorithm allowsoptimally efficient use of the arrays for this purpose. We believe such adesign will prove useful for transcription factor binding siteidentification and other biological problems.

Mintseris, Julian; Eisen, Michael B.

2006-07-07T23:59:59.000Z

415

Transposon-containing DNA cloning vector and uses thereof  

DOE Patents [OSTI]

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.

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

1997-01-01T23:59:59.000Z

416

Transposon-containing DNA cloning vector and uses thereof  

DOE Patents [OSTI]

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.

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

1997-07-08T23:59:59.000Z

417

Alternative Methods for Human Identification: Mitochondrial DNA Base Composition Profiling  

E-Print Network [OSTI]

Profiling by ESI-TOF Mass Spectrometry Kevin Kiesler Research Biologist, Applied Genetics Group Forensics · Why use Mass Spectrometry? · Abbott / Ibis Biosciences PLEX-ID Instrument · PLEX-ID mtDNA 2.0 Assay://remf.dartmouth.edu/images/mammalianLungTEM/source/8.html #12;Applied Genetics mtDNA Genotyping for Human I.D. · Mutations in mtDNA occur naturally

Perkins, Richard A.

418

Synthetic DNA minor groove-binding drugs  

Science Journals Connector (OSTI)

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][1,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5?-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

B.S.Praveen Reddy; S.Murari Sondhi; J.William Lown

1999-01-01T23:59:59.000Z

419

Thermodynamic relations for DNA phase transitions  

E-Print Network [OSTI]

The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The thermodynamic approach is based on the hypothesis of impenetrability of the force in the zipped state. The melting and the unzipping transitions are considered in the same framework and compared with the existing statistical model results. The analysis is then extended to a possible continuous unzipping transition.

Poulomi Sadhukhan; Somendra M. Bhattacharjee

2014-01-21T23:59:59.000Z

420

Mechanism of aerobic biological destabilisation of wool scour effluent emulsions  

Science Journals Connector (OSTI)

Wool scouring effluent is a highly polluted industrial wastewater in which the main pollutant, wool wax, is held in a stable oil-in-water emulsion by non-ionic detergent. The use of microbial action to cause emulsion destabilisation has been proposed as a new treatment strategy for this effluent stream. This strategy aims at improving aerobic treatment performance by physically removing the high-COD, slowly bio-degradable wool wax from the system without bio-degradation. The mechanism by which an aerobic-mixed culture destabilises the wool scouring effluent emulsion was investigated. Our results show that destabilisation is due to partial bio-degradation of both the scouring detergent and the wool wax. Cleavage of the wool wax esters was the first stage in wax degradation, when 40–50% of wax was de-emulsified. Over the same period, detergent degradation was low, at 7–21%. With further incubation, detergent degradation increased, aiding further breakdown of the emulsion. The degradation of the detergent, a nonylphenol ethoxylate, resulted in both a reduction in molar concentration (of up to 82%) and a shortening of the ethoxylate chain length. The latter reduced the hydrophile–lipophile balance (HLB) from 12 to approximately 7, thereby reducing the ability of the residual detergent to stabilise the emulsion. Analysis of the emulsified and de-emulsified wax fractions could not identify a group of compounds that were preferentially de-emulsified based on molecular weight or polarity. These findings will assist in using a de-emulsification strategy in both existing and new treatment systems in order to save on aeration costs and treatment times for biological treatment of this highly polluted wastewater.

Andrew J. Poole; Ralf Cord-Ruwisch; F. William Jones

2005-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Low-cost, Rapid DNA Sequencing Technique - Energy Innovation...  

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

Biofuels Advanced Materials Advanced Materials Find More Like This Return to Search Low-cost, Rapid DNA Sequencing Technique Oak Ridge National Laboratory Contact ORNL About This...

422

Ergonomics in DNA Sequencing: Standing Down to Ergonomics  

E-Print Network [OSTI]

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

Naca, Christine

2009-01-01T23:59:59.000Z

423

Spectral Study of DNA Adsorption on Natural and Synthetic Silicates  

Science Journals Connector (OSTI)

Adsorption and interaction capacity of DNA with three types of natural silicates (chrysotile, crocidolite, clinoptilolite) and one synthetic Y zeolite were studied. The influence of ... pretreatment of silicates ...

R. Stanescu-Dumitru; C. Mandravel…

1997-01-01T23:59:59.000Z

424

The Fleet DNA Project (Fact Sheet), NREL (National Renewable...  

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

Fleet DNA Project aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel...

425

Solvent resistant microfluidic DNA synthesizer{ Yanyi Huang,{a  

E-Print Network [OSTI]

a microfluidic DNA synthesizer out of perfluoropolyether (PFPE), an elastomer with excellent chemical characterization of the products.6 We previously reported a photocurable perfluoropolyether (PFPE) elastomer, which

Huang, Yanyi

426

Fleet DNA Project - Data Dictionary for Public Download Files  

SciTech Connect (OSTI)

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.

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

2014-09-01T23:59:59.000Z

427

DNA-inspired materials for 'bottom-up' nanotechnology.  

E-Print Network [OSTI]

??DNA is a remarkable material that is both an inspiration for polymer nanotechnology and a versatile building block for assembling well-defined nanostructures. To create polymeric… (more)

Ishihara, Yoshihiro.

2007-01-01T23:59:59.000Z

428

DNA Gridiron Nanostructures Based on Four-Arm Junctions  

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

and scaffolds of increasing complexity is one of the important challenges in nanotechnology. We present a design strategy to create gridiron-like DNA structures. A series of...

429

DNA Nanostructures as Models for Evaluating the Role of Enthalpy...  

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

American Chemical Society Year: 2011 Volume: 133 Pages: 4490-4497 ABSTRACT: DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned...

430

Nanoparticle diffraction gratings for DNA detection on photopatterned glass substrates  

E-Print Network [OSTI]

Sendroiu and R. M. Corn: Nanoparticle diffraction gratingsSendroiu and R. M. Corn: Nanoparticle diffraction gratingsthe principle of the nanoparticle-based DNA detection assay

Sendroiu, Luliana E; Corn, Robert M

2008-01-01T23:59:59.000Z

431

Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures  

SciTech Connect (OSTI)

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.

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)

2014-06-09T23:59:59.000Z

432

DNA Origami Directed Self-Assembly of Discrete Silver Nanoparticle...  

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

Self-Assembly of Discrete Silver Nanoparticle Architectures Source: Angewandte Chemie International Edition Year: 2010 Volume: 49 Pages: 2700-2704 ABSTRACT: DNA origami...

433

Methods for parallel amplification of single DNA molecules  

E-Print Network [OSTI]

2006) BEAMing: single? molecule PCR on microparticles in Mutation  detection and single?molecule counting using Amplification of DNA Single Molecules by Linear Rolling 

McElfish, Erin Marie

2009-01-01T23:59:59.000Z

434

High-Performance Integrated Genetic Analyzers for Forensic DNA Typing  

E-Print Network [OSTI]

Encoded evidence: DNA in forensic analysis. Nature Reviewspopulations. Journal of Forensic Sciences 48, 908-911 (identity testing. Journal of Forensic Sciences 51, 253-265 (

Liu, Peng

2009-01-01T23:59:59.000Z

435

Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair  

Science Journals Connector (OSTI)

...agents to treat human cancer. Grant support: U.S. NIH grants GM47251, ES12512, and GM57479...Biology of DNA Repair Program grant CA92584 (A.E. Tomkinson...University of Maryland, School of Pharmacy Computer-Aided Drug Design Center...

Xi Chen; Shijun Zhong; Xiao Zhu; Barbara Dziegielewska; Tom Ellenberger; Gerald M. Wilson; Alexander D. MacKerell, Jr.; and Alan E. Tomkinson

2008-05-01T23:59:59.000Z

436

Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA  

Science Journals Connector (OSTI)

...Boehringer Mannheim; other protein Mr standards were from Bio-Rad. Plasmid pBR322 DNA...tivity in corresponding fractions. Protein standards along left ordinate are (in order of...dG-dC) 2.1 2.4 Poly(dG-dC,dmSC)* 70.1 105.4 Poly(dC) 0.003...

T H Bestor; V M Ingram

1983-01-01T23:59:59.000Z

437

Mechanical Engineering Department Seminar Series  

E-Print Network [OSTI]

Mechanical Engineering Department Seminar Series Rational Mechanics of Viral Shells: Is Continuum Theory a Stretch? William S. Klug Associate Professor, Mechanical & Aerospace Engineering, University-assembly. The capacity of these shells to respond structurally and mechanically to physical and chemical stimuli also

Eustice, Ryan

438

07SCHOOL OF MECHANICAL ENGINEERING  

E-Print Network [OSTI]

, mechanical with nuclear engineering, and medical engineering. Engineers qualified in all these areas play MECHANICAL ENGINEERING MECHANICAL WITH NUCLEAR ENGINEERING MEDICAL ENGINEERING OTHER COURSES TO CONSIDER Entryrequirementsandhowtoapply Modules MedicalEngineering(MEng,BEng) MechanicalwithNuclearEngineering(MEng,BEng) MechanicalEngineering

Dimitrova, Vania

439

A fluorescence method to detect photo-activated repair of UV-induced DNA damage in marine organisms  

SciTech Connect (OSTI)

After UV exposure, marine microorganisms may re-activate their photosynthetic systems or regain their pre-exposure metabolic rates, but they will not long survive, nor grow or reproduce, if they cannot repair DNA or ERN damage. Several repair mechanisms, including nucleotide excision repair and photo-reactivation, are known in terrestrial organisms, but there is little information on either process in marine microorganisms. Photo-reactivation may be especially important near the ocean surface where a few meters difference in vertical position or a few hours difference in time may alleviate UV-irradiation stress yet still provide sufficient light for photoactivated repair processes. We have developed a relatively simple, sensitive method to measure the activity of the photo-reactivation enzyme, photolyase, by fluorometry. UV irradiation causes adjacent thymine nucleotides in DNA to form cyclobutane dimers. Photolyase attaches to the dimerized DNA then breaks the dimers in a reaction catalyzed by visible light, thereby allowing restoration of cross-strand base pairing. Our assay for photolyase activity involves a dimerized synthetic DNA and DNA-specific fluorochromes with affinity for thymine-rich regions of DNA. When thymine dimers are present, fluorescence of these dyes is reduced. As dimers are repaired, fluorescence increases, allowing us to demonstrate the presence of photolyase and measure its activity using conventional fluorometers available in most marine laboratories. Photo-reactivation activity has been unambiguously demonstrated in samples of coastal seawater. In preliminary investigations, cells taken from surface slicks did not have enhanced photo-repair capabilities relative to cells collected 5 meters below the surface. Additional tests of the method and measurements of photo-repair activities of surface and subsurface organisms will be made during the SLIX-89 Surface Microlayer Experiment in October 1989.

Carlson, D.J.; Mordy, C.W.; Nelson, K. (Oregon State Univ., Corvallis (United States))

1990-01-09T23:59:59.000Z

440

Specific amino acid substitutions in bacterioopsin: replacement of a restriction fragment in the structural gene by synthetic DNA fragments containing altered codons  

SciTech Connect (OSTI)

To study the mechanism of light-dependent proton translocation by bacteriorhodopsin, we have introduced single-codon changes in the gene so as to produce the following specific amino acid substitutions in the protein: Tyr-185 to Phe, Pro-186 to Leu, Trp-189 to Phe, Ser-193 to Ala, and Glu-194 to Gln. The strategy involved replacement of a 62-base-pair restriction fragment by synthetic DNA duplexes containing the modified nucleotide sequences. This required a unique restriction site (Xho I) at Ile-203 which was created by oligonucleotide-directed point mutagenesis. The six DNA duplexes corresponding to the modified native and mutant restriction fragments were all prepared by DNA ligase-catalyzed joining of chemically synthesized deoxyribooligonucleotides. The bacterioopsin expression plasmids reconstructed by using the synthetic DNA fragments were characterized by restriction analysis and DNA sequence determination. An extremely rapid, efficient, and general method for purification of the synthetic oligonucleotides and of DNA fragments was developed. 32 references, 6 figures.

Lo, K.M.; Jones, S.S.; Hackett, N.R.; Khorana, H.G.

1984-04-01T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

Phosphorylation of the DNA-binding domain of nonhistone high-mobility group I protein by cdc2 kinase: Reduction of binding affinity  

SciTech Connect (OSTI)

Mammalian high-mobility group I nonhistone protein (HMG-I) is a DNA-binding chromatin protein that has been demonstrated both in vitro and in vivo to be localized to the A + T-rich sequenced of DNA. Recently an unusual binding domain peptide, the A{center dot}T-hook motif, that mediates specific interaction of HMG-I with the minor groove of DNA in vitro has been described. Inspection of the A{center dot}T-hook region of the binding domain showed that it matches the consensus sequence for phosphorylation by cdc2 kinase. Here the authors demonstrate that HMG-I is a substrate for phosphorylation by purified mammalian cdc2 kinase in vitro. The site of phosphorylation by this enzyme is a threonine residue at the amino-terminal end of the principal binding-domain region of the protein. Labeling of mitotically blocked mouse cells with ({sup 32}P)phosphate demonstrates that this same threonine residue in HMG-I is also preferentially phosphorylated in vivo. These finding indicate that cdc2 phosphorylation may significantly alter the DNA-binding properties of the HMG-I proteins. Becuase many cdc2 substrated are DNA-binding proteins, these results further suggest that alteration of the DNA-binding affinity of a variety of proteins is an important general component of the mechanism by which cdc2 kinase regulates cell cycle progression.

Reeves, R.; Nissen, M.S. (Washington State Univ., Pullman (United States)); Langan, T.A. (Univ. of Colorado, Denver (United States))

1991-03-01T23:59:59.000Z

442

Mechanical Operations and Maintenance  

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

Holiday Work Status Holiday Work Status Mechanical Operations & Maintenance Group APS Storage Ring Magnets The Advanced Photon Source (APS) at the Argonne National Laboratory is a national synchrotron-radiation research facility funded by the U.S. Department of Energy. Using high-brilliance x-ray beams from the APS, an international community of scientists conducts forefront basic and applied research in the fields of material science, biological science, physics, chemistry, environmental, geophysical and planetary science. The 1.1-km circumference APS facility consists of several major subsystems including magnets, vacuum chambers, radio-frequency cavities, diagnostics instrumentation, x-ray absorbers and apertures, and cooling water subsystems. Each of these subsystems contains hundreds of mechanical

443

Mechanics of collective unfolding  

E-Print Network [OSTI]

Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and structure of the folding-u...

Caruel, M; Truskinovsky, L

2015-01-01T23:59:59.000Z

444

Time in quantum mechanics  

E-Print Network [OSTI]

OF CONTENTS I. INTRODUCTION II. HISTORICAL DEVELOPMENT A. Classical Mechanics B. Quantum Theory . C. The Problem 3 4 6 III. TIME ATOMS AND DISCRETE TIME A. The Earliest Applications of Atomistic and Discrete Time . . . . . B. The Radiating Electron... . C. Quantum Field Theory 8 10 l2 IV. TIME OPERATOR FORMULATIONS 16 A. Advocates Against a Time Operator . B. The Possibility of a Time Operator C, Advocates in Favor of a Time Operator D. A Restricted Time Delay Operator: Scattering Theory...

Chapin, Kimberly R.

2012-06-07T23:59:59.000Z

445

Relativistic viscoelastic fluid mechanics  

SciTech Connect (OSTI)

A detailed study is carried out for the relativistic theory of viscoelasticity which was recently constructed on the basis of Onsager's linear nonequilibrium thermodynamics. After rederiving the theory using a local argument with the entropy current, we show that this theory universally reduces to the standard relativistic Navier-Stokes fluid mechanics in the long time limit. Since effects of elasticity are taken into account, the dynamics at short time scales is modified from that given by the Navier-Stokes equations, so that acausal problems intrinsic to relativistic Navier-Stokes fluids are significantly remedied. We in particular show that the wave equations for the propagation of disturbance around a hydrostatic equilibrium in Minkowski space-time become symmetric hyperbolic for some range of parameters, so that the model is free of acausality problems. This observation suggests that the relativistic viscoelastic model with such parameters can be regarded as a causal completion of relativistic Navier-Stokes fluid mechanics. By adjusting parameters to various values, this theory can treat a wide variety of materials including elastic materials, Maxwell materials, Kelvin-Voigt materials, and (a nonlinearly generalized version of) simplified Israel-Stewart fluids, and thus we expect the theory to be the most universal description of single-component relativistic continuum materials. We also show that the presence of strains and the corresponding change in temperature are naturally unified through the Tolman law in a generally covariant description of continuum mechanics.

Fukuma, Masafumi; Sakatani, Yuho [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan)

2011-08-15T23:59:59.000Z

446

Twisting and Bending Stress in DNA Minicircles  

E-Print Network [OSTI]

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of \\textit{66-bps} whose bending angle is $\\sim 6^{o} $. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at $\\tau =\\,315K$. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.

Marco Zoli

2014-03-25T23:59:59.000Z

447

Antibody-mediated neutralization of Ebola virus can occur by two distinct mechanisms  

SciTech Connect (OSTI)

Human Ebola virus causes severe hemorrhagic fever disease with high mortality and there is no vaccine or treatment. Antibodies in survivors occur early, are sustained, and can delay infection when transferred into nonhuman primates. Monoclonal antibodies (mAbs) from survivors exhibit potent neutralizing activity in vitro and are protective in rodents. To better understand targets and mechanisms of neutralization, we investigated a panel of mAbs shown previously to react with the envelope glycoprotein (GP). While one non-neutralizing mAb recognized a GP epitope in the nonessential mucin-like domain, the rest were specific for GP1, were neutralizing, and could be further distinguished by reactivity with secreted GP. We show that survivor antibodies, human KZ52 and monkey JP3K11, were specific for conformation-dependent epitopes comprising residues in GP1 and GP2 and that neutralization occurred by two distinct mechanisms; KZ52 inhibited cathepsin cleavage of GP whereas JP3K11 recognized the cleaved, fusion-active form of GP.

Shedlock, Devon J., E-mail: shedlock@mail.med.upenn.ed [Biodefense Research Section, Vaccine Research Center, National Institute for Allergy and Infectious Disease, National Institutes of Health, 40 Convent Drive, MSC 3005, Bethesda, MD 20814 (United States); Bailey, Michael A., E-mail: mike.bailey@taurigroup.co [Biodefense Research Section, Vaccine Research Center, National Institute for Allergy and Infectious Disease, National Institutes of Health, 40 Convent Drive, MSC 3005, Bethesda, MD 20814 (United States); Popernack, Paul M. [Biodefense Research Section, Vaccine Research Center, National Institute for Allergy and Infectious Disease, National Institutes of Health, 40 Convent Drive, MSC 3005, Bethesda, MD 20814 (United States); Cunningham, James M. [Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115 (United States); Burton, Dennis R. [Department of Immunology, Scripps Research Institute, La Jolla, CA 92037 (United States); Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037 (United States); Sullivan, Nancy J., E-mail: nsullivan@nih.go [Biodefense Research Section, Vaccine Research Center, National Institute for Allergy and Infectious Disease, National Institutes of Health, 40 Convent Drive, MSC 3005, Bethesda, MD 20814 (United States)

2010-06-05T23:59:59.000Z

448

Subunit interactions and protein-DNA interactions of the Drosophila melanogaster small nuclear RNA activating protein complex  

E-Print Network [OSTI]

was then replaced with synthetic DNA sequence encoding theprepared as follows: synthetic DNA containing a translationPSEB. I then ligated in synthetic DNA that reconstituted the

Titus, Mitchell

2007-01-01T23:59:59.000Z

449

Correlation between Point Mutations in NS2 and the Viability and Cytopathogenicity of Bovine Viral Diarrhea Virus Strain Oregon Analyzed with an Infectious cDNA Clone  

Science Journals Connector (OSTI)

...exchange of a single amino acid within NS2 of BVDV Oregon can reduce NS2-3 cleavage. Most striking was...frame. The BVDV Oregon sequence codes for an S at this position, whereas...Oregon sequence led to reduction of NS2-3 cleavage efficiency to 50 of...

Beate M. Kümmerer; Gregor Meyers

2000-01-01T23:59:59.000Z

450

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations  

Science Journals Connector (OSTI)

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations ... Future extensive molecular mechanical MD simulations exploring the stability of the various states would be very beneficial, although they are outside the scope of the present work. ... Here, we discuss the functions and mechanisms of action of three such crosslinkers: the motors kinesin-5 and kinesin-14, and the non-motor MAPs of the Ase1p family. ...

Matthew J. McGrath; I.-F. Will Kuo; Shigehiko Hayashi; Shoji Takada

2013-05-23T23:59:59.000Z

451

How noisy and replicable are DNA microarray data?  

Science Journals Connector (OSTI)

This paper analyses variability in highly replicated measurements of DNA microarray data conducted on nylon filters and Affymetrix GeneChips with different cDNA targets, filters, and imaging technology. Replicability is assessed quantitatively using correlation analysis as a global measure and differential expression analysis and ANOVA at the level of individual genes.

Suman Sundaresh; She-pin Hung; G. Wesley Hatfield; Pierre Baldi

2005-01-01T23:59:59.000Z

452

Affinity Purification of Plasmid DNA by Temperature-Triggered Precipitation  

E-Print Network [OSTI]

Affinity Purification of Plasmid DNA by Temperature-Triggered Precipitation Jan Kostal, Ashok purification method, which takes advantage of the DNA- binding affinity and specificity of the bacterial increasing the temper- ature, ELP undergoes a reversible phase transition from water-soluble forms

Chen, Wilfred

453

cDNA Synthesis and Labeling Aime M. Dudley  

E-Print Network [OSTI]

cDNA Synthesis and Labeling Aimée M. Dudley We use the Atlas Glass Labeling Kit from Clontech by the polymerase, since the aminoallyl-dUTP is incorporated during the cDNA synthesis step and the dyes of all Ts synthesized by my favorite oligo synthesis company with no purification. I resuspended

Dudley, Aimee

454

New algebraic constructions for pooling design in DNA library screening  

Science Journals Connector (OSTI)

Pooling design is an important mathematical tool in DNA library screening. It has been showed that using pooling design, the number of tests in DNA library screening can be greatly reduced. In this paper, we present some new algebraic constructions for pooling design.

Zengti Li; Suogang Gao; Hongjie Du; Yan Shi; Weili Wu

2010-01-01T23:59:59.000Z

455

ATP AND DNA AS MICROBIAL PARAMETERS IN THE ALIMENTARY TRACT  

E-Print Network [OSTI]

ATP AND DNA AS MICROBIAL PARAMETERS IN THE ALIMENTARY TRACT J. WOLSTRUP K. JENSEN A. JUST I. The aim of the present work was to investi- gate the use of ATP and DNA as parameters for microbial activity and biomass in the ali- mentary tract of cows and pigs. ATP was selected because of the promising

Paris-Sud XI, Université de

456

DNA damage-site recognition by lysine conjugates  

Science Journals Connector (OSTI)

...with potent photoactivated “warheads” § (33, 34) and satisfy...envisioned that the hydrophobic “warheads” may occupy a hydrophobic...DNA is involved in the “warhead” activation step. We irradiated...3. Comparison between the intact DNA duplex A and constructs B–E. The constructs...

Boris Breiner; Jörg C. Schlatterer; Igor V. Alabugin; Serguei V. Kovalenko; Nancy L. Greenbaum

2007-01-01T23:59:59.000Z

457

FDA backs off attempt to control private DNA research  

Science Journals Connector (OSTI)

... concluded that it probably lacks the legal authority to regulate re-combinant DNA research in private industry, as it 'had previously announced its intention to do following a directive from ... ago, however, the NIH's Recombinant DNA Advisory Committee passed a resolution recommending that private industry be legally required to observe the guidelines. It is now up to Mr ...

David Dickson

1979-06-07T23:59:59.000Z

458

Energy and Technology Review: Unlocking the mysteries of DNA repair  

SciTech Connect (OSTI)

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

Quirk, W.A.

1993-04-01T23:59:59.000Z

459

Computing Handbook Set -Computer Science (Volume I) Chapter: DNA Computing  

E-Print Network [OSTI]

Computing Handbook Set - Computer Science (Volume I) Chapter: DNA Computing Sudhanshu Garg, Reem. DNA computing is a class of molecular computing that does computation by the use of reactions chemistry, biochemistry, physics, material science, and computer science. This chapter surveys the field

Reif, John H.

460

cDNA encoding a polypeptide including a hevein sequence  

DOE Patents [OSTI]

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.

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

1993-02-16T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

Nuclear magnetic resonance analysis of protein–DNA interactions  

Science Journals Connector (OSTI)

...review-article Review articles 1004 30 15 Nuclear magnetic resonance analysis of protein-DNA...instrumental advances in solution-state nuclear magnetic resonance have opened up the...structural biology|protein-DNA complex|nuclear magnetic resonance| 1. Introduction...

2011-01-01T23:59:59.000Z

462

NMR Studies of DNA Oligomerers and Their Interactions with Minor Groove Binding Ligands  

E-Print Network [OSTI]

the minor groove of A-T synthetic DNA polymers by volume anda linearized plasmid and synthetic DNA oligomers (Sigurdssonused to cleave DNA, diagram of netropsin-diazene Synthetic

Fagan, P.A.

2010-01-01T23:59:59.000Z

463

Closely related DNA sequences specify distinct patterns of developmental expression in Drosophila melanogaster.  

Science Journals Connector (OSTI)

...New York 14853. Three short synthetic DNA sequences, which are closely...Drosophila melanogaster. | Three short synthetic DNA sequences, which are closely...Accepted 9 March 1990 Three short synthetic DNA sequences, which are closely...

H Xiao; J T Lis

1990-06-01T23:59:59.000Z

464

Optimization of a rapid nonisotopic DNA probe assay for Plasmodium falciparum in the Gambia.  

Science Journals Connector (OSTI)

...Urbana 61801. An enzyme-linked synthetic DNA probe which hybridizes to repetitive...Gambia. | An enzyme-linked synthetic DNA probe which hybridizes to repetitive...April 1991 An enzyme-linked synthetic DNA probe which hybridizes to repetitive...

G L McLaughlin; C Decrind; R Dayal-Drager; M Hassan-King; S Subramanian; B M Greenwood

1991-07-01T23:59:59.000Z

465

Quantitative study of Helicobacter pylori in gastric mucus by competitive PCR using synthetic DNA fragments.  

Science Journals Connector (OSTI)

...mucus by competitive PCR using synthetic DNA fragments T Furuta E Kaneko M...method using various amounts of synthetic DNA fragments containing the same...mucus by competitive PCR using synthetic DNA fragments. | Helicobacter pylori...

T Furuta; E Kaneko; M Suzuki; H Arai; H Futami

1996-10-01T23:59:59.000Z

466

Synthetic DNA probes for detection of enterotoxigenic Clostridium perfringens strains isolated from outbreaks of food poisoning.  

Science Journals Connector (OSTI)

...research-article Research Article Synthetic DNA probes for detection of enterotoxigenic...potential to produce enterotoxin. Synthetic DNA probes for detection of enterotoxigenic...American Society for Microbiology Synthetic DNA Probes for Detection of Enterotoxigenic...

M Van Damme-Jongsten; J Rodhouse; R J Gilbert; S Notermans

1990-01-01T23:59:59.000Z

467

Immunochemical Studies of DNA Modified by cis-Dichlorodiammineplatinum(II) in Vivo and in Vitro  

Science Journals Connector (OSTI)

...not formed in several modified synthetic DNA's and RNA's. At least two...not formed in several modified synthetic DNA's and RNA's. At least two...not formed in several modified synthetic DNA's and RNA's. At least two...

Bernard Malfoy; Brigitte Hartmann; Jean-Pierre Macquet; Marc Leng

1981-10-01T23:59:59.000Z

468

DNA hybridization for assessment of response of Plasmodium falciparum to chloroquine therapy.  

Science Journals Connector (OSTI)

...the accuracy of PFR1-AP, a synthetic DNA hybridization probe conjugated...the accuracy of PFR1-AP, a synthetic DNA hybridization probe conjugated...the accuracy of PFR1-AP, a synthetic DNA hybridization probe conjugated...

G L McLaughlin; P Deloron; A Y Huong; C Sezibera; G H Campbell

1988-09-01T23:59:59.000Z

469

Development of new tools for the production of plasmid DNA biopharmaceuticals  

E-Print Network [OSTI]

DNA vaccines and gene therapies that use plasmid DNA (pDNA) as a vector have gained attention in recent years for their good safety profile, ease of manufacturing, and potential to treat a host of diseases. With this ...

Bower, Diana M. (Diana Morgan)

2012-01-01T23:59:59.000Z

470

Engineering of bacterial strains and vectors for the production of plasmid DNA  

E-Print Network [OSTI]

The demand for plasmid DNA (pDNA) is anticipated to increase significantly as DNA vaccines and non-viral gene therapies enter phase 3 clinical trials and are approved for use. This increased demand, along with renewed ...

Prather, Kristala L. Jones

471

Abstract 1516: Automated circulating DNA purification from large volumes of plasma  

Science Journals Connector (OSTI)

...Automated circulating DNA purification from large volumes of plasma...The current commercial DNA purification methods limit researchers...microl of nuclease-free water in either plates or tubes...Automated circulating DNA purification from large volumes of plasma...

Sydnor T. Withers; Mary Dressler; and Cristopher A. Cowan

2014-10-01T23:59:59.000Z

472

E-Print Network 3.0 - anchored dna substrates Sample Search Results  

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

show... that the binding of the -domain to DNA is not required for anchoring to DNA, as looping is still observed for Fts... in the new DNA tether (Supplementary ... Source:...

473

Mechanical Systems Qualification Standard  

Broader source: Energy.gov (indexed) [DOE]

61-2008 61-2008 June 2008 DOE STANDARD MECHANICAL SYSTEMS QUALIFICATION STANDARD DOE Defense Nuclear Facilities Technical Personnel U.S. Department of Energy AREA TRNG Washington, D.C. 20585 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. DOE-STD-1161-2008 ii This document is available on the Department of Energy Technical Standards Program Web Site at http://www.hss.energy.gov/nuclearsafety/techstds/ DOE-STD-1161-2008 iv INTENTIONALLY BLANK DOE-STD-1161-2008 v TABLE OF CONTENTS ACKNOWLEDGMENT................................................................................................................ vii PURPOSE ....................................................................................................................................1

474

Fields and Quantum Mechanics  

E-Print Network [OSTI]

The quantum field theories (QFT) constructed in [1,2] include phenomenology of interest. The constructions approximate: scattering by $1/r$ and Yukawa potentials in non-relativistic approximations; and the first contributing order of the Feynman series for Compton scattering. To have a semi-norm, photon states are constrained to transverse polarizations and for Compton scattering, the constructed cross section deviates at large momentum exchanges from the cross section prediction of the Feynman rules. Discussion includes the incompatibility of canonical quantization with the constructed interacting fields, and the role of interpretations of quantum mechanics in realizing QFT.

Glenn Eric Johnson

2014-12-21T23:59:59.000Z

475

Insulation Mechanisms of in vivo Biomolecular Circuits Kayzad S. Nilgiriwala, Phillip M. Rivera and Domitilla Del Vecchio  

E-Print Network [OSTI]

Insulation Mechanisms of in vivo Biomolecular Circuits Kayzad S. Nilgiriwala, Phillip M. Rivera,2,3). It has been theoretically shown that a system can be insulated from retroactivity by using high gain, effectively insulating the cycle from retroactivity by downstream DNA targets. Hence, phosphorylation cycles

Del Vecchio, Domitilla

476

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

Open Energy Info (EERE)

DNA-52 DNA-52 Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home NEPA Document Collection for: NV-020-08-DNA-52 DNA at {{{GeothermalArea}}} for Geothermal/Exploration, {{{NEPA_Name}}} General NEPA Document Info Energy Sector Geothermal energy Environmental Analysis Type DNA Applicant Gerlach Geothermal LLC Geothermal Area {{{GeothermalArea}}}"{{{GeothermalArea}}}" cannot be used as a page name in this wiki. Project Location Project Phase Geothermal/Exploration Techniques Thermal Gradient Holes Comments NOI for TGH at Gavvs Valley Time Frame (days) Application Time 14 Participating Agencies Lead Agency BLM Funding Agency none provided Managing District Office Winnemucca Managing Field Office BLM Black Rock Field Office Funding Agencies none provided

477

Use of synthetic DNA in expression of foreign proteins  

Science Journals Connector (OSTI)

Synthetic \\{DNAs\\} and oligonucleotides, which can be prepared conveniently by combining chemical synthesis and enzymatic methods, have been used extensively in recombinant DNA research. Examples include total gene synthesis, probes for the isolation of specific genes from cDNA or genomic libraries, linkers containing specific restriction sites for cloning, primers for DNA and RNA sequencing, and primers for the construction of specific mutations (either deletion, insertion or point mutations) by oligonucleotide-directed site-specific mutagenesis. This article reviews recent advances in the chemical and enzymatic synthesis of oligo- and polynucleotides and the application of synthetic DNA to the expression of foreign proteins. The synthesis of genes, including structural genes and regulatory genes are reviewed. Oligonucleotide-directed site-specific mutagenesis and use of synthetic DNA to optimize foreign protein expression are also discussed.

Hansen M. Hsiung

1986-01-01T23:59:59.000Z

478

Quantum Mechanics Action of ELF Electromagnetic Fields on Living Organisms  

Science Journals Connector (OSTI)

There is presently an intense discussion if extremely low frequency electromagnetic field (ELF?EMF) exposure has consequences for human health. This include exposure to structures and appliances from this range of frequency in the electromagnetic (EM) spectrum. Biological effects of such exposures have been noted frequently although the implications for specific health effects is not that clear. The basic interactions mechanisms between such fields and living matter is unknown. Numerous hypotheses have been suggested although none is convincingly supported by experimental data. Various cellular components processes and systems can be affected by EMF exposure. Since it is unlikely that EMF can induce DNA damage directly most studies have examined EMF effects on the cell membrane level general and specific gene expression and signal transduction pathways. Even more a large number of studies have been performed regarding cell proliferation cell cycle regulation cell differentiation metabolism and various physiological characteristics of cells. The aim of this letter is present the hypothesis of a possible quantum mechanic effect generated by the exposure of ELF EMF an event which is compatible with the multitude of effects observed after exposure. Based on an extensive literature review we suggest that ELF EMF exposure is able to perform such activation restructuring the electronic level of occupancy of free radicals in molecules interacting with DNA structures.

J. J. Godina?Nava

2010-01-01T23:59:59.000Z

479

Conflicting patterns of nucleotide diversity between mtDNA and nDNA in the Moorish gecko, Tarentola mauritanica  

E-Print Network [OSTI]

RNA) for 154 specimens, and a total of 1876 bp from three nuclear genes (ACM4, MC1R and Rag2) for 51 specimens- pean clade presents a higher nucleotide diversity for the nuclear genes when compared to the combined mtDNA dataset. These analyses suggest that the low mtDNA variability that characterises the European

Carranza, Salvador

480

Agrobacterium May Delay Plant Nonhomologous End-Joining DNA Repair via XRCC4 to Favor T-DNA Integration  

Science Journals Connector (OSTI)

...benthamiana. Supplemental Figure 3. Estimation of At-XRCC4 Transcript Level...plants are sensitive to ionizing radiation and defective in T-DNA integration...rates in higher plants by low-dose irradiation: Are DNA repair...tumefaciens transformation of the radiation hypersensitive Arabidopsis...

Zarir E. Vaghchhipawala; Balaji Vasudevan; Seonghee Lee; Mustafa R. Morsy; Kirankumar S. Mysore

2012-10-12T23:59:59.000Z

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer  

E-Print Network [OSTI]

provide information about dye-DNA interactions. Comparison of Texas Red (TR), fluorescein, and tetramethyl- rhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for biophysical studies employing such conjugates.... Time-resolved anisotropy studies demonstrate that the TR- and TAMRA-aptamer anisotropy decays are dominated by the overall rotation of the aptamer, whereas the fluorescein-aptamer anisotropy decay displays a subnanosecond rotational correlation time...

Wilson, George S.; Unruh, Jay R.; Gokulrangan, Giridharan; Lushington, Gerald H.; Johnson, Carey K.

2005-05-01T23:59:59.000Z

482

Radiation-generated Short DNA Fragments May Perturb Non-homologous End-joining and Induce Genomic Instability  

Science Journals Connector (OSTI)

......itatively similar to the observations obtained with synthetic DNA fragments, supporting the importance of DNA size dependency...were qualitatively similar to those stimulated by short synthetic DNA fragments, supporting the importance of DNA size dependency......

Dalong Pang; Thomas A. Winters; Mira Jung; Shubhadeep Purkayastha; Luciane R. Cavalli; Sergey Chasovkikh; Bassem R. Haddad; Anatoly Dritschilo

2011-05-01T23:59:59.000Z

483

E-Print Network 3.0 - ainulaadne dna anals Sample Search Results  

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

31, 2005; Accepted September 18, 2005 ABSTRACT Peptide nucleic acid (PNA) is a synthetic DNA mimic... is capable of sequence-specific targeting of complementary dsDNA...

484

Folding of a DNA Hairpin Loop Structure in Explicit SolventUsingRepli...  

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

Folding of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations. Folding of a DNA Hairpin Loop Structure in Explicit Solvent...

485

E-Print Network 3.0 - alignment improves dna Sample Search Results  

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

details of initiator proteins for DNA replication have provided clues... + domains in ORC contain a conserved structural element that, in DnaA, promotes formation of a right...

486

E-Print Network 3.0 - activates dna polymerase Sample Search...  

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

DNA polymerases has under-gone a striking expansion in the past decade. Since Summary: primer terminus on the -phosphorus105 . In vitro assays for DNA polymerase activity...

487

E-Print Network 3.0 - arbitrarily amplified dna Sample Search...  

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

given DNA sequence millions of times. A. Denaturation: DNA is denatured. B. Annealing: Primer... acronyms associated with molecular markers AFLP Amplified Fragment Length...

488

E-Print Network 3.0 - altered dna polymerase Sample Search Results  

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

University in St. Louis Collection: Biology and Medicine 9 Very Efficient TemplatePrimer-Independent DNA Synthesis by Thermophilic DNA Polymerase in the Presence of a...

489

E-Print Network 3.0 - ancient human dna Sample Search Results  

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

validating ampli- fication of human DNA. Here, we take advantage of two large ancient... Shapiro, Reimer C. Dobberstein, ancient DNA in bone? Is amino acid racemization a useful...

490

E-Print Network 3.0 - automated one-step dna Sample Search Results  

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

Studies, Department of Marine Benthic Ecology and Evolution, Collection: Biology and Medicine ; Environmental Sciences and Ecology 4 Nanotechnology with DNA DNA Nanodevices...

491

E-Print Network 3.0 - alpha-1 foundation dna Sample Search Results  

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

Medicine ; Materials Science ; Physics 76 Conductivity of a single DNA duplex bridging a carbon nanotube gap Summary: Conductivity of a single DNA duplex bridging a carbon...

492

College of Engineering Mechanical Engineering  

E-Print Network [OSTI]

College of Engineering Mechanical Engineering Core 2.0 Completion Checklist Mechanical Engineering Science IN CHMY 141 (CHEM 131) 6 Research and Creative Experience R EMEC 489R & EMEC 499 R (ME 404R & ME

Dyer, Bill

493

Mechanical engineering COLLEGE of ENGINEERING  

E-Print Network [OSTI]

. Mechanical engineering is a broad, versatile and creative discipline concerned with conversion of energyMechanical engineering COLLEGE of ENGINEERING DepartmentofMechanicalEngineering CollegeofEngineering 5050AnthonyWayneDrive Detroit,MI48202 College of engineering t Educating future engineers for 80 years

Berdichevsky, Victor

494

Exploiting mechanical biomarkers in microfluidics  

E-Print Network [OSTI]

Exploiting mechanical biomarkers in microfluidics Xiaole Maoa and Tony Jun Huang*b DOI: 10.1039/c2 mechanical biomarkers in microfluidic devices. This trend makes sense because microfluidic devices often of mechanical biomarker- based microfluidic applications. We believe that these examples are just the tip

495

MASTER OF SCIENCE MECHANICAL ENGINEERING  

E-Print Network [OSTI]

MASTER OF SCIENCE IN MECHANICAL ENGINEERING 75 DEVELOPMENT OF A MODEL TO PREDICT AND ASSESS SURFACE Master of Science in Mechanical Engineering-December 2000 Advisors: Charles N. Calvano, Department of Mechanical Engineering David W. Byers, Naval Surface Warfare Center-Carderock Division Survivability has

496

Apoptosis as a Mechanism for Low Dose Radiation-and Amifostine-Mediated  

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

Apoptosis as a Mechanism for Low Dose Radiation- and Amifostine-Mediated Apoptosis as a Mechanism for Low Dose Radiation- and Amifostine-Mediated Chromosomal Inversion Responses Pam Sykes Flinders University and Medical Centre Abstract Low dose radiation and the chemical radioprotector amifostine have both been shown to protect cells from the immediate and delayed effects of radiation exposure. They display a number of distinct similarities including their ability to protect cells against radiation-induced DNA damage, radiation-induced cell death and metastases formation. Amifostine, which protects cells from the toxic effects of ionizing radiation, has a broad range of activities including free radical scavenging, polyamine-like DNA binding, and induction of hypoxia and redox-regulated genes. Amifostine’s ability to protect cells is often

497

Mechanics of Peridynamic Membranes  

National Nuclear Security Administration (NNSA)

JBAidun AdvMatSci090831 JBAidun AdvMatSci090831 1 Accurate Prediction of Dynamic Fracture with Peridynamics John B. Aidun & Stewart A. Silling Multiscale Dynamic Material Modeling Sandia National Laboratories Prague, Czech Republic August 30 - September 3, 2009 Joint U.S.-Russian Conference on Advances in Materials Science SAND2009-5095C Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. JBAidun AdvMatSci090831 2 Fracture Mechanics Theory and Dynamic Fracture * Onset of crack growth can be accurately predicted * Crack growth speed and direction cannot! Wanted: A successful method for simulating Dynamic Fracture * Such a method must be able to reproduce the

498

Vehicle rear suspension mechanism  

SciTech Connect (OSTI)

A vehicle rear suspension mechanism is described which consists of: a suspension member connected with a vehicle body; wheel hub means supporting a rear wheel having a wheel center plane for rotation about a rotating axis; and connecting means for connecting the wheel hub means with the suspension member. The connecting means include ball joint means having a pivot center located forwardly of and below the rotating axis of the rear wheel and connecting the wheel hub means to the suspension member pivotably about the pivot center, first resilient means located between the wheel hub means and the suspension member rearwardly of and above the rotating axis of the rear wheel, and second resilient means located between the wheel hub means and the suspension member forwardly of and above the rotating axis of the rear wheel.

Kijima, T.; Maebayashi, J.

1986-08-05T23:59:59.000Z

499

Mechanically expandable annular seal  

DOE Patents [OSTI]

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

Gilmore, R.F.

1983-07-19T23:59:59.000Z

500

PEBBLES Mechanics Simulation Speedup  

SciTech Connect (OSTI)

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

Joshua J. Cogliati; Abderrafi M. Ougouag

2010-05-01T23:59:59.000Z