Sample records for dna cleavage mechanism

  1. Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage

    E-Print Network [OSTI]

    Williams, Loren

    Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage recently described a set of anthraquinone derivatives that act as photonucleases.6 Three classes

  2. DNA cleavage and opening reactions of human topoisomerase II are regulated via Mg2-

    E-Print Network [OSTI]

    Hohng, Sung Chul

    DNA cleavage and opening reactions of human topoisomerase II are regulated via Mg2ţ- mediated dynamic bending of gate-DNA Sanghwa Leea,b,1 , Seung-Ryoung Junga,b,1 , Kang Heoa,b , Jo Ann W. Bylc intrinsic topological problems of double- stranded DNA. As part of its essential cellular functions, the en

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

    E-Print Network [OSTI]

    Mecham, Robert

    . For both the serine and matrix met- alloproteinases, catalysis of peptide bond cleavage in insoluble). Elastases are heterogeneous with differing substrate specificities and cata- lytic mechanisms. In fact

  4. Mechanistic studies of bleomycin-mediated double-stranded DNA cleavage and structural studies of DNA containing normal and 4'-oxidized abasic sites

    E-Print Network [OSTI]

    Chen, Jingyang, Ph. D. Massachusetts Institute of Technology

    2006-01-01T23:59:59.000Z

    In order to examine the role of partial intercalation in double-stranded (ds) DNA cleavage mediated by a single bleomycin (BLM), a bulky group ([-cyclodextrin) was chemically attached to the polyamine tail of BLM A5 to ...

  5. 4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack of Hydrogen

    E-Print Network [OSTI]

    Tullius, Thomas D.

    4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack by oxidative damage of the DNA backbone but instead is the result of nucleophilic attack by peroxide. A singleSaccharomyces cerevisae, whichactivatesthephosphodiester for attack by thediffusible smallnucleophile. While Flp

  6. Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV

    E-Print Network [OSTI]

    Liphardt, Jan

    Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single Eco proposed as ``plasmon rulers'' based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic

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

    E-Print Network [OSTI]

    Gates, Kent. S.

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

  8. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    that promote cell death. Several poisons have been successfully exploited in the clinic as antibiotics such as ciprofloxacin (against bacterial topoisomerases) and as...

  9. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in2, 2003Tool ofTopo II: An Enzyme Target forTopo II:

  10. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in2, 2003Tool ofTopo II: An Enzyme Target forTopo

  11. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in2, 2003Tool ofTopo II: An Enzyme Target

  12. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in2, 2003Tool ofTopo II: An Enzyme TargetTopoisomerase

  13. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in2, 2003Tool ofTopo II: An Enzyme

  14. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solidSynthesisAppliances » Top Innovative

  15. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solidSynthesisAppliances » Top InnovativeTopoisomerase II

  16. Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA

    E-Print Network [OSTI]

    Williams, Loren

    30332-0400 ReceiVed May 20, 1998 Abstract: Irradiation of the anthraquinone derivative N,N-Bis(3 interactions are observed in the intercalated complex, indicating that the ground-state anthraquinone and DNA (Rh),7 and a series of anthraquinone (AQ) derivatives8 provides a model for natural oxidative

  17. Photochemistry and Photobiology, 2005, 81: 8995 Photoinduced DNA Cleavage and Cellular Damage in Human Dermal

    E-Print Network [OSTI]

    Turro, Claudia

    1 Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD . Furthermore, upon irradiation with visible light, DAP is able to nick plasmid DNA in the presence of oxygen. The concentration of DAP that resulted in 50% cell death was 172 6 9 lM in the dark and 13 6 1 lM after irradiation

  18. Carbon Nanotube DNA Sensor and Sensing Mechanism

    E-Print Network [OSTI]

    Le Roy, Robert J.

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

  19. DNA Deformation Energy as an Indirect Recognition Mechanism in

    E-Print Network [OSTI]

    Lathrop, Richard H.

    DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions Kimberly A. Senear Abstract--Proteins that bind to specific locations in genomic DNA control many basic cellular. Deformation energy, which models the energy required to bend DNA from its native shape to its shape when bound

  20. Crystal structures of [lamda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

    SciTech Connect (OSTI)

    Zhang, Jinjin; McCabe, Kimberly A.; Bell, Charles E. (OSU)

    2011-08-10T23:59:59.000Z

    The {lambda} exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of {lambda} exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of {lambda} exonuclease in complex with DNA at 1.88-{angstrom} resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg{sup 2+} ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of {lambda} exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

  1. DNA Twist Elasticity: Mechanics and Thermal Fluctuations

    E-Print Network [OSTI]

    Supurna Sinha; Joseph Samuel

    2010-11-30T23:59:59.000Z

    The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that thermal fluctuations play an important role in determining molecular elastic properties, but a full theoretical treatment of the problem of twist elasticity of fluctuating ribbons using the simplest worm like chain model (WLC) remains elusive. In this paper, we approach this problem by taking first a mechanical approach and then incorporating thermal effects in a quadratic approximation applying the Gelfand-Yaglom (GY) method for computing fluctuation determinants. Our study interpolates between mechanics and statistical mechanics in a controlled way and shows how profoundly thermal fluctuations affect the elasticity of semiflexible polymers. The new results contained here are: 1) a detailed study of the minimum energy configurations with explicit expressions for their energy and writhe and plots of the extension versus Link for these configurations. 2) a study of fluctuations around the local minima of energy and approximate analytical formulae for the free energy of stretched twisted polymers derived by the Gelfand Yaglom method. We use insights derived from our mechanical approach to suggest calculational schemes that lead to an improved treatment of thermal fluctuations. From the derived formulae, predictions of the WLC model for molecular elasticity can be worked out for comparison against numerical simulations and experiments.

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

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

    DNA-Programmed Assembly of Plasmon Rulers. (a) 40 nm goldtrajectories for 40 bps plasmon rulers recorded at 85 Hzthe enzyme is bound to the plasmon rulers in the absence of

  3. Phase diagram of mechanically stretched DNA: The salt effect

    E-Print Network [OSTI]

    Amar Singh; Navin Singh

    2014-09-05T23:59:59.000Z

    The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified to incoporate the solvent effect and the cations present in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.

  4. amide bond cleavage: Topics by E-print Network

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

    the reactions of vanadyl ion and found that incubation of DNA with vanadyl ion and hydrogen peroxide (H202) led to intense DNA cleavage. ESR spin trapping demonstrated that...

  5. 'Wume '14 Number 13 1986 Nucleic Aclds Research Specific cleavage of lunetoplast minicircle DNA ft-om Leishmania tarentolae by mung bean

    E-Print Network [OSTI]

    Simpson, Larry

    -om Leishmania tarentolae by mung bean nuclease and identification of several additional minicircle sequenceŁŁ were cleaved by mung bean nuclease in the presence of formamide, yielding unit length linear molecules was not a requirement for cleavage, as linearized network-derived or cloned minicircles were also cleaved by mung bean

  6. DNA . DNA

    E-Print Network [OSTI]

    1. DNA . , . , . . DNA DNA . , DNA . DNA . DNA . DNA DNA DNA . DNA [6, 7, 8]. DNA . DNA NACST/Sim DNA/DNA

  7. Cleavage of nucleic acids

    DOE Patents [OSTI]

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

    2007-12-11T23:59:59.000Z

    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.

  8. Cleavage of nucleic acids

    DOE Patents [OSTI]

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

    2010-11-09T23:59:59.000Z

    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.

  9. Electrochemical DNA Hybridization Detection Using DNA Dohyoung Kwon,a

    E-Print Network [OSTI]

    Kwak, Juhyoun

    Full Paper Electrochemical DNA Hybridization Detection Using DNA Cleavage Dohyoung Kwon,a Kyuwon method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture

  10. Diffusion-based DNA target colocalization by thermodynamic mechanisms

    E-Print Network [OSTI]

    Antonio Scialdone; Mario Nicodemi

    2011-05-04T23:59:59.000Z

    In eukaryotic cell nuclei, a variety of DNA interactions with nuclear elements occur, which, in combination with intra- and inter- chromosomal cross-talks, shape a functional 3D architecture. In some cases they are organized by active, i.e. actin/myosin, motors. More often, however, they have been related to passive diffusion mechanisms. Yet, the crucial questions on how DNA loci recognize their target and are reliably shuttled to their destination by Brownian diffusion are still open. Here, we complement the current experimental scenario by considering a physics model, in which the interaction between distant loci is mediated by diffusing bridging molecules. We show that, in such a system, the mechanism underlying target recognition and colocalization is a thermodynamic switch-like process (a phase transition) that only occurs if the concentration and affinity of binding molecules is above a threshold, or else stable contacts are not possible. We also briefly discuss the kinetics of this "passive-shuttling" process, as produced by random diffusion of DNA loci and their binders, and derive predictions based on the effects of genomic modifications and deletions.

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

    E-Print Network [OSTI]

    Lohman, Timothy M.

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

  12. DNA repair is the target of novel antibiotics

    E-Print Network [OSTI]

    Gunderson, Carl Wayne

    2007-01-01T23:59:59.000Z

    W. & A. M. Segall, (2006) DNA repair, a novel antibacterialjunction-trapping peptides induce DNA damage and chromosomePeptide inhibitors of DNA cleavage by tyrosine recombinases

  13. DNA DNA DNA (d)DNA DNA DNA

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

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

    E-Print Network [OSTI]

    Dinner, Aaron

    A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT Jie serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all trajectories of molecu- larly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT

  15. Recent developments in single-molecule DNA mechanics Zev Bryant1,2

    E-Print Network [OSTI]

    Bryant, Zev

    Recent developments in single-molecule DNA mechanics Zev Bryant1,2 , Florian C Oberstrass1 University, Stanford, CA 94305, USA Corresponding author: Bryant, Zev (zevry@stanford.edu) Current Opinion

  16. DNA DNA . DNA

    E-Print Network [OSTI]

    1. DNA DNA , . . DNA ( ) DNA "exhaustive " . Boolean , 40 2 40 10 12 pico mole . DNA . 20 3-SAT DNA NP-complete [1]. [2, 3]. DNA

  17. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  18. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OF CALCIUM SULFATE: A REVIEWThis rcportJ itDNA-Binding

  19. DNA -DNA--

    E-Print Network [OSTI]

    Glykos, Nikolaos

    #12;#12;#12;8.1 DNA - . DNA- - (DNA-binding domains) ( 100 ). - DNA- - -, DNA. - -- - DNA. 173 8 DNA : -- 8.1 8.2 8.3 Cro - 8.4 Cro 8.5 DNA- - 8.6 Cro DN 8

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

    E-Print Network [OSTI]

    Rocha, M S

    2015-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Not Available

    1988-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Modell, Joshua W.

    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 ...

  3. Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide

    E-Print Network [OSTI]

    Florescu, Ana-Maria; 10.1063/1.3626870

    2011-01-01T23:59:59.000Z

    In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation of long DNA sequences by adjusting slightly the base pairing contribution. The adjusted model leads to (i) critical temperatures for long homogeneous sequences that are in good agreement with both experimental ones and those obtained from statistical models, (ii) a realistic step-like denaturation behaviour for long inhomogeneous sequences, and (iii) critical forces at ambient temperature of the order of 10 pN, close to measured values. The adjusted model furthermore supports the conclusion that the thermal denaturation of long homogeneous sequences corresponds to a first-order phase transition and yields a critical exponent for the critical force equal to sigma=0.70. This model is both geometrically and energetically realistic, in the sense that the helical structure and th...

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

    SciTech Connect (OSTI)

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

    2005-04-06T23:59:59.000Z

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

  5. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07T23:59:59.000Z

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

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

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

    double helix. A protein called DNA polymerase does most of this work, adding nucleotides complementary to the template's nucleotides. But before polymerase builds the...

  7. Structure and mechanism of the UvrA?UvrB DNA damage sensor

    SciTech Connect (OSTI)

    Pakotiprapha, Danaya; Samuels, Martin; Shen, Koning; Hu, Johnny H.; Jeruzalmi, David (Harvard)

    2012-04-17T23:59:59.000Z

    Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, {approx}80 {angstrom} from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.

  8. An unprecedented nucleic acid capture mechanism for excision of DNA damage

    SciTech Connect (OSTI)

    Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)

    2010-11-18T23:59:59.000Z

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

  9. Sustained water cleavage by visible light

    SciTech Connect (OSTI)

    Borgarello, E.; Kiwi, J.; Pelizzetti, E.; Visca, M.; Graetzel, M.

    1981-10-21T23:59:59.000Z

    Sustained cleavage of water by 4 quanta of visible light is achieved in aqueous solutions by using a bifunctional redox catalyst composed of Pt and RuO/sub 2/ cosupported by colloidal TiO/sub 2/ particles. A photochemical model system containing Ru(bpy)/sub 3//sup 2 +/ as a sensitizer and methyl viologen (MV/sup 2 +/) as an electron relay is used to test the effect of catalyst composition, sensitizer concentration, pH, and temperature on the efficiency of light-induced water decomposition. Electron relay free systems also exhibit high photoactivity. Direct band gap irradiation by uv light leads to efficient water cleavage in the absence of sensitizer and relay.

  10. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

    1. , . DNA, RNA, Protein [1-4]. DNA . DNA A, T, G, C . DNA , DNA DNA . , DNA DNA . DNA DNA . , PCR , , DNA [5]. DNA DNA , DNA

  11. Mechanism of mismatch recognition revealed by human MutS[beta] bound to unpaired DNA loops

    SciTech Connect (OSTI)

    Gupta, Shikha; Gellert, Martin; Yang, Wei (NIH)

    2012-04-17T23:59:59.000Z

    DNA mismatch repair corrects replication errors, thus reducing mutation rates and microsatellite instability. Genetic defects in this pathway cause Lynch syndrome and various cancers in humans. Binding of a mispaired or unpaired base by bacterial MutS and eukaryotic MutS{alpha} is well characterized. We report here crystal structures of human MutS{beta} in complex with DNA containing insertion-deletion loops (IDL) of two, three, four or six unpaired nucleotides. In contrast to eukaryotic MutS{alpha} and bacterial MutS, which bind the base of a mismatched nucleotide, MutS{beta} binds three phosphates in an IDL. DNA is severely bent at the IDL; unpaired bases are flipped out into the major groove and partially exposed to solvent. A normal downstream base pair can become unpaired; a single unpaired base can thereby be converted to an IDL of two nucleotides and recognized by MutS{beta}. The C-terminal dimerization domains form an integral part of the MutS structure and coordinate asymmetrical ATP hydrolysis by Msh2 and Msh3 with mismatch binding to signal for repair.

  12. A New Mechanism for DNA Alterations Induced by Alpha Particles Such as Those Emitted by Radon and Radon Progeny

    E-Print Network [OSTI]

    Bruce E. Lehnert; Edwin H. Goodwin

    The mechanism(s) by which alpha (a) particles like those emitted from inhaled radon and radon progeny cause their carcinogenic effects in the lung remains unclear. Although direct nuclear traversals by a-particles may be involved in mediating these outcomes, increasing evidence indicates that a particles can cause alterations in DNA in the absence of direct hits to cell nuclei. Using the occurrence of excessive sister chromatid exchanges (SCE) as an index of DNA damage in human lung fibroblasts, we investigated the hypothesis that a-particles may induce DNA damage through the generation of extracellular factors. We have found that a relatively low dose of a-particles can result in the generation of extracellular factors, which, upon transfer to unexposed normal human cells, can cause excessive SCE to an extent equivalent to that observed when the cells are directly irradiated with the same irradiation dose. A short-lived, SCEinducing factor(s) is generated in a-irradiated culture medium containing serum in the absence of cells. A more persistent SCE-inducing factor(s), which can survive freeze-thaw and is heat labile is produced by fibroblasts after exposure to the a-particles. These results indicate that the initiating target for a-particle-induced genetic changes can be larger than a cell's nucleus or even a whole cell. How transmissible factors like those observed here in vitro may extend to the in vivo condition in the context of a-particle-induced carcinogenesis in the respiratory tract remains to be determined. Environ Health Perspect 1 05(Suppl 5):1095-1101 (1997) Key words: alpha particles, radon/radon progeny, indirect radiation effects, high LET radiation,

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

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01T23:59:59.000Z

    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.

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our InstagramStructure of All-Polymer Solar Cells ImpedesStructure of DNA-Bound FEN1

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our InstagramStructure of All-Polymer Solar Cells ImpedesStructure of DNA-Bound

  16. ataxin-3 protein cleavage: Topics by E-print Network

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

    Page Topic Index 1 FUSION OF CONDITIONAL RANDOM FIELD AND SIGNALP FOR PROTEIN CLEAVAGE SITE PREDICTION Engineering Websites Summary: FUSION OF CONDITIONAL RANDOM FIELD AND...

  17. Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models

    E-Print Network [OSTI]

    Buyukdagli, Sahin; 10.1016/j.cplett.2009.11.061

    2010-01-01T23:59:59.000Z

    In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that separates zipped from unzipped DNA sequences in mechanical unzipping experiments is a power-law in the temperature-force plane. We also prove that for the investigated models the corresponding critical exponent is proportional to the critical exponent alpha, which characterizes the behaviour of the specific heat in the neighbourhood of the critical temperature for thermal denaturation.

  18. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

    SciTech Connect (OSTI)

    Wang, Yanli; Juranek, Stefan; Li, Haitao; Sheng, Gang; Wardle, Greg S.; Tuschl, Thomas; Patel, Dinshaw J.; (MSKCC); (HHMI)

    2009-10-21T23:59:59.000Z

    The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg{sup 2+}-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.

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

    SciTech Connect (OSTI)

    Horton, John R.; Borgaro, Janine G.; Griggs, Rose M.; Quimby, Aine; Guan, Shengxi; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Zhu, Zhenyu; Cheng, Xiaodong (Emory-MED); (NE Biolabs)

    2014-07-03T23:59:59.000Z

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

  20. MECHANISM AND FUNCTION OF SPLICEOSOMAL CLEAVAGE IN FISSION YEAST

    E-Print Network [OSTI]

    Kannan, Ram

    2013-08-31T23:59:59.000Z

    antagonizes the second step of splicing in the context of TER1 suggests that the BS-U2 snRNA interactions are disrupted after the first step and thus earlier than previously thought. The slow transition from first to second step triggers the Prp22 DEx...

  1. alpha-dependent aggrecan cleavage: Topics by E-print Network

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

    in both strand cleavage reactions. These structures differ Monnat, Ray 46 Refining the model for selective cleavage at acidic residues in arginine-containing protonated...

  2. Molecular Quantum Mechanics 2010: From Methylene to DNA and Beyond Conference Support

    SciTech Connect (OSTI)

    None

    2013-05-15T23:59:59.000Z

    This grant was $12500 for partial support of an international conference, Molecular Quantum Mechanics 2010, which was held on the campus of the University of California, Berkeley, from 24 to 29 May 2010. The conference involved more than 250 participants. The conference schedule ran from as early as 8:00 AM to as late as 10:30 PM at night, in order to accommodate six historical lectures, 16 plenary lectures, 42 invited talks and two very strong poster sessions containing 143 contributed posters. Since 1989, the Molecular Quantum Mechanics (MQM) series of international conferences has show- cased the frontiers of research in quantum chemistry with a strong focus on basic theory and algorithms, as well as highlights of topical applications. Both were strongly in evidence at MQM 2010. At the same time as embracing the future, the MQM conferences also honour the lifetime contributions of some of the most prominent scientists in the field of theoretical and computational quantum chemistry. MQM 2010 recognised the work of Prof. Henry F. ‘Fritz’ Schaefer of the Center for Computational Chemistry at the University of Georgia, who was previously on the faculty at Berkeley The travel of invited speakers was partially covered by sponsorships from Dell Computer, Hewlett-Packard, Journal of Chemical Theory and Computation, Virginia Tech College of Science, Molecular Physics, Q-Chem Inc and the American Institute of Physics. By contrast, the conference grant from the Department of Energy was used to provide fellowships and scholarships to enable graduate students and postdoctoral fellows to attend the meeting, and thereby broaden the participation of young scientists at a meeting where in the past most of the attendees have been more senior faculty researchers. We believe that we were very successful in this regard: 118 students and postdocs attended out of the total of 256 participants. In detail, the DOE sponsorship money was partially used for dormitory scholarships that covered the cost of shared accommodation for students and postdocs at Berkeley dormitories. This covered the $200-$305 cost of a shared room for the 5-day duration of the conference. The only condition of these scholarships was that the awardee must present a poster at the meeting. Approximately $7565 was spent for these dormitory scholarships. The remaining expenditures of $4800 was used for 12 merit scholarships which were awarded to students whose poster presentations were judged the best at the conference. This amount covered a significant part of their travel and registration fees.

  3. Scientific Correspondence Cleavage of Bipartite Substrates by Rice and Maize

    E-Print Network [OSTI]

    Gopalan, Venkat

    -exchange chromato- graphic and density gradient fractionation pro- cedures, nuclear RNase P was partially purified of the well- studied Escherichia coli RNase P as a standard, we first confirmed the accurate cleavage of pt

  4. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

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

    2012-10-16T23:59:59.000Z

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

  5. Mechanistic Examination of C?-C? Bond Cleavages of Tryptophan...

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

    (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+,...

  6. Microbial cleavage of organic C-S bonds

    DOE Patents [OSTI]

    Kilbane, J.J. II.

    1994-10-25T23:59:59.000Z

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

  7. DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action

    E-Print Network [OSTI]

    Hergenrother, Paul J.

    . A battery of in vitro assays readily distinguishes between DNA intercalation, DNA groove binding-targeting drugs for cancer and beyond, the further discovery and characterization of such compounds are of considerable interest. This review outlines diagnostic experiments useful in characterizing noncovalent drug

  8. Application of electron backscattered diffraction to cleavage fracture in duplex stainless steel

    SciTech Connect (OSTI)

    Kim, S.; Marrow, T.J.

    1999-05-21T23:59:59.000Z

    The mechanical properties and corrosion resistance of duplex stainless steel (DSS) are generally superior to conventional austenite or ferrite grades. DSSs can have yield strengths twice the austenite grades, while retaining good ductility and toughness properties. Commercial wrought duplex stainless steels, either plates or rod, are processed by hot rolling followed by a solution annealing treatment to optimize the austenite-ferrite ratio and dissolve any pre-existing secondary phases. Processing may lead to a significant anisotropy in mechanical properties. For example, the tensile properties in cold-rolled sheet of duplex stainless steel (22Cr5Ni) reveals anisotropy of strength, i.e., the transverse direction tensile strength is 7.3% higher than tensile strength in the rolling direction (RD). It was also shown in a study of the effect of crack orientation on the impact properties of the same steel, that when the crack was oriented parallel to the direction of elongation of the austenite phase, the crack could grow along the more brittle ferrite phase for a longer distance before encountering the more ductile austenite. This decreased impact toughness. These are examples of microstructure texture. Crystallographic texture may also have an effect on properties that are related to specific crystallographic planes; such as brittle cleavage and stress corrosion cracking. This paper describes the application of electron backscattered diffraction (EBSD) to study cleavage fracture and crystal texture in age-hardened DSS.

  9. Transferability of cleavage fracture parameters between notched and cracked geometries

    E-Print Network [OSTI]

    Boyer, Edmond

    and specimen geometry dependence of cleavage fracture micromechanisms of a French pressure vessel steel (A508 that only NT tests with a mean fracture strain lower than 25% have to be considered to make sure ; ¢ 50 £ C ]. Also a unique set of Weibull parameters was found to describe all the NT tests over

  10. CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL

    E-Print Network [OSTI]

    Boyer, Edmond

    CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL S. R. Bordet1 , B. Tanguy1 , S vessel (RPV) steel. In this purpose, different WPS fracture test results obtained on compact tensile (CT fractographic investigations and finite element (FE) calculations, demonstrate a strong material aspect to WPS

  11. Nanotechnology with DNA DNA Nanodevices

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

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

  12. DNA microarray (spot) .

    E-Print Network [OSTI]

    1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

  13. Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA

    E-Print Network [OSTI]

    Wang, Wei Hua

    Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA Wei (Received 17 July 2012; published 20 November 2012) DNA wrapping is an important mechanism for chromosomal DNA packaging in cells and viruses. Previous studies of DNA wrapping have been performed mostly

  14. Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor

    SciTech Connect (OSTI)

    Jin, Tengchuan; Perry, Andrew; Jiang, Jiansheng; Smith, Patrick; Curry, James A.; Unterholzner, Leonie; Jiang, Zhaozhao; Horvath, Gabor; Rathinam, Vijay A.; Johnstone, Ricky W.; Hornung, Veit; Latz, Eicke; Bowie, Andrew G.; Fitzgerald, Katherine A.; Xiao, T. Sam (UMASS, MED); (Bonn); (Trinity); (PMCI-A); (NIH)

    2012-05-21T23:59:59.000Z

    Recognition of DNA by the innate immune system is central to antiviral and antibacterial defenses, as well as an important contributor to autoimmune diseases involving self DNA. AIM2 (absent in melanoma 2) and IFI16 (interferon-inducible protein 16) have been identified as DNA receptors that induce inflammasome formation and interferon production, respectively. Here we present the crystal structures of their HIN domains in complex with double-stranded (ds) DNA. Non-sequence-specific DNA recognition is accomplished through electrostatic attraction between the positively charged HIN domain residues and the dsDNA sugar-phosphate backbone. An intramolecular complex of the AIM2 Pyrin and HIN domains in an autoinhibited state is liberated by DNA binding, which may facilitate the assembly of inflammasomes along the DNA staircase. These findings provide mechanistic insights into dsDNA as the activation trigger and oligomerization platform for the assembly of large innate signaling complexes such as the inflammasomes.

  15. DNA Computing Hamiltonian path

    E-Print Network [OSTI]

    Hagiya, Masami

    2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

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

    E-Print Network [OSTI]

    Gates, Kent. S.

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

  17. Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate

    SciTech Connect (OSTI)

    Changela, Anita; DiGate, Russell J.; Mondragon, Alfonso (NWU); (Phil. Col. Pharmacy)

    2010-03-05T23:59:59.000Z

    Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5{prime} phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.

  18. DNA UPTAKE BY TRANSFORMABLE BACTERIA

    SciTech Connect (OSTI)

    LACKS,S.A.

    1999-09-07T23:59:59.000Z

    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.

  19. 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...

  20. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2013-01-01T23:59:59.000Z

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

  2. DNA Copyright

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2011-01-01T23:59:59.000Z

    of architecture and computer software. Sequences of DNA should also be acknowledged as eligible for copyright protection. Unaltered genomic DNA sequences would seem poor candidates for copyright protection. The case is stronger for copyright protection...

  3. DNA demethylation by DNA repair

    E-Print Network [OSTI]

    Gehring, Mary

    Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...

  4. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09T23:59:59.000Z

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

  5. Cleavage of carbon-sulfur bonds in coal and substituted dibenzyl sulfides

    SciTech Connect (OSTI)

    Green, T.K.; Wang, L.; Estill, W.J.; Bixler, B. [Western Kentucky Univ., Bowling Green, KY (United States)

    1996-10-01T23:59:59.000Z

    S-methylation of a bituminous coal using {sup 13}C-enriched methyl iodide in the presence of silver tetrafluoroborate produces significant quantities of trimethylsulfonium ion as determined by {sup 13}C NMR. This result suggests that carbon-sulfur bonds in coal are being cleaved. In an effort to determine the types of structures in coal responsible for this ion, a series of model substituted dibenzyl sulfides were S-methylated. The substrates included 4,4{prime}dimethoxydibenzylsulfide (1), 4,4{prime}dimethyldibenzylsulfide (2), dibenzylsulfide (3), 4,4{prime}dichlorodibenzylsufide (4). All substrates are cleaved to varying degrees in refluxing DCE (83{degrees}C) to produce a mixture of methyldibenzyl-, dimethylbenzyl- and trimethylsulfonium ions. The relative amounts of these ions depends on the substituent, with the degree of C-S bond cleavage increasing with the electron-donating ability of the substituent in the order (1) > (2) > (3) > (4). A mechanism is proposed consistent with this substituent effect which involves an intermediate benzyl carbocation - sulfide ion-dipole complex.

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

    DOE Patents [OSTI]

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

    1995-04-11T23:59:59.000Z

    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.

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

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

    O-H Bond Cleavage: Methanol on TiO2(110). Abstract: We investigated methanol adsorption and dissociation on bridge-bonded oxygen vacancies of TiO2(110) (1×1) surface...

  8. Crystallographic Evidence for Water-assisted Photo-induced Peptide Cleavage in the Stony Coral

    E-Print Network [OSTI]

    Ikura, Mitsuhiko

    Crystallographic Evidence for Water-assisted Photo-induced Peptide Cleavage in the Stony Coral 3-2, Suita, Osaka 565-0871, Japan A coral fluorescent protein from Trachyphyllia geoffroyi, Kaede

  9. Negative Self-Regulation of TLR9 Signaling by Its N-Terminal Proteolytic Cleavage Product

    E-Print Network [OSTI]

    Ploegh, Hidde

    TLR signaling is essential to innate immunity against microbial invaders and must be tightly controlled. We have previously shown that TLR9 undergoes proteolytic cleavage processing by lysosomal proteases to generate two ...

  10. The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an ;Ajar; Intermediate Conformation in the Nucleotide Selection Mechanism

    SciTech Connect (OSTI)

    Wu, Eugene Y.; Beese, Lorena S. (Duke)

    2011-10-10T23:59:59.000Z

    To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established 'open' and 'closed' states. In this 'ajar' conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.

  11. DNA Pendant

    E-Print Network [OSTI]

    Hacker, Randi; Tsutsui, William

    2007-11-14T23:59:59.000Z

    Broadcast Transcript: It's a symbol of commitment. It's a memento mori. It's the DNA pendant offered by Japan's Eiwa Industry and it's two, two, two things in one. Using genetic extraction, Eiwa removes the DNA from, say, a strand of hair or a...

  12. A Mechanism of Haloalkene-Induced Renal

    E-Print Network [OSTI]

    Wolfgang Dekant; Spyridon Vamvakas; Andreas Kochling; Wolfgang Kanhai; Dirk Muller; Dietrich Henschler

    Several halogenated alkenes are nephrotoxic; some others induce renal tubular adenocarcinomas in rodents after lifelong administration. A bioactivation mechanism accounting for the organ-selective tumor induction has been elucidated: conjugation of the parent compounds with glutathione (GSH), catalyzed by hepatic GSH S-transferases, results in the formation of haloalkyl and halovinyl glutathione S-conjugates. Formation of S-conjugates (identified by NMR and mass spectrometry) could be demonstrated with trichloroethene, tetrachloroethene, hexachlorobutadiene, perfluoropropene, trichlorotrifluoropropene, and dichloroacetylene in incubations with rat liver microsomes and in the isolated perfused rat liver. The GSH conjugates formed are eliminated from the rat liver with the bile and may be translocated to the kidney, intact or after metabolism to the corresponding cysteine S-conjugates that are metabolized in the kidney by renal tubular cysteine conjugate 3-lyase (P-lyase) to reactive intermediates, most likely thioacylchlorides and thioketenes. Interaction of these potent electrophiles with DNA [demonstrated for intermediates formed from S-(1,2,3,4,4-pentachlorobutadienyl)-L-cysteine] causes mutagenicity in bacteria, genotoxicity in cultured renal cells, and cytotoxicity in kidney cells. As an alternative to 3-lyase-catalyzed cleavage, the cysteine S-conjugates may be acetylated to the corresponding mercapturic acids, which have been identified in urine. The ability of the kidney to concentrate GSH and cysteine S-conjugates and the intensive metabolism of GSH S-conjugates to cysteine S-conjugates in this organ are evidently responsible for the organotropic carcinogenicity.

  13. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo­Yong Shin 1 , Eun Jeong the complexity of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  14. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo-Yong Shin1 , Eun Jeong of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  15. (gene expression) DNA (DNA microarrays).

    E-Print Network [OSTI]

    Athens, University of

    Lymphoblastic Leukemia - ALL, 25 Acute Myeloid Leukemia - AML) µ 7129 [10]. µ µ µ µ µ µ µ µ DNA. 62 µ, 22 40 , µ 2000 [6]. µ 72 µ µ (47 Acute

  16. Synthesis and enzymatic cleavage of dual-ligand quantum dots Sarah L. Sewell a

    E-Print Network [OSTI]

    cleavage by matrix metalloprotease-7 (MMP-7). The QDs were further functionalized with folic acid, a ligand functionalized with both the MMP-7 cleavable substrate and folic acid were successfully synthesized molecule, ubiquitous cancer targeting ligands. In this work, we have designed and fabricated a nanoparticle

  17. Temperature-Controlled Regioselectivity in the Reductive Cleavage of p-Methoxybenzylidene Acetals

    E-Print Network [OSTI]

    Wei, Alexander

    Temperature-Controlled Regioselectivity in the Reductive Cleavage of p-Methoxybenzylidene Acetals The regioselective ring opening of pyranosidic 4,6-p-methoxybenzylidene acetals with BH3/Bu2BOTf in THF can be tuned-sensitive functional groups, including allyl and enol ethers. The presence of water does not interfere with reductive

  18. Reversible Cleavage of Carbon-Carbon Bonds in Benzonitrile Using Nickel(0)

    E-Print Network [OSTI]

    Jones, William D.

    Reversible Cleavage of Carbon-Carbon Bonds in Benzonitrile Using Nickel(0) Juventino J. Garcia 3, 2000 Summary: The nickel(0) fragment [(dippe)Ni] has been found to -coordinate to the CN bond efficient and reversible. The nickel dimer [(dippe)NiH]2 has been reported to be capable of cleaving the C

  19. Cleavage of Carbon-Carbon Bonds in Alkyl Cyanides Using Nickel(0)

    E-Print Network [OSTI]

    Jones, William D.

    Cleavage of Carbon-Carbon Bonds in Alkyl Cyanides Using Nickel(0) Juventino J. Garci´a,*, Alma Are of alkyl cyanides afforded nickel(0) compounds of the type [(dippe)Ni(2 -RCN)], where R ) Me, Et, Pr, i Pr cyanides using [(dippe)NiH]2, leading to the formation of an 2- nitrile complex of nickel(0), which

  20. Low-Energy (0.1 eV) Electron Attachment SS Bond Cleavage

    E-Print Network [OSTI]

    Simons, Jack

    Low-Energy (0.1 eV) Electron Attachment S­S Bond Cleavage Assisted by Coulomb Stabilization Department of Chemistry, University of Gdansk, Gdansk, Poland Received 12 September 2004; accepted 13 October], very low-energy elec- trons are attached to the gaseous sample, after which specific bonds break

  1. ##### SAT Engine ####### _ ############ DNA ###### _

    E-Print Network [OSTI]

    Hagiya, Masami

    ##### SAT Engine ####### _ ############ DNA ###### _ # # # #y # # #yy # # # #yy ###### DNA #################################### ############### ##################### 6 ## 10 ##### ### DNA ############### (Sakamoto et al., Science, Vol.288, pp.1223-122* *6

  2. Cleavage-like fracture of austenite in duplex stainless steel

    SciTech Connect (OSTI)

    Foct, J. (Univ. de Lille (France)); Akdut, N. (Inst. fuer Metallkunde und Metallphysik, Aachen (Germany))

    1993-07-15T23:59:59.000Z

    Nitrogen alloying of stainless steel has proved to be extremely successful for mechanical and corrosion properties. For duplex stainless steel, which appears to be very promising for industrial application, the beneficial influence of nitrogen has also been established for contents of about 0.2 wt-%. Duplex structures are found in many alloys and systems as, for instance, in Cu- and Ti-alloys and in stainless steel. They all are characterized by a mixture of similar amounts of two phases whose plastic behaviors are different from one another. In the case of duplex stainless steel the matrix phase is usually ferrite. However, by increasing the nitrogen content and therefore the stability of austenite, it is shown in the present work that austenite can also become the matrix. Because the partition coefficient of nitrogen between [alpha] and [gamma] is large, it is also possible to harden the [gamma] phase more than [alpha]. The question this paper attempts to answer is whether or not nitrogen alloying can exchange the roles of the [alpha] and the [gamma] phases with respect to mechanical properties.

  3. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA

    E-Print Network [OSTI]

    1. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA DNA [2]. DNA DNA , . , , 2 , DNA 4 . DNA 4 A(Adenine), C(Cytosine), G(Guanine), T(Thymine) 2 4 . , . 1 mole 6x10 23 DNA DNA . , . DNA NP-complete [1, 2], [2

  4. Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

    SciTech Connect (OSTI)

    Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; F., Lawrence

    2008-02-18T23:59:59.000Z

    Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.

  5. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

    DNA Topology: Fundamentals Sergei M Mirkin, University of Illinois at Chicago, Illinois, USA Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA

  6. Tops and Writhing DNA

    E-Print Network [OSTI]

    Joseph Samuel; Supurna Sinha

    2010-11-30T23:59:59.000Z

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

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

    E-Print Network [OSTI]

    Qiao, Yu, 1972-

    2002-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tesfatsion, Leigh

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

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

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

    B. M. , Liphardt, J. & Alivisatos, A. P. (2005) NatureD. , Williams, S. C. & Alivisatos, A. P. (2002) Journal ofSiu, M. , Agarwal, H. , Alivisatos, A. P. & Liphardt, J. (

  11. DNA polymerase with modified processivity

    DOE Patents [OSTI]

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

    1999-01-01T23:59:59.000Z

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

  12. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30T23:59:59.000Z

    DNA computer. The existing models from which a few DNA computing algorithms have been developed are not sufficiently powerful and robust, however, to attract potential users. This thesis has described research performed to build a new DNA computing...

  13. Synthesis of DNA

    DOE Patents [OSTI]

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

    2008-11-18T23:59:59.000Z

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

  14. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  15. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Pruteanu, Mihaela

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

  17. DNA repair modulates the vulnerability of the developing brain to alkylating agents

    E-Print Network [OSTI]

    Samson, Leona D.

    Neurons of the developing brain are especially vulnerable to environmental agents that damage DNA (i.e., genotoxicants), but the mechanism is poorly understood. The focus of the present study is to demonstrate that DNA ...

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

    E-Print Network [OSTI]

    Zhu, Guangyu

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

  19. Natural DNA sequencing by synthesis

    E-Print Network [OSTI]

    Roller, Eric E.

    2011-01-01T23:59:59.000Z

    labeled nucleotides by DNA polymerases. Biotechniques, 2005.S.A. , et al. , Multiplexed DNA sequencing-by-synthesis.Assembly of High-Density DNA Arrays for Genomic Analyses.

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

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

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

  2. Nickel-promoted reductive C-S bond cleavage: A model for the first step in the reaction promoted by methyl coenzyme M reductase

    SciTech Connect (OSTI)

    Mikyung Cha; Shoner, S.C.; Kovacs, J.A. (Univ. of Washington, Seattle (United States))

    1993-04-28T23:59:59.000Z

    Sulfur-ligated Ni complexes are of interest as active-site models of the Ni-containing enzymes hydrogenase (H[sub 2]-ase), methyl coenzyme M reductase (Me-CoM reductase), and Co-dehydrogenase (CODH). Me-CoM reductase catalyzes the last step in the reaction sequence which converts CO[sub 2] to CH[sub 4] in methanogenic bacteria. This step involves the cleavage of the methyl thioether C-S bond of the substrate methyl coenzyme M (Me-S-CoM). Ni(I) is believed to be the active species responsible for promoting this reaction. However, it has been difficult to probe the mechanism by which this occurs, since Me-CoM reductase rapidly loses activity upon breakage of whole cells during purification. Only one Ni complex, Ni[sup II](dioxo[16]aneN[sub 5]), has been shown to induce stoichiometric methane formation from Me-S-CoM; however, the mechanism proposed to explain this reaction is difficult to understand, and involves a Ni(II/III), as opposed to a Ni(I/II), redox couple. Other nickel complexes have been shown to desulfurize thioethers in the presence of reducing agents (e.g., LiAlH[sub 4]); however, the reactive Ni species have not been characterized. As part of a systematic study aimed at determining the influence of the local Ni coordination environment on reactivity, the authors have synthesized a series of structurally related sulfur-ligated Ni(II) complexes, including Ni[sup II]L[sub S5] (1). Since redox changes (Ni(III) [yields] Ni(II) and/or Ni(II) [yields] Ni(I)) appear to play an important role in the mechanisms of the enzymes mentioned above, the authors have also examined the redox chemistry of these molecules. Herein, they report a Ni-promoted reductive C-S bond cleavage reaction that represents a plausible chemical model for the first step in the reaction promoted by Ni in Me-CoM reductase. 30 refs., 4 figs.

  3. Physical process Mechanical mechanisms

    E-Print Network [OSTI]

    Berlin,Technische Universität

    1 Physical process Generation · Mechanical mechanisms F = m·a · Electric/Magnetic mechanisms F = B·i·l · Fluid dynamic/Hydraulic mechanisms q, p, ij · Thermal/Optical #12;2 Source unit

  4. DNA conjugation andDNA conjugation and reversibility onreversibility on

    E-Print Network [OSTI]

    Rubloff, Gary W.

    DNA conjugation andDNA conjugation and reversibility onreversibility on chitosan surfaceschitosan surfaceschitosan surfaceschitosan surfaces Rubloff Research Group Accomplishments #12;DNA conjugation and reversibility onDNA conjugation and reversibility on chitosan surfaceschitosan surfaces Accomplishment Single

  5. The influence of crenulation cleavage development on the bulk elastic and seismic properties of phyllosilicate-rich rocks

    E-Print Network [OSTI]

    Vel, Senthil

    -rich, crustal rocks. We calculated the bulk elastic properties and resulting wave velocities for rock samplesThe influence of crenulation cleavage development on the bulk elastic and seismic properties of phyllosilicate-rich rocks Félice M.J. Naus-Thijssen a, , Andrew J. Goupee b , Scott E. Johnson a , Senthil S. Vel

  6. Capstan friction model for DNA ejection from bacteriophages

    E-Print Network [OSTI]

    Sandip Ghosal

    2013-01-09T23:59:59.000Z

    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.

  7. Meta-DNA: synthetic biology via DNA nanostructures and

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands

  8. Quantitive DNA Fiber Mapping

    E-Print Network [OSTI]

    Lu, Chun-Mei

    2009-01-01T23:59:59.000Z

    of California. Lu et al. : DNA Fiber Mapping page - 35 Lu etal. : DNA Fiber Mapping page - 36 a b c d e f g OV P1 cloneSp6 end T7 end Lu et al. : DNA Fiber Mapping page - 37 a b c

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

    E-Print Network [OSTI]

    Ewald, Sarah Elisabeth

    2010-01-01T23:59:59.000Z

    receptor DC: dendritic cell pDC: plasmacytoid dendritic celltaken up by plasmacytoid DCs (pDC) and elicit large amountsare also components of the pDC-MyD88 signaling complex (

  10. DNA Sequencing apparatus

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

    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.

  11. DNA: structure, dense phases, charges, interactions

    E-Print Network [OSTI]

    Potsdam, Universität

    DNA: structure, dense phases, charges, interactions #12;Outline 1. DNA: structure, charges, dense phases 2. Counterion and DNA condensation 3. ES DNA-DNA interactions 4. DNA toroidal structures 5. Interactions of real DNA helices 6. DNA-DNA ES recognition 7. DNA melting in aggregates 8. Azimuthal

  12. Inhibition of DNA Supercoiling-dependent Transcriptional Activation by a Distant B-DNA to Z-DNA Transition*

    E-Print Network [OSTI]

    Benham, Craig J.

    that a supercoiling-dependent, DNA structural transmission mechanism of this type is responsible for the integration over other alterna- tives, primarily because the change from right-handed helix to left-handed helix). In this way one can alter the destabilization characteristics of other local regions without changing

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

    SciTech Connect (OSTI)

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

    2002-01-01T23:59:59.000Z

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

  14. (2) DNA O(n^5) Quorum-Sensing Lux

    E-Print Network [OSTI]

    Hagiya, Masami

    - 1 - ( ) ( ) DNA RNA DNA RNA DNA DNA 2 DNA #12;- 2 - 17 6 (1) (2) DNA O(n^5) (3) Quorum-Sensing Lux (4) (5) LMNtal ambient LMNtal (1) (2) DNA (3) DNA (4) DNA (5) DNA (1) DNA ANP-96 (Precision System Science ) (2) RTRACS DNA RTRACS (3) in vivo in vivo (4) DNA trans cis 1/10 (5) DNA-PNA DNA DNA DNA DNA DNA

  15. Structural Basis for Substrate Specificity and Mechanism of NAcetylDneuraminic Acid Lyase from Pasteurella multocida

    E-Print Network [OSTI]

    Fisher, Andrew J.

    pyruvate and N-acetyl-D-mannosamine. Although equilibrium favors sialic acid cleavage, these enzymes can of excess pyruvate. Engineering these enzymes to synthesize structurally modified natural sialic acidsStructural Basis for Substrate Specificity and Mechanism of NAcetylDneuraminic Acid Lyase from

  16. DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic linkages

    E-Print Network [OSTI]

    Swigon, David

    DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic Accepted 28 October 2011 Available online 12 November 2011 Keywords: DNA mechanics Overstretching Discrete elastic model Simplex algorithm Bifurcations a b s t r a c t Stretching experiments on single DNA

  17. DNA Sensing by Field-Effect Transistors Based on Networks of Carbon Nanotubes

    E-Print Network [OSTI]

    Rogers, John A.

    DNA Sensing by Field-Effect Transistors Based on Networks of Carbon Nanotubes Ee Ling Gui, Lain mechanism of electrical detection of deoxyribonucleic acid (DNA) hybridization for Au- and Cr level alignment between electrode and SWCNTs can be affected by DNA immobilization and hybridization

  18. DNA polymerases in adaptive immunity Jean-Claude Weill and Claude-Agns Reynaud

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 DNA polymerases in adaptive immunity Jean-Claude Weill and Claude-Agnčs Reynaud Institut National DNA-repair machinery of the cell. Strikingly, these general mechanisms are usually diverted from. In this Review, we focus on the contribution of a set of DNA polymerases discovered in the last decade

  19. DNA is a co-factor for its own replication in Xenopus egg extracts

    E-Print Network [OSTI]

    DNA is a co-factor for its own replication in Xenopus egg extracts Ronald Lebofsky1 , Antoine M a physiological mechanism, and thus represent a powerful system to understand vertebrate DNA replication. Surprisingly, DNA repli- cation in this system is highly sensitive to plasmid concentration, being undetectable

  20. Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH{sub 2}BrI

    SciTech Connect (OSTI)

    Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J. [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)] [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2013-11-21T23:59:59.000Z

    It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (n{sub X}) to a carbon-halogen antibonding orbital (?*{sub C-X}). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH{sub 2}BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH{sub 2}BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH{sub 2}Br + I radical pairs, iso-CH{sub 2}Br-I, and iso-CH{sub 2}I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH{sub 2}Br-I. Both iso-CH{sub 2}Br-I and iso-CH{sub 2}I-Br are observed in cyclohexane with a ratio of ?2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH{sub 2}I-Br photoproduct as well as iso-CH{sub 2}Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH{sub 2}Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ?1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH{sub 2}BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

  1. DNA nanotechnology: understanding and optimisation through simulation

    E-Print Network [OSTI]

    Thomas E. Ouldridge

    2014-11-07T23:59:59.000Z

    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.

  2. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01T23:59:59.000Z

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

  3. Multiprotein DNA looping

    E-Print Network [OSTI]

    Jose M. G. Vilar; Leonor Saiz

    2006-06-19T23:59:59.000Z

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  4. Regulation of DNA repair by parkin

    SciTech Connect (OSTI)

    Kao, Shyan-Yuan, E-mail: shyan-yuan_kao@meei.harvard.edu [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)] [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)

    2009-05-01T23:59:59.000Z

    Mutation of parkin is one of the most prevalent causes of autosomal recessive Parkinson's disease (PD). Parkin is an E3 ubiquitin ligase that acts on a variety of substrates, resulting in polyubiquitination and degradation by the proteasome or monoubiquitination and regulation of biological activity. However, the cellular functions of parkin that relate to its pathological involvement in PD are not well understood. Here we show that parkin is essential for optimal repair of DNA damage. Parkin-deficient cells exhibit reduced DNA excision repair that can be restored by transfection of wild-type parkin, but not by transfection of a pathological parkin mutant. Parkin also protects against DNA damage-induced cell death, an activity that is largely lost in the pathological mutant. Moreover, parkin interacts with the proliferating cell nuclear antigen (PCNA), a protein that coordinates DNA excision repair. These results suggest that parkin promotes DNA repair and protects against genotoxicity, and implicate DNA damage as a potential pathogenic mechanism in PD.

  5. Application of elastic-plastic fracture mechanics to marine structures 

    E-Print Network [OSTI]

    Pathi, Amarkumar

    1991-01-01T23:59:59.000Z

    , be able to support the loads that are applied during its operating lifetime. The structural integrity of components can be assured by knowledge of the material used in their construction. The fracture behavior of a given structure or material depends... or fatigue cracks. Ship structures operate in or near the ductile-brittle transition region, where the failure mechanism is unstable cleavage. Consequently materials are characterized by a transition temperature region above which they may be safely used...

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

    SciTech Connect (OSTI)

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

    2009-05-11T23:59:59.000Z

    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.

  7. Ubiquitylation, neddylation and the DNA damage response

    E-Print Network [OSTI]

    Brown, Jessica S.; Jackson, Stephen P.

    2015-04-01T23:59:59.000Z

    major families: RING (really interesting new gene), HECT (homology to E6AP car- boxyl-terminus) and RBR (ring between ring) [102,103]. The transcription, respectively [88] trans-lesion synthesis (TLS) TLS is a DNA damage bypass mechanism tha It employs... depends on RNF4 binding to SUMO2/3 polymeric chains and subsequent RNF4 dimerization [183]. In addition to its role in promoting the turnover of proteins, RNF4 might also be important for the formation of hybrid SUMO/ubiquitin chains at DNA damage sites...

  8. Visualizing DNA What is it?

    E-Print Network [OSTI]

    Rose, Michael R.

    Visualizing DNA #12;What is it? Gel electrophoresis is one of the techniques scientists use to look at the DNA they have. This technique separates DNA by size. #12;How does it work? First a gel is prepared. Gels

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

    SciTech Connect (OSTI)

    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

    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.

  10. Mechanisms of chemical phototoxicity

    SciTech Connect (OSTI)

    Yurkow, E.J.

    1989-01-01T23:59:59.000Z

    Psoralens in combination with ultraviolet light (PUVA) are phototoxic and potent modulators of epidermal cell growth and differentiation. Using an in vitro cell culture model, the effects of psoralens and UVA light on the growth of epidermal cells were investigated. It was found that psoralen and UVA light interact synergistically to inhibit the growth of cells in culture. This synergism was also observed in the ability of PUVA to inhibit DNA synthesis, decrease cell survival, cause mutations and form psoralen-DNA adducts. Using a cell culture model for the differentiation of melanocytes, PUVA was also found to be a potent inducer of melanogenesis as evidenced by its ability to increase cellular tyrosinase, the enzyme responsible for melanin biosynthesis. Results from these studies indicate that PUVA can induce dramatic alterations in the growth rate and differentiation state of cells at dosage levels which are associated with minimal DNA damage. These findings are in conflict with the general assumption that the biological effects of psoralens and UVA light are associated with their ability to bind covalently to and cross-link DNA. Therefore, the author investigated the possibility that sites of action, other than DNA, are involved in the mechanism(s) by which photoactivated psoralens modulate epidermal cell growth and differentiation. The author's laboratory has found that mammalian epidermal cells contain specific, saturable, high-affinity binding sites for the psoralens that are distinct from DNA. This receptor for the psoralens, photolabeled with ({sup 3}H)-8-methoxysporalen, was visualized following sodium dodecyl sulfatepolyacrylamide gel electrophoresis. The psoralen receptor is shown to be a 22,000 dalton protein located in nonnuclear fractions of cell extracts.

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

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2005-10-01T23:59:59.000Z

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

  13. Carbon-carbon bond cleavage of 1,2-hydroxy ethers b7 vanadium(V) dipicolinate complexes

    SciTech Connect (OSTI)

    Hanson, Susan K [Los Alamos National Laboratory; Gordon, John C [Los Alamos National Laboratory; Thorn, David L [Los Alamos National Laboratory; Scott, Brian L [Los Alamos National Laboratory; Baker, R Tom [Los Alamos National Laboratory

    2009-01-01T23:59:59.000Z

    The development of alternatives to current petroleum-based fuels and chemicals is becoming increasingly important due to concerns over climate change, growing world energy demand, and energy security issues. Using non-food derived biomass to produce renewable feedstocks for chemicals and fuels is a particularly attractive possibility. However, the majority of biomass is in the form of lignocellulose, which is often not fully utilized due to difficulties associated with breaking down both lignin and cellulose. Recently, a number of methods have been reported to transform cellulose directly into more valuable materials such as glucose, sorbitol, 5-(chloromethyl)furfural, and ethylene glycol. Less progress has been made with selective transformations of lignin, which is typically treated in paper and forest industries by kraft pulping (sodium hydroxide/sodium sulfide) or incineration. Our group has begun investigating aerobic oxidative C-C bond cleavage catalyzed by dipicolinate vanadium complexes, with the idea that a selective C-C cleavage reaction of this type could be used to produce valuable chemicals or intermediates from cellulose or lignin. Lignin is a randomized polymer containing methoxylated phenoxy propanol units. A number of different linkages occur naturally; one of the most prevalent is the {beta}-O-4 linkage shown in Figure 1, containing a C-C bond with 1,2-hydroxy ether substituents. While the oxidative C-C bond cleavage of 1,2-diols has been reported for a number of metals, including vanadium, iron, manganese, ruthenium, and polyoxometalate complexes, C-C bond cleavage of 1,2-hydroxy ethers is much less common. We report herein vanadium-mediated cleavage of C-C bonds between alcohol and ether functionalities in several lignin model complexes. In order to explore the scope and potential of vanadium complexes to effect oxidative C-C bond cleavage in 1,2-hydroxy ethers, we examined the reactivity of the lignin model complexes pinacol monomethyl ether (A), 2-phenoxyethanol (B), and 1,2-diphenyl-2-methoxyethanol (C) (Figure 1). Reaction of (dipic)V{sup V}(O)O{sup i}Pr (1a) or (dipic)V{sup v}(O)OEt (lb) with A, B, or C in acetonitrile yielded new vanadium(V) complexes where the alcohol-ether ligand was bound in a chelating fashion. From the reaction of 1b with pinacol monomethyl ether (A) in acetonitrile solution, (dipic)V{sup v}(O)(pinOMe) (2) (PinOMe = 2,3-dimethyl-3-methoxy-2-butanoxide) was isolated in 61 % yield. Reaction of 1b with 2-phenoxyethanol (B) in acetonitrile gave the new complex (dipic)V{sup v}(O)(OPE) (3) (OPE = 2-phenoxyethoxide), which was isolated in 76% yield. In a similar fashion, 1a reacted with 1,2-diphenyl-2-methoxyethanol (C) to give (dipic)V(O)(DPME) (4) (DPME = 1,2-diphenyl-2-methoxyethoxide), which was isolated in 39% yield. Complexes 2, 3, and 4 were characterized by {sup 1}H NMR and IR spectroscopy, elemental analysis, and X-ray crystallography. Compared to the previously reported vanadium(V) pinacolate complex (dipic)V(O)(pinOH) the X-ray structure of complex 2 reveals a slightly shorter V = O bond, 1.573(2) {angstrom} vs 1.588(2) {angstrom} for the pinOH structure. Complexes 3 and 4 display similar vanadium oxo bond distances of 1.568(2) {angstrom} and 1.576(2) {angstrom}, respectively. All three complexes show longer bonds to the ether-oxygen trans to the oxo (2.388(2) {angstrom} for 2, 2.547(2) {angstrom} for 3, and 2.438(2) {angstrom} for 4) than to the hydroxy-oxygen in the pinOH structure (2.252(2) {angstrom}).

  14. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA chips -- Integrated Chemical Circuits for DNADiagnosis and DNA computers Akira Suyama, Associate Professor Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo DNA chips are si l i con­ or glass­based smal l surfaces on which many DNA ol i gonuc l eotides are i

  16. Focus: DNA probes

    SciTech Connect (OSTI)

    Not Available

    1986-11-01T23:59:59.000Z

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  17. Effect of electric field on exfoliation of nanoplates Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109

    E-Print Network [OSTI]

    Lu, Wei

    Effect of electric field on exfoliation of nanoplates Wei Lua Department of Mechanical Engineering assist or retard exfoliation depending on the angle between a collection of plates and the field. A critical electric field strength for exfoliation is predicted. Structural refinement occurs by cleavage

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

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

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

    2014-12-01T23:59:59.000Z

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

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

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

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

    2014-12-01T23:59:59.000Z

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

  20. -DNA 1217 BK21-IT,

    E-Print Network [OSTI]

    - DNA 1217 BK21-IT, (MEC) (NRL) . . : : : : syshin@bi.snu.ac.kr ihlee@bi.snu.ac.kr btzhang@bi.snu.ac.kr 2004 9 16 2005 10 14 - DNA (DNA Sequence Design using -Multiobjective Evolutionary Algorithm) (Soo-Yong Shin) (In-Hee Lee) (Byoung-Tak Zhang) DNA

  1. Damage and rupture mechanisms in an austenoferritic duplex steel

    SciTech Connect (OSTI)

    Verhaeghe, B.; Louchet, F.; Brechet, Y. [LTPCM-CNRS, St. Martin d`Heres (France). Groupe Physique du Metal] [LTPCM-CNRS, St. Martin d`Heres (France). Groupe Physique du Metal; Massoud, J.P. [EDF, Moret sur Loing (France)] [EDF, Moret sur Loing (France)

    1997-05-01T23:59:59.000Z

    The influence of ageing on damage and rupture mechanisms in an austenoferritic duplex stainless steel is studied using conventional straining and impact toughness testing at 20 C and 320 C, and in situ SEM straining at 20 C. While the as-received alloy fails in a ductile mode, damage in the aged material starts with cleavage nucleation in ferrite. The authors show that, owing to the bipercolated topology of the alloy, these cleavage cracks can propagate while passing round austenite ligaments whose plastic stretching controls the crack extension. The variations with strain of both the crack size and the average crack separation are computed analytically and their comparison gives a good prediction of ductility.

  2. Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the acyl-enzyme Complex for an Intermolecular Self-Cleavage Reaction

    SciTech Connect (OSTI)

    Lee,J.; Feldman, A.; Delmas, B.; Paetzel, M.

    2007-01-01T23:59:59.000Z

    Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH{sub 2}-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-{angstrom} resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser{sup 633}O{gamma} forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala{sup 716}, of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-{angstrom} resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ({approx}19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.

  3. Intermediate DNA at low added salt: DNA bubbles slow the diffusion of short DNA fragments

    E-Print Network [OSTI]

    Tomislav Vuletic; Sanja Dolanski Babic; Ticijana Ban; Joachim Raedler; Francoise Livolant; Silvia Tomic

    2011-01-05T23:59:59.000Z

    We report a study of DNA (150 bp fragments) conformations in very low added salt $DNA concentration range $0.0015\\leq c \\leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 DNA has the diffusion coefficient, $D_p$ reduced below the values for both ssDNA coils and native dsDNA helices of similar polymerization degree $N$. Thus, this DNA population can not be a simple mix of dsDNA and of ssDNA which results from DNA melting. Here, melting occurs due to a reduction in screening concomitant with DNA concentration being reduced, in already very low salt conditions. The intermediate DNA is rationalized through the well known concept of fluctuational openings (DNA bubbles) which we postulate to form in AT-rich portions of the sequence, without the strands coming apart. Within the bubbles, DNA is locally stretched, while the whole molecule remains rod-like due to very low salt environment. Therefore, such intermediate DNA is elongated, in comparison to dsDNA, which accounts for its reduced $D_p$.

  4. Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human

    E-Print Network [OSTI]

    Boyer, Edmond

    have direct implications for the cell entry mechanism of SARS-CoV along the respiratory system and the susceptibility of a recombinant native full-length S-protein trimer (triSpike) of the severe acute respiratory

  5. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect (OSTI)

    Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L. (Harvard)

    2012-05-14T23:59:59.000Z

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

  6. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Turro, Claudia

    ,8-anthraquinone disulfonate (AQ2-) was utilized,17 whose negative charge precludes its binding to the polyanionic

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

    SciTech Connect (OSTI)

    Hess, Peter [Institute of Physical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D-69120 Heidelberg (Germany)

    2014-08-07T23:59:59.000Z

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

  9. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection...

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

    Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Hairpin DNA Switch for Ultrasensitive...

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

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Drennan, Catherine L.

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

  13. A synthetic autonomous rotary nanomotor made from and fuelled by DNA

    E-Print Network [OSTI]

    Dunn, Katherine E

    2015-01-01T23:59:59.000Z

    DNA nanostructures are made using synthetic DNA strands, the sequences of which are designed such that they will self-assemble into the desired form by hybridization of complementary domains. Various structures and devices have been presented, including DNA tweezers, nanorobots and a range of linear motors such as bipedal walkers. Inspiration for the latter is drawn from naturally occurring molecular motors like kinesin. This paper describes a concept for an autonomous rotary nanomotor made from DNA, which utilizes the well-known and widely-studied phenomenon of toehold-mediated DNA strand displacement. The motor is to be driven by a series of strand displacement reactions, the order of which is controlled by steric constraints arising from the secondary structure of the DNA strands comprising the motor mechanism. The capabilities of DNA motors would be extended significantly if autonomous rotary motion could be achieved. The device has a range of potential applications, including molecular computation and si...

  14. DNA Structural Nanotechnology Duke University

    E-Print Network [OSTI]

    Reif, John H.

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

  15. Sensing DNA - DNA as nanosensor: a perspective towards nanobiotechnology

    E-Print Network [OSTI]

    Ralf Metzler; Tobias Ambjoernsson

    2005-08-20T23:59:59.000Z

    Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out about the solvent conditions such as ionic strength, presence of binding proteins, etc. By measuring dynamical quantities in particular, rather sensitive nanoprobes may be constructed with contemporary instruments.

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

    E-Print Network [OSTI]

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

  17. Detailed Architecture of a DNA Translocating Machine: The High-resolution Structure of the Bacteriophage

    E-Print Network [OSTI]

    Rossmann, Michael G.

    . The structure suggests a translocation mechanism in which the longitudinal displacement of the DNA along its of the best known. f29 is a small double- stranded DNA bacteriophage that infects Bacillus subtilis cells from its distal part. Electron microscopy studies, based on two- dimensional projections and three

  18. DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents

    E-Print Network [OSTI]

    Cai, Long

    DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents Here we present a completely new DNA decontamination reagent DNA-ExitusPlus. In comparison with conventional products, DNA solutions for effective DNA decontamination. DNA decontamination reagents use three different molecular prin

  19. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01T23:59:59.000Z

    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.

  20. DNA waves and water

    E-Print Network [OSTI]

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

    2010-12-23T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Silverman, Scott K.

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

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

    E-Print Network [OSTI]

    Ang, Wee Han

    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 ...

  3. Mitochondrial DNA variation in populations of Peromyscus eremicus from the Sonoran and Chihuahuan Deserts

    E-Print Network [OSTI]

    Walpole, Deric King

    1995-01-01T23:59:59.000Z

    DNA divergence suggests a lack of gene flow between the two races and supports the hypothesis that these groups represent distinct species. Pliocene or late Pleistocene pluvial-interpluvial climatic fluctuations are implicated as the primary isolating mechanism...

  4. Allele-specific enzymatic amplification of. beta. -globin genomic DNA for diagnosis of sickle cell anemia

    SciTech Connect (OSTI)

    Wu, D.Y.; Ugozzoli, L.; Pal, B.K.; Wallace, B. (Beckman Research Institute of the City of Hope, Duarte, CA (USA))

    1989-04-01T23:59:59.000Z

    A rapid nonradioactive approach to the diagnosis of sickle cell anemia is described based on an allele-specific polymerase chain reaction (ASPCR). This method allows direct detection of the normal or the sickle cell {beta}-globin allele in genomic DNA without additional steps of probe hybridization, ligation, or restriction enzyme cleavage. Two allele-specific oligonucleotide primers, one specific for the sickle cell allele and one specific for the normal allele, together with another primer complementary to both alleles were used in the polymerase chain reaction with genomic DNA templates. The allele-specific primers differed from each other in their terminal 3{prime} nucleotide. Under the proper annealing temperature and polymerase chain reaction conditions, these primers only directed amplification on their complementary allele. In a single blind study of DNA samples from 12 individuals, this method correctly and unambiguously allowed for the determination of the genotypes with no false negatives or positives. If ASPCR is able to discriminate all allelic variation (both transition and transversion mutations), this method has the potential to be a powerful approach for genetic disease diagnosis, carrier screening, HLA typing, human gene mapping, forensics, and paternity testing.

  5. Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA

    E-Print Network [OSTI]

    Gates, Kent. S.

    Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially

  6. Photofragmentation in linked donor-acceptor molecules. Intramolecular single electron transfer induced cleavage of a 1,2-diamine

    SciTech Connect (OSTI)

    Leon, J.W.; Whitten, D.G. (Univ. of Rochester, NY (United States))

    1993-09-08T23:59:59.000Z

    Two intramolecular donor-acceptor molecules which fragment by a single electron transfer initiated cation radical carbon-carbon bond cleavage have been synthesized and their photoreactivity studied. The intramolecular [open quotes]diads[close quotes] consist of a 1,2-diamine linked via an ester bond to either an anthraquinone or a 9,10-dicyanoanthracene electron-acceptor chromophore. As the covalent linkage between the donor and acceptor chromophores prevents solvent separation of the photogenerated radical ion pair, these systems provide a [open quotes]clock[close quotes] to examine directly competition between fragmentation and back electron transfer. The linked anthraquinone molecule fragments efficiently, with quantum yields approaching 80%, despite the inability of the photoproduced radical ions to separate. These high yields may be attributed to a slow, spin-forbidden back electron transfer and a rapid fragmentation. In contrast, the quantum yields for the dicyanoanthracene diad (reactive singlet) are markedly lower, less than 0.001 in benzene. The reactivity of comparable intermolecular donor-acceptor combinations is also reported. 54 refs., 3 figs., 2 tabs.

  7. Heterolytic Cleavage of H2 by Bifunctional Manganese(I) Complexes: Impact of Ligand Dynamics, Electrophilicity, and Base Positioning

    SciTech Connect (OSTI)

    Hulley, Elliott B.; Helm, Monte L.; Bullock, R. Morris

    2014-12-01T23:59:59.000Z

    We report the synthesis, characterization, and reactivity with H2 of a series of MnI complexes of the type [(P-P)Mn(L2)CO]+ (L2 = dppm, bppm, or (CO)2; P-P = PPhNMePPh or PPh2 NBn2 ) that bear pendant amine ligands designed to function as proton relays. The pendant amine was found to function as a hemilabile ligand; its binding strength is strongly affected by the ancillary ligand environment around Mn. Tuning the electrophilicity of the Mn center leads to systems capable of reversible heterolytic cleavage of the H-H bond. The strength of pendant amine binding can be balanced to protect the Mn center while still leading to facile reactivity with H2. Neutral amine-bearing MnIH species were found to react with one-electron oxidants and, after proton and electron transfer reactions, regenerate MnI cationic species. The reactivity presented herein indicate that the Mn complexes we have developed are a promising platform for Mn-based H2 oxidation electrocatalyst development. The 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 DOE.

  8. Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

    E-Print Network [OSTI]

    Christian Matek; Thomas E. Ouldridge; Jonathan P. K. Doye; Ard A. Louis

    2014-04-10T23:59:59.000Z

    Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For example, loop formation in the Lac operon can regulate the expression of key genes, and DNA supercoiling is closely correlated to rhythmic circardian gene expression in cyanobacteria. Supercoiling is also important for large scale organisation of the genome in both eukaryotic and prokaryotic cells. DNA can respond to torsional stress by writhing to form looped structures called plectonemes, thus transferring energy stored as twist into energy stored in bending. Denaturation bubbles can also relax torsional stress, with the enthalpic cost of breaking bonds being compensated by their ability to absorb undertwist. Here we predict a novel regime where bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. These tip bubbles can occur for both positive and negative supercoiling and greatly reduce plectoneme diffusion by a pinning mechanism. They can cause plectonemes to preferentially localise to AT rich regions, because bubbles more easily form there. The tip-bubble regime occurs for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.

  9. DNA attachment to support structures

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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).

  10. 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...

  11. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynami...

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

    B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations....

  12. Controlling DNA Methylation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration would likeConstitution And BylawsMetal-Organic FrameworksControlling DNA

  13. GENETIC AND MOLECULAR ANALYSIS OF DNA DAMAGE REPAIR AND TOLERANCE PATHWAYS.

    SciTech Connect (OSTI)

    SUTHERLAND, B.M.

    2001-07-26T23:59:59.000Z

    Radiation can damage cellular components, including DNA. Organisms have developed a panoply of means of dealing with DNA damage. Some repair paths have rather narrow substrate specificity (e.g. photolyases), which act on specific pyrimidine photoproducts in a specific type (e.g., DNA) and conformation (double-stranded B conformation) of nucleic acid. Others, for example, nucleotide excision repair, deal with larger classes of damages, in this case bulky adducts in DNA. A detailed discussion of DNA repair mechanisms is beyond the scope of this article, but one can be found in the excellent book of Friedberg et al. [1] for further detail. However, some DNA damages and paths for repair of those damages important for photobiology will be outlined below as a basis for the specific examples of genetic and molecular analysis that will be presented below.

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

    SciTech Connect (OSTI)

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

    2012-09-17T23:59:59.000Z

    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).

  15. DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* ,

    E-Print Network [OSTI]

    Podgornik, Rudolf

    309 DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* , Parsegian The forces that govern DNA interactions - such as electrostatic interactions, hydration, and fluctuation forces - that treat DNA about the physical forces and energies that involve DNA molecules is to ask whether there is more to DNA

  16. & Mechanical Engineering

    E-Print Network [OSTI]

    Zhou, Chongwu

    , robotics, and the development of new tools for integrated approaches to concurrent engineeringAME Aerospace & Mechanical Engineering #12;Aerospace and Mechanical Engineers design complex Engineering (AME) students conduct basic and applied research within and across the usual disciplinary

  17. Condensation of circular DNA

    E-Print Network [OSTI]

    E. L. Starostin

    2013-04-05T23:59:59.000Z

    A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.

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

    E-Print Network [OSTI]

    Shell, Scarlet Sara

    2008-01-01T23:59:59.000Z

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

  19. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    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. The sequences of...

  20. Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis

    E-Print Network [OSTI]

    Bashir, Rashid

    conventional semi- conductor processes, thereby facilitating mass fabrication and size tunability-beam-based sputtering and surface-tension-driven shrinking processes.[2,4,7] Other techniques for creating indivi- dual failure in SiO2 structures),[5] limited nanopore lifetime, electrical noise,[14,15] and a lack of chemical

  1. WRN Exonuclease Structure, Molecular Mechanism, and DNA End Processing Role

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

    found that the lanthanide europium does not support WRN-exoM A position 28 . The two europium ion sites in WRN-exo areof nuclease activity by europium. Instead, the Eu 3+ M A and

  2. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract Management Fermi SitePART I SECTION ADMSE ElectronDNADNA origami:

  3. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OF CALCIUM SULFATE: A REVIEWThis rcportJ it

  4. The TGA codons are present in the open reading frame of selenoprotein P cDNA

    SciTech Connect (OSTI)

    Hill, K.E.; Lloyd, R.S.; Read, R.; Burk, R.F. (Vanderbilt Univ., Nashville, TN (United States))

    1991-03-11T23:59:59.000Z

    The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelled with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.

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

    SciTech Connect (OSTI)

    Peng, Jamy C.

    2007-05-05T23:59:59.000Z

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

  6. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K. (Chicago, IL)

    1998-01-01T23:59:59.000Z

    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.

  7. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10T23:59:59.000Z

    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.

  8. Normalized cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

    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.

  9. Mechanism of DNA Polymerization Catalyzed by Sulfolobus solfataricus P2 DNA Polymerase IV

    E-Print Network [OSTI]

    Suo, Zucai

    . Fiala and Zucai Suo*,,§ Department of Biochemistry, Ohio State Biochemistry Program, Ohio State, The Ohio State UniVersity, Columbus, Ohio 43210 ReceiVed September 26, 2003; ReVised Manuscript Recei the energy of nucleotide binding is used to drive a rate-limiting protein conformational change preceding

  10. DNA Synthesis across an Abasic Lesion by Human DNA Polymerase I

    SciTech Connect (OSTI)

    Nair, Deepak T.; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.; (Sinai); (Texas-MED)

    2009-05-22T23:59:59.000Z

    Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase{sup I} (Pol{sup I}) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Pol in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the 'void' opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Pol's small preference for insertion of dGTP over other nucleotides opposite this common lesion.

  11. Huntington's disease: underlying molecular mechanisms and emerging

    E-Print Network [OSTI]

    Morimoto, Richard

    transcriptional mechanism also dictates the expression of polygluta- mine proteins. Here, we summarize the key with no disease modifying treatments available [1]. At the molecular level, HD is caused by a CAG trinu- cleotide is composed of proteins involved in transcription, DNA maintenance, cell cycle regulation, cellular orga

  12. Transcriptional Control of DNA-Based Nanomachines

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    on responses to stimuli or the cell's environ- ment. So far, nanomachines have been controlled with DNA rather be performed by these devices in well-defined steps. Recently, a DNA machine that binds, carries, and releases the manual addition of a "fuel" strand, consisting of single stranded DNA (ssDNA) that affects

  13. Unnatural nucleotides for DNA sequencing

    E-Print Network [OSTI]

    Jacutin, Swanee E

    1997-01-01T23:59:59.000Z

    Fluorescent nucleotide analogs were prepared and tested to find surrogate structures that are: (i) incorporated by DNA polymerases; (ii) spectroscopically distinct for each fluorescent tag; and (iii) easily deprotected at the 3'-position under mild...

  14. Mammalian DNA Repair. Final Report

    SciTech Connect (OSTI)

    None

    2003-01-24T23:59:59.000Z

    The Gordon Research Conference (GRC) on Mammalian DNA Repair was held at Harbortown Resort, Ventura Beach, CA. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

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

    E-Print Network [OSTI]

    Shapiro, Beth

    reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from (Lydolph et al. 2005). Also uncertain is whether the DNA is extracellular and bound to clay minerals

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

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: A DNA-Based Approach to Synthetic Biology Harish Chandran1 harish@cs.duke.edu Nikhil taken here is to develop a biochemical system which we call meta-DNA (abbre- viated as mDNA), based entirely on strands of DNA as the only component molecules. Our work leverages prior work

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

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions Harish Chandran for desired functionality. The approach of this paper is to develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based entirely on strands of DNA as the only component molecule. Our work leverages

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

    E-Print Network [OSTI]

    DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays-interacting DNA oligonucleotides for applications in DNA arrays and biosensors is demonstrated. This strategy mismatches with the complements of all the other members in the set. These "DNA word" sets are denoted as nbm

  19. New Catalytic DNA Biosensors for Radionuclides and Metal ions

    SciTech Connect (OSTI)

    Lu, Yi

    2005-06-01T23:59:59.000Z

    In vitro selection for DNAzymes that are catalytically active with UO22+ ions as the metal cofactor has been completed. The 10th generation pool of DNA was cloned and sequenced. A total of 84 clones were sequenced and placed into families based on sequence alignments. Selected members of each family were 5-labeled with 32P and amplified using PCR. Activity assays were conducted using the isotopically labeled DNAzymes in order to determine which sequences were the most active. The secondary structures of the two most active sequences, called Clone 13 and Clone 39, were determined using the computer program Mfold. A cleavage rate of approximately 1 min-1 in the presence of 10 uM UO22+ was observed for both clones. Clone 39 was determined to be the best candidate for truncation to create a trans-cleaving DNAzyme, based on its secondary structure. An enzyme strand, called 39E, and a substrate strand, called 39DS, were designed by truncating the cis-cleaving DNAzyme. An alternative enzyme strand, called 39Ec, was also assayed with the 39DS substrate. This strand was designed so that the two binding arms were perfectly complimentary, unlike 39E, which formed three mismatched base pairs with 39DS. Both 39E and 39Ec were found to be active, with a rate of approximately 1 min-1 in the presence of 10 uM UO22+. A preliminary UO22+ binding curve was obtained for the 39Ec/39DS trans-cleaving system. The enzyme is active with UO22+ concentrations as low as 1 nM. Based on the preliminary binding curve data, the apparent UO22+ binding constant is approximately 330 nM, and kmax is approximately 1 min-1.

  20. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

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

  1. Quantum Confinement in Hydrogen Bond of DNA and RNA

    E-Print Network [OSTI]

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

    2015-02-09T23:59:59.000Z

    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.

  2. Quantum Confinement in Hydrogen Bond of DNA and RNA

    E-Print Network [OSTI]

    Santos, da Silva dos; Ricotta, Regina Maria

    2015-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

  5. DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics

    E-Print Network [OSTI]

    Nguyen, Gael; Howorka, Stefan; Siwy, Zuzanna S.

    2011-01-01T23:59:59.000Z

    Nonexponential kinetics of DNA escape from alpha-hemolysin2010), (iii) the speed of DNA transport (Meller et al. 2001;0AJ, UK G. Nguyen et al. : DNA Strands in Single Nanopores

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

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

    interactions of p53 with DNA: when flexibility serves2006). Structural basis of DNA recognition by p53 tetramers.Z. (2010). Diversity in DNA recognition by p53 revealed by

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

  8. Quantitative measurement and modeling of the DNA damage signaling network : DNA double-strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2009-01-01T23:59:59.000Z

    DNA double-strand breaks (DSB) are one of the major mediators of chemotherapy-induced cytotoxicity in tumors. Cells that experience DNA damage can initiate a DNA damage-mediated cell-cycle arrest, attempt to repair the ...

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

    E-Print Network [OSTI]

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

    2015-04-16T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

  13. DNA Guided Self-Assembly of Nanocrystals for Optoelectronic Devices /

    E-Print Network [OSTI]

    Noh, Hyunwoo

    2013-01-01T23:59:59.000Z

    Lithographically Confined DNA Origami. Nat. Nanotech. 2010,and Orientation of Individual DNA Shapes on LithographicallyB. ; Yan, H. ; Liu, Y. DNA-Origami-Directed Self- Assembly

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

    SciTech Connect (OSTI)

    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

    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.

  15. Computational mechanics

    SciTech Connect (OSTI)

    Goudreau, G.L.

    1993-03-01T23:59:59.000Z

    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.

  16. High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices

    E-Print Network [OSTI]

    Reif, John H.

    of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major specific high-fidelity DNA hybridization reactions for tar- get strands of arbitrary length. Our protocol acid strands is the most basic of all reactions involving nucleic acids and a major component of most

  17. Computational mechanics

    SciTech Connect (OSTI)

    Raboin, P J

    1998-01-01T23:59:59.000Z

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

  18. Reprogramming the Mechanism of Action of Chlorambucil by Coupling to a GQuadruplex Ligand

    E-Print Network [OSTI]

    Di Antonio, Marco; McLuckie, Keith I. E.; Balasubramanian, Shankar

    2014-04-03T23:59:59.000Z

    Reprogramming the Mechanism of Action of Chlorambucil by Coupling to a G-quadruplex Ligand Marco Di Antonio,‡,† Keith I. E. McLuckie† and Shankar Balasubramanian ‡,†,§ ‡Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge... excision repair (NER) enzymes to overcome intra-strand crosslinks and repair T-T di- mers. 15 NER recognizes the damaged DNA strand, ex- cises it and replaces it with freshly synthesized DNA. 15 Because of its importance to DNA repair after UV expo...

  19. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01T23:59:59.000Z

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

  20. Towards Privacy Preserving of Forensic DNA Databases

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14T23:59:59.000Z

    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...

  1. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  2. DNA Microarrays An R Tutorial

    E-Print Network [OSTI]

    Qiu, Weigang

    Analysis & R Tutorial #12;DNA Microarrays An R Tutorial R: Graphics and Statistics beyond Excel R: an Open Source statistical package (http://www.r-project.org) RStudio: a Graphic User Interface to R (http(stock) # median > range(stock) # mim and max > sum(stock) # sum > var(stock) # variance > sd(stock) # standard

  3. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

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

    1991-01-01T23:59:59.000Z

    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).

  4. Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P.

    E-Print Network [OSTI]

    Thoms, Brian C; Chamberlain, Joel; Engelke, David R; Gegenheimer, Peter Albert

    2000-01-01T23:59:59.000Z

    neighbor is itali- cized+) Inspection of Figure 4 shows that these oligo- nucleotides could result only from cleavage at the normal RNase P site, –ApUp21Afp11GpC– for pre-G1Phe and –ApUp 21Afp11ApC– for pre-A1Phe+ In contrast, RNase P treatment...Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P BRIAN C. THOMAS,1,2,5 JOEL CHAMBERLAIN,3,6 DAVID R. ENGELKE,3,4 and PETER GEGENHEIMER1,2 1Department of Molecular Biosciences, The University of Kansas, 2045 Haworth...

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

    E-Print Network [OSTI]

    Podgornik, Rudolf

    Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids Ame, University of Ljubljana, Ljubljana, Slovenia ABSTRACT DNA toroids that form inside the bacteriophage capsid glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor

  6. Probe and method for DNA detection

    SciTech Connect (OSTI)

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

    2013-07-02T23:59:59.000Z

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

  7. DNA Sequencing via Electron Tunneling Michael Zwolak

    E-Print Network [OSTI]

    Zwolak, Michael

    DNA Sequencing via Electron Tunneling Michael Zwolak Department of Physics Oregon State University-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced of "personalized medicine" is hampered today by the high cost and slow speed of DNA sequencing methods. We

  8. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

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

  9. Random mtDNA mutations modulate proliferation capacity in mouse embryonic fibroblasts

    SciTech Connect (OSTI)

    Kukat, Alexandra [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden) [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Edgar, Daniel [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden)] [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Bratic, Ivana [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden) [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Maiti, Priyanka [Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany)] [Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Trifunovic, Aleksandra, E-mail: aleksandra.trifunovic@ki.se [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden) [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany)

    2011-06-10T23:59:59.000Z

    Highlights: {yields} Increased mtDNA mutations in MEFs lead to high level of spontaneous immortalization. {yields} This process is independent of endogenous ROS production. {yields} Aerobic glycolysis significantly contributes to spontaneous immortalization of MEFs. -- Abstract: An increase in mtDNA mutation load leads to a loss of critical cells in different tissues thereby contributing to the physiological process of organismal ageing. Additionally, the accumulation of senescent cells that display changes in metabolic function might act in an active way to further disrupt the normal tissue function. We believe that this could be the important link missing in our understanding of the molecular mechanisms of premature ageing in the mtDNA mutator mice. We tested proliferation capacity of mtDNA mutator cells in vitro. When cultured in physiological levels of oxygen (3%) their proliferation capacity is somewhat lower than wild-type cells. Surprisingly, in conditions of increased oxidative stress (20% O{sub 2}) mtDNA mutator mouse embryonic fibroblasts exhibit continuous proliferation due to spontaneous immortalization, whereas the same conditions promote senescence in wild-type cells. We believe that an increase in aerobic glycolysis observed in mtDNA mutator mice is a major mechanism behind this process. We propose that glycolysis promotes proliferation and allows a fast turnover of metabolites, but also leads to energy crisis due to lower ATP production rate. This could lead to compromised replication and/or repair and therefore, in rare cases, might lead to mutations in tumor suppressor genes and spontaneous immortalization.

  10. DNA and the Genetic Code June 14, 2011

    E-Print Network [OSTI]

    Guevara-Vasquez, Fernando

    DNA and the Genetic Code June 14, 2011 DNA and the Genetic Code #12;Protein synthesis The genetic synthesis requires two steps: transcription and translation. DNA and the Genetic Code #12;DNA DNA development. DNA is comprised of 4 bases: guanine (G), adenine (A), cytosine (C), and thymine (T). The bases

  11. Photodegradation of oligomeric polyesters containing anthraquinone and 1,2-diamine units. Single electron transfer induced cation radical bond cleavage in the solid state

    SciTech Connect (OSTI)

    Leon, J.W.; Whitten, D.G. (Univ. of Rochester, NY (United States))

    1995-03-01T23:59:59.000Z

    Oligomeric polyesters containing light-absorbing anthraquinone electron acceptor chromophores and fragmentable 1,2-diamine donors have been synthesized. Irradiation with [lambda] [ge] 340 nm in solution or as solid films results in photooxidative C-C bond cleavage of the 1,2-diamine units yielding essentially the same products in either case. The solid state photodegradation reaction was monitored using size exclusion chromatography and was found to be substantially less efficient than the corresponding solution reaction. This is attributed to an inefficient forward electron transfer step and the possibility of an induced reversibility of the fragmentation. The efficiency of photodegradation is suggested to be dependent on the donor/acceptor orientations in the solid state. 49 refs., 11 figs., 1 tab.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

  13. Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63

    SciTech Connect (OSTI)

    Chen, Chen; Gorlatova, Natalia; Herzberg, Osnat (Maryland)

    2012-05-02T23:59:59.000Z

    We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120{sup o}. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.

  14. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

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

  15. Binary electrokinetic separation of target DNA from background DNA primers.

    SciTech Connect (OSTI)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01T23:59:59.000Z

    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

  16. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  17. In Situ Live Cell Sensing of Multiple Nucleotides Exploiting DNA/RNA Aptamers and Graphene Oxide Nanosheets

    SciTech Connect (OSTI)

    Wang, Ying; Li, Zhaohui; Weber, Thomas J.; Hu, Dehong; Lin, Chiann Tso; Li, Jinghong; Lin, Yuehe

    2013-07-23T23:59:59.000Z

    Adenosine-5’-triphosphate (ATP) and guanosine-5’-triphosphate (GTP) are primary energy resources and function coordinately for numerous reactions such as microtubule assembly, insulin secretion and ion channel regulation. We have developed a novel DNA/RNA aptamer- graphene oxide nanosheet (GO-nS) sensing platform that can selectively and simultaneously detect ATP and GTP in live cells. A fluorescent tag is covalently attached to aptamers and fluorescence is quenched upon binding of aptamer to the GO-nS. Fluorescently tagged aptamers that selectively bind ATP or GTP were isolated from an aptamer library and were adsorbed onto GO-nS. Upon incubation with targets (ATP and/or GTP), the aptamers readily dissociated from GO-nS and the fluorescent signal was recovered. By covalently attaching fluorophores, both ATP and GTP sensing aptamers could be exploited to simultaneously visualize aptamer dissociation in live cells. In addition, the GO-nS appear to be biocompatible and protect the adsorbed DNA/RNA aptamers from enzymatic cleavage. Our results support the application of aptamer/GO-nS as a sensing platform for nucleotides in living cells and have implications for the development of additional sensor platforms for other bio-molecules that show selective interactions with aptamers and other biomarkers.

  18. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01T23:59:59.000Z

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

  19. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13T23:59:59.000Z

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

  20. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13T23:59:59.000Z

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

  1. Extrusion of an Imperfect Palindrome to a Cruciform in Superhelical DNA: Complete Determination of

    E-Print Network [OSTI]

    Benham, Craig J.

    of Energetics Using a Statistical Mechanical Model Craig J. Benham1 , Anne G. Savitt2 and William R. Bauer2 * 1 at the base of an imperfect cruciform can successfully compete with extension of the cruciform arms. # 2002 that structures more com- plex than the standard DNA double helix are bio- logically important. These include

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

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2014-05-19T23:59:59.000Z

    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) Ĺ 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.

  4. DNA Bubble Life Time in Denaturation

    E-Print Network [OSTI]

    Zh. S. Gevorkian; Chin-Kun Hu

    2010-10-11T23:59:59.000Z

    We have investigated the denaturation bubble life time for a homogeneous as well as for a heterogeneous DNA within a Poland-Scheraga model. It is shown that at criticality the bubble life time for a homogeneous DNA is finite provided that the loop entropic exponent c>2 and has a scaling dependence on DNA length for c<2. Heterogeneity in the thermodynamical limit makes the bubble life time infinite for any entropic exponent.

  5. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01T23:59:59.000Z

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

  6. Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation

    E-Print Network [OSTI]

    Shrivastav, Nidhi

    The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they ...

  7. DNA Directed Assembly Probe for Detecting DNA-Protein Interaction in Microarray Format

    E-Print Network [OSTI]

    Ng, Jin Kiat

    Quantifying DNA-protein interaction using DNA microarrays are gaining increasing attention due to their ability to profile specificity of interactions in a high-throughput manner. This paper describes a new approach that ...

  8. Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA

    E-Print Network [OSTI]

    Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore among individual nucleotides (nt). The system must be capable of differentiating among the four bases

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

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

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

  10. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18T23:59:59.000Z

    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.

  11. Local compression properties of double-stranded DNA based on a dynamic simulation

    E-Print Network [OSTI]

    Xiaoling Lei; Wenpeng Qi; Haiping Fang

    2013-03-13T23:59:59.000Z

    The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deducing by external loads is helpful to understand the biological process, and important to DNA-based nanomechanical devices.

  12. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

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

    2011-03-29T23:59:59.000Z

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

  13. SnapShot: DNA Polymerases II Mammals

    E-Print Network [OSTI]

    Foti, James J.

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

  14. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

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

  15. Nucleotide capacitance calculation for DNA sequencing

    SciTech Connect (OSTI)

    Lu, Jun-Qiang [ORNL; Zhang, Xiaoguang [ORNL

    2008-01-01T23:59:59.000Z

    Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nano-gap electrodes may not sufficient to be used as a stand alone method for rapid DNA sequencing, the capacitance of the nucleotides should be taken into consideration in any GHz-frequency electric measurements and may also serve as an additional criterion for identifying the DNA sequence.

  16. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16T23:59:59.000Z

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

  17. Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine

    SciTech Connect (OSTI)

    Haranczyk, Maciej; Gutowski, Maciej S.

    2007-02-01T23:59:59.000Z

    hanges of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotoides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps.

  18. DNA

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

    algorithms that we have developed to see the inner workings of molecular machines," said Thomas Terwilliger, a senior Los Alamos scientist and Laboratory Fellow. In this case,...

  19. DNA

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OF CALCIUM SULFATE: A REVIEWThis rcportJ it cdrives

  20. DNA nanotechnology DOI: 10.1002/smll.200500464

    E-Print Network [OSTI]

    Li, Jiali

    DNA nanotechnology DOI: 10.1002/smll.200500464 Towards Rapid DNA Sequencing: Detecting Single- Stranded DNA with a Solid-State Nanopore Hao Yan* and Bingqian Xu* Keywords: · DNA · sequencing · single for rapid detection of single DNA molecules and their sequences. Two types of nanopores have been used

  1. Sequence specific alkylation of DNA by hairpin pyrroleimidazole polyamide conjugates

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Sequence specific alkylation of DNA by hairpin pyrrole­imidazole polyamide conjugates Nicholas R predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA for covalent reaction at specific DNA sequences and thereby inhibit DNA­protein interactions. Site

  2. Sequence Recognition of DNA by Protein-Induced Conformational Transitions

    E-Print Network [OSTI]

    Williams, Loren

    Sequence Recognition of DNA by Protein-Induced Conformational Transitions Derrick Watkins1 The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA

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

    E-Print Network [OSTI]

    Meller, Amit

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

  4. A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation

    E-Print Network [OSTI]

    Deaton, Russell J.

    lelism, capacity, and power. This potential, however, is limited by the constraints imposed by the DNA chemistry 1]. Adleman 2] introduced a way to solve combina- torial optimization problems with DNA- mental reaction in DNA based computation is hydro- gen bonding between Watson-Crick complement base pairs

  5. alkyladenine dna glycosylase: Topics by E-print Network

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

    recognition and repair by 3-methyladenine DNA glycosylase I (TAG) Audrey H Metz1II), Helicobacter pylori 3mA DNA glycosylase (MagIII), yeast methyladenine DNA glycosylase...

  6. Single Stranded DNA Induced Assembly of Gold Nanoparticles

    E-Print Network [OSTI]

    Yang, Jun

    The binding affinity of single stranded DNA (ssDNA) for gold nanoparticle surface is studied in this work. The data indicate that the strength of interaction between ssDNA and Au particle surface is closely related to the ...

  7. Single molecule analysis of DNA electrophoresis in microdevices

    E-Print Network [OSTI]

    Randall, Greg C

    2006-01-01T23:59:59.000Z

    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 ...

  8. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

    DNA topology confers sequence specificity to nonspecific architectural proteins Juan Weia , Luke of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles

  9. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    431. Kunkel, T.A. (2004) DNA replication fidelity. J Biol1996) Generation of an endogenous DNA- methylating agent bypombe Mag1 alkylpurine DNA glycosylase. EMBO Rep, 12, 1286-

  10. Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

    E-Print Network [OSTI]

    Dekker, Cees

    Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels Derek Stein,, Zeno Deurvorst on this understanding by demonstrating how a nanofluidic device with integrated electrodes can preconcentrate DNA. KEYWORDS Nanofluidic, DNA, electrokinetic, concentration M iniature fluidic devices are having an important

  11. Allostery through protein-induced DNA bubbles

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

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

    2015-03-12T23:59:59.000Z

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

  12. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-01-01T23:59:59.000Z

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

  13. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-10-18T23:59:59.000Z

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

  14. Dynamics and control of DNA sequence amplification

    SciTech Connect (OSTI)

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

    2014-10-28T23:59:59.000Z

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

  15. DNA Motif Representation with Nucleotide Dependency

    E-Print Network [OSTI]

    Chin, Francis Y.L.

    DNA Motif Representation with Nucleotide Dependency Francis Chin1 and Henry Leung1 1 Department, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot

  16. Atomic force microscopy of biochemically tagged DNA

    SciTech Connect (OSTI)

    Ogletree, D.F.; Kolbe, W.; Spengler, S.; Salmeron, M. (Lawrence Berkeley Laboratory, CA (United States)); Hansma, H.G.; Bezanilla, M. (Univ. of California, Santa Barbara (United States)); Sano, T.; Smith, C.S.; Cantor, C.R. (Boston Univ., MA (United States))

    1993-05-01T23:59:59.000Z

    Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein. 25 refs., 5 figs.

  17. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

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

    2006-06-06T23:59:59.000Z

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

  18. Elastic and Proton Dynamics of the DNA

    E-Print Network [OSTI]

    V. L. Golo

    2008-03-28T23:59:59.000Z

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

  19. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2011-07-05T23:59:59.000Z

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

  20. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2006-08-01T23:59:59.000Z

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

  1. DNA tethering characterization, enzyme-mediated DNA looping under tension, and nucleosome stability in the force measuring optical tweezers

    E-Print Network [OSTI]

    Gemmen, Gregory John

    2006-01-01T23:59:59.000Z

    M. & Schiessel, H. (2004). DNA spools under tension. Phys.accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol.elasticity of lambda-phage DNA. Science . 265 : 1599–1600.

  2. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    from DNA containing dIMP residues by the Escherichia coli,from DNA containing dIMP residues by the Escherichia coli,

  3. 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....

  4. ap dna endonuclease: Topics by E-print Network

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

    specificity Raines, Ronald T. 2 A DNA and restriction enzyme implementation of Turing Ma (Turing machines; Universal Turing machines; recombinant DNA; nonpalindromic...

  5. adenovirus dna sequences: Topics by E-print Network

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

    description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly...

  6. andribosomal dna sequences: Topics by E-print Network

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

    description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly...

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

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

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

  8. 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...

  9. adapting dna microarray: Topics by E-print Network

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

    Gene Expression Analysis & R Tutorial 12;DNA Microarrays An R Tutorial Functional Genomics Qiu, Weigang 3 Research tools known as DNA microarrays are Biology and Medicine...

  10. archived dna microarrays: Topics by E-print Network

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

    Gene Expression Analysis & R Tutorial 12;DNA Microarrays An R Tutorial Functional Genomics Qiu, Weigang 3 Research tools known as DNA microarrays are Biology and Medicine...

  11. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    a nucleotide from the DNA double helix to its active site to access damaged nucleotides. But unlike AGT and most other known DNA nucleotide-flipping proteins, this...

  12. DNA Replication via Entanglement Swapping

    E-Print Network [OSTI]

    Onur Pusuluk; Cemsinan Deliduman

    2011-03-31T23:59:59.000Z

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

  13. Abstract DNA-type systems

    E-Print Network [OSTI]

    Diederik Aerts; Marek Czachor

    2005-12-22T23:59:59.000Z

    An abstract DNA-type system is defined by a set of nonlinear kinetic equations with polynomial nonlinearities that admit soliton solutions associated with helical geometry. The set of equations allows for two different Lax representations: A von Neumann form and a Darboux-covariant Lax pair. We explain why non-Kolmogorovian probability models occurring in soliton kinetics are naturally associated with chemical reactions. The most general known characterization of soliton kinetic equations is given and a class of explicit soliton solutions is discussed. Switching between open and closed states is a generic behaviour of the helices. The effect does not crucially depend on the order of nonlinearity (i.e. types of reactions), a fact that may explain why simplified models possess properties occuring in realistic systems. We explain also why fluctuations based on Darboux transformations will not destroy the dynamics but only switch between a finite number of helical structures.

  14. 2013 INORGANIC REACTION MECHANISMS GORDON RESEARCH CONFERENCE (MARCH 3-8, 2013 - HOTEL GALVEZ, GALVESTON TX)

    SciTech Connect (OSTI)

    Abu-Omar, Mahdi M.

    2012-12-08T23:59:59.000Z

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

  15. Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA

    E-Print Network [OSTI]

    Richardson, Charles C.

    Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft

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

    E-Print Network [OSTI]

    Fedele?, Bogdan I

    2009-01-01T23:59:59.000Z

    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 ...

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

    DOE Patents [OSTI]

    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

    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.

  18. Method of quantitating dsDNA

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2009-10-02T23:59:59.000Z

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

  20. , btzhang}@bi.snu.ac.kr Boosted DNA Computing for Evolutionary Graphical Structure Learning

    E-Print Network [OSTI]

    PLM (Probabilistic Library Model PLM PLM DNA bead seperation PCR (Polymerase Chain Reaction) PLM PLM DNA DNA PLM PLM PLM PLM DNA PLM PLM evolutionary graph structure PLM DNA &$$) Jc`" '& Bc" %6 #12

  1. DNA looping: the consequences and its control

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-09-26T23:59:59.000Z

    The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of DNA looping in its natural context and how they propagate to the cellular behavior through gene regulation. The results of connecting the molecular properties with cellular physiology indicate that looping of DNA in vivo is much more complex and easier than predicted from current models and reveals a wealth of previously unappreciated details.

  2. DNA adsorption at liquid/solid interfaces

    E-Print Network [OSTI]

    Carine Douarche; Robert Cortčs; Steven J. Roser; Jean-Louis Sikorav; Alan Braslau

    2008-09-26T23:59:59.000Z

    DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through chemical grafting of a homogeneous organicmonomolecular layer of N-(2-aminoethyl) dodecanamide on an oxide-free monocrystalline Si(111) wafer. The adsorbed dsDNA is found to embed into the soft monolayer which is deformed in the process. The surface coverage is very high and this adsorbed layer is expected to display 2D nematic ordering.

  3. Heavy Mobile Equipment Mechanic (One Mechanic Shop)

    Broader source: Energy.gov [DOE]

    The position is a Heavy Mobile Equipment Mechanic (One Mechanic Shop) located in Kent, Washington, and will be responsible for the safe and efficient operation of a field garage performing...

  4. 8-oxoguainine enhances bending of DNA that favors binding of glycosylases

    SciTech Connect (OSTI)

    John H. Miller

    2003-04-23T23:59:59.000Z

    Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G19:C6 base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation and Na+ counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G19. Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    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...

  7. Nucleotide insertion initiated by van der Waals interaction during polymerase beta DNA replication

    E-Print Network [OSTI]

    Arulsamy, Andrew Das

    2011-01-01T23:59:59.000Z

    Immortality will remain a fantasy for as long as aging is determined by the erroneous biochemical reactions during a particular DNA replication. The replication and base excision repair mechanism, associated to eukaryotic DNA polymerase-beta enzyme are central to maintaining a healthy cell. Here, we give a series of unambiguous theoretical analyses and prove that the exclusive biochemical reaction involved in a single nucleotide insertion into the DNA primer can be efficiently tracked using the renormalized van der Waals interaction of the stronger type, and the Hermansson blue-shifting hydrogen bond effect. We found that there are two biochemical steps involved to complete the insertion of a single dCTP into the 3' end of a DNA primer. First, the O3' (from a DNA primer) initiates the nucleophilic attack on P_alpha?(from an incoming dCTP), in response, O3_alpha (bonded to P_alpha) retaliates by interacting with H' (bonded to O3'). These interactions are shown to be strongly interdependent and require the form...

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

    DOE Patents [OSTI]

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

    2013-06-25T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-07-26T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    DeSalle, Rob

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

  11. DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION

    E-Print Network [OSTI]

    DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION Mona A. Sheikh, Shriram Compressed Sensing (CS) and demonstrate its utility in DNA array decoding. In a CS DNA microarray, the array spots identify DNA sequences that are shared between multiple organisms, thereby reduc- ing the number

  12. DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications

    E-Print Network [OSTI]

    Weiss, Sharon

    DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications Jenifer L. Lawrie for improving the sensitivity of label-free optical biosensors based on in-situ synthesis of DNA probes within was utilized as the sensor structure. Synthesis of DNA probe, as well as sensing of target DNA, was verified

  13. DNA Translocation Governed by Interactions with Solid-State Nanopores

    E-Print Network [OSTI]

    Meller, Amit

    DNA Translocation Governed by Interactions with Solid-State Nanopores Meni Wanunu, Jason Sutin, Ben dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7­5 nm. Our with DNA length by two power laws: for short DNA molecules, in the range 150­3500 bp, we find an exponent

  14. DNA Compression Challenge Revisited: a Dynamic Programming Approach

    E-Print Network [OSTI]

    Lonardi, Stefano

    DNA Compression Challenge Revisited: a Dynamic Programming Approach Behshad Behzadi and Fabrice Le Fessant LIX, Ecole Polytechnique, Paris, FRANCE June 21 2005 B. Behzadi, F. Le Fessant (LIX) DNA Compression June 21 2005 1 / 38 #12;Outline 1 DNA Compression Challenge 2 Tools and Methods 3 DNA Compression

  15. DNA Computing: A Research University of Western Ontario

    E-Print Network [OSTI]

    Kari, Lila

    31 DNA Computing: A Research Snapshot Lila Kari University of Western Ontario Kalpana Mahalingam ........................................... 31-6 31.5 DNA Memory ................................................... 31-8 Nested Primer Molecular Memory · Organic DNA Memory · Design of DNA Sequences 31.6 Computation in Living Cells

  16. Deoxyribose oxidation chemistry and endogenous DNA adducts

    E-Print Network [OSTI]

    Zhou, Xinfeng

    2006-01-01T23:59:59.000Z

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

  17. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08T23:59:59.000Z

    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

  18. Linear Thermodynamics of Rodlike DNA Filtration

    E-Print Network [OSTI]

    Li, Zirui

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

  19. Intriguing DNA Editor Has a Structural Trigger

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

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

  20. A model for melting of confined DNA

    E-Print Network [OSTI]

    Werner, E; Ambjörnsson, T; Mehlig, B

    2015-01-01T23:59:59.000Z

    When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.

  1. The Initiation of Bacterial DNA Replication

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

    that the ATP-DnaA active site is in a closed configuration, which allows it to bind nucleotides using conserved residues from neighboring AAA+ protomers. The precise geometry of...

  2. RecA acts in trans to allow replication of damaged DNA by DNA polymerase V

    E-Print Network [OSTI]

    Cox, Michael M.

    , Michael M. Cox2 , Roger Woodgate3 & Myron F. Goodman1 The DNA polymerase V (pol V) and RecA proteins

  3. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

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

  4. Mechanical Engineering & Thermal Group

    E-Print Network [OSTI]

    Mojzsis, Stephen J.

    Mechanical Engineering & Thermal Group The Mechanical Engineering (ME) & Thermal Group at LASP has · STOP (Structural, Thermal, and Optical Performance) analyses of optical systems Thermal engineers lead evolved with the complexity of instrument design demands, LASP mechanical engineers develop advanced

  5. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    and the Department of Mechanical Engineering Tufts University Retooling Our Energy Ecosystem: challengesMechanical engineering Department Seminar Robert J. Hannemann The Gordon Institute and Chair of the Tufts Department of Mechanical Engineering. His technical and academic interests

  6. DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack W. Szostak*

    E-Print Network [OSTI]

    Heller, Eric

    DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack TNA is capable of antiparallel, Watson-Crick base-pairing with complementary DNA, RNA, and TNA oligo- nucleotides.2 This property is remarkable, given that the TNA repeat unit is one atom shorter than that of DNA

  7. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering It is a new beginning for innovative fundamental and applied and consolidation of bulk nanocrystalline materials using mechanical alloying, the alloy development and synthesis

  8. 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...

  9. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Lin, Xi

    Mechanical engineering Department Seminar Ju Li Professor MIT Electrochemical-mechanical actions computational and experimental research on mechanical properties of materials, and energy storage and conversion Refreshments served at 10:45 AM The creation of a nanoscale electrochemical and mechanical testing platform

  10. Transport in hybrid electronic devices based on a modified DNA nucleoside (deoxyguanosine)

    E-Print Network [OSTI]

    R. Rinaldi; E. Branca; R. Cingolani; R. Di Felice; E. Molinari; S. Masiero; G. P. Spada; G. Gottarelli; A. Garbesi

    2000-06-26T23:59:59.000Z

    We report on a new class of hybrid electronic devices based on a DNA nucleoside (deoxyguanosine lipophilic derivative) whose assembled polymeric ribbons interconnect a submicron metallic gate. The device exhibits large conductivity at room temperature, rectifying behaviour and strong current-voltage hysteresis. The transport mechanism through the molecules is investigated by comparing films with different self-assembling morphology. We found that the main transport mechanism is connected to pi-pi interactions between guanosine molecules in adjacent ribbons, consistently with the results of our first-principles calculations.

  11. Role of CYP1B1 in PAH-DNA adduct formation and breast cancer risk

    SciTech Connect (OSTI)

    Goth-Goldstein, Regine; Russell, Marion L.; Muller, A.P.; Caleffi, M.; Eschiletti, J.; Graudenz, M.; Sohn, Michael D.

    2010-04-01T23:59:59.000Z

    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.

  12. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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.

  13. Kinetics and mechanism of the oxidation of propylene to allyl acetate in solutions of palladium clusters

    SciTech Connect (OSTI)

    Stolyarov, I.P.; Vargaftik, M.N.; Moiseev, I.I.

    1988-05-01T23:59:59.000Z

    The kinetics of the oxidative acetoxylation of propylene to allyl acetate in solutions of the clusters Pd/sub 561/Phen/sub 60/(OAc)/sub 180/ and Pd/sub 561/Phen/sub 80/(PF/sub 6/) have been studied by gas-liquid chromatography over the range 40-90/degree/C. It has been established that the rate of reaction is proportional to the concentrations of propylene and the clusters in solution and its dependence on the concentrations of O/sub 2/ and acetic acid is represented by a Michaelis type of equation. For high partial O/sub 2/ pressures inhibition of the reaction by oxygen is observed. A mechanism is proposed for the reaction, according to which the cleavage of the C-H bond in the coordinated olefin molecule to form an allyl complex takes place at the limiting stage.

  14. Conditions for positioning of nucleosomes on DNA

    E-Print Network [OSTI]

    Michael Sheinman; Ho-Ryun Chung

    2015-04-29T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    2011-01-18T23:59:59.000Z

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

  16. Dynamic cluster-scaling in DNA

    E-Print Network [OSTI]

    A. Bershadskii

    2010-08-07T23:59:59.000Z

    It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are relevant to both types of nucleotide pair-bases interactions: hydrogen bonds and stacking interactions. It is shown that taking into account the cluster-scaling properties can help to improve heterogeneous models of the DNA dynamics. Two human genes: BRCA2 and NRXN1, have been considered as examples.

  17. Internal pipe attachment mechanism

    DOE Patents [OSTI]

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

    1994-12-13T23:59:59.000Z

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

  18. Localization of positive charge in DNA induced by its interaction with environment

    E-Print Network [OSTI]

    Dmitry B. Uskov; Alexander L. Burin

    2008-06-06T23:59:59.000Z

    Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the interaction $\\lambda$ with the local environment which attempts to trap charge. To determine which interaction dominates we investigated charge quantum states in various $(GC)_{n}$ sequences choosing DNA parameters satisfying experimental data for the balance of charge transfer rates $G^{+} \\leftrightarrow G_{n}^{+}$, $n=2,3$ \\cite{FredMain}. We show that experimental data can be consistent with theory only assuming $b\\ll \\lambda$ meaning that charge is typically localized within the single $G$ site. Consequently any DNA sequence including the one consisting of identical base pairs behaves more like an insulating material then a molecular conductor. Our theory can be verified experimentally, for instance measuring balance of charge transfer reactions $G^{+} \\leftrightarrow G_{n}^{+}$, $n \\geq 4$ and comparing the experimental results with our predictions.

  19. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    SciTech Connect (OSTI)

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07T23:59:59.000Z

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of ?-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming D. salina nuclear genome sequence, placing D. salina in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.

  20. Studies of the chemical mechanisms of flavoenzymes 

    E-Print Network [OSTI]

    Sobrado, Pablo

    2004-09-30T23:59:59.000Z

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

  1. Studies of DNA dynamics in slit-like nanochannel confinement

    E-Print Network [OSTI]

    Balducci, Anthony (Anthony G.)

    2008-01-01T23:59:59.000Z

    The ability to visually observe single DNA molecules has greatly improved our understanding of polymer physics, from gel electrophoresis to the theology of dilute (and even concentrated) polymer solutions. The use of DNA ...

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

    E-Print Network [OSTI]

    Bajaj, Manish G. (Manish Gopal)

    2005-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Elmouelhi, Ahmed (Ahmed M.), 1979-

    2003-01-01T23:59:59.000Z

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

  4. Protein-DNA interaction, random walks and polymer statistics

    E-Print Network [OSTI]

    Slutsky, Michael

    2005-01-01T23:59:59.000Z

    In Part I of the thesis, a general physical framework describing the kinetics of protein- DNA interaction is developed. Recognition and binding of specific sites on DNA by proteins is central for many cellular functions ...

  5. Role of DNA repair protein ERCC1 in skin cancer 

    E-Print Network [OSTI]

    Song, Liang

    2009-01-01T23:59:59.000Z

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

  6. Mitigating security issues in the evolving DNA synthesis industry

    E-Print Network [OSTI]

    Turlington, Ralph Donald, III

    2013-01-01T23:59:59.000Z

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

  7. Defining functional DNA elements in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

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

  8. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V. (Okemos, MI)

    2000-10-03T23:59:59.000Z

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

  9. A model for sample stacking in microcapillary DNA electrophoresis

    E-Print Network [OSTI]

    Srivastava, Alok Kumar, 1967-

    2002-01-01T23:59:59.000Z

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

  10. Local alignment of generalized k-base encoded DNA sequence

    E-Print Network [OSTI]

    Homer, Nils; Nelson, Stanley F; Merriman, Barry

    2010-01-01T23:59:59.000Z

    k-base encoded DNA sequence BMC Bioinformatics 2010, 11:347similarities in the amino acid sequence of two proteins. Jof two-base encoded DNA sequence. BMC Bioinformatics 2009,

  11. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

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

    1983-10-18T23:59:59.000Z

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

  12. Photoelectrochemical array platform for genomic scale DNA synthesis

    E-Print Network [OSTI]

    Emig, Christopher Joseph

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Park, Sunho

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

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

    E-Print Network [OSTI]

    Chen, Xiaojia

    2009-05-15T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2012-01-01T23:59:59.000Z

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

  16. Graduate School Engineering Mechanics

    E-Print Network [OSTI]

    Franssen, Michael

    Mechanics c/o Eindhoven University of Technology PO Box 513, building W-hoog 2.113 5600 MB Eindhoven NL Tel on Engineering Mechanics, a joint initiative of the Eindhoven and Delft Universities of Technology Mechanics c/o Eindhoven University of Technology PO Box 513, building W-hoog 2.113 5600 MB Eindhoven NL

  17. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

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

  18. UNSATURATED SOIL MECHANICS IMPLEMENTATION

    E-Print Network [OSTI]

    Minnesota, University of

    UNSATURATED SOIL MECHANICS IMPLEMENTATION DURING PAVEMENT CONSTRUCTION QUALITY ASSURANCE Mn !! Performance Based Construction QA !! Unsaturated Soil Mechanics !! What We've Learned !! Next Steps #12.6-6.0 5 - 7 19 0.8 5 7 - 9 24 1.1 4 9 - 11 28 1.2 4 #12;Unsaturated Soil Mechanics #12;Fundamentals

  19. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering An experimental methodology is presented for mechanism Yang is a second graduate student in the department of mechanical engineering of ASU. He received his Jian Yang School for Engineering of Matter, Transport and Energy Arizona State University October 5

  20. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    efficient energy systems. Evelyn N. Wang is an Associate Professor in the Mechanical Engineering DepartmentMechanical engineering Department Seminar Evelyn Wang Depaprtment of Mechanical Engineering MIT Nanoengineered Surfaces: Transport Phenomena and Energy Applications 11:00 AM Friday, 5 April 2013 Room 245, 110

  1. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Mechanical engineering Department Seminar Domitilla Del Vecchio Department of Mechanical. A near future is envisioned in which re- engineered bacteria will turn waste into energy and kill cancer, she joined the Department of Mechanical Engineering and the Laboratory for Information and Decision

  2. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    in Mechanical Engineering at the School for Engineering of Matter, Transport and Energy, working in Dr. MarcusMechanical & Aerospace Engineering The atomization of a liquid jet by a high speed cross.S.E. degree in mechanical engineering from Amirkabir University of Technology in 2006 and M.S. degree

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

    E-Print Network [OSTI]

    Bernstein, Bradley E.

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

  4. Beyond DNA origami: the unfolding prospects of

    E-Print Network [OSTI]

    Walter, Nils G.

    for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and futureOpinion Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology Nicole

  5. Rewritable Memory by Controllable Nanopatterning of DNA

    E-Print Network [OSTI]

    Pierce, Niles A.

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

  6. Reprogramming DNA Methylation in Bovine Cells by Knocking Down DNA Methyltransferase-1 with RNA Interference 

    E-Print Network [OSTI]

    Stroud, Todd

    2010-01-20T23:59:59.000Z

    Embryos derived by somatic cell nuclear transfer (SCNT) produce few pregnancies that result in a live, healthy offspring. This has largely been attributed to the aberrant reprogramming of the somatic cell DNA used for ...

  7. DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics

    E-Print Network [OSTI]

    Nguyen, Gael; Howorka, Stefan; Siwy, Zuzanna S.

    2011-01-01T23:59:59.000Z

    Kathawalla et al. 1989; Heng et al. 2005; Keyser et al.due to the electric ?eld (Heng et al. 2005; Randall et al.DNA analysis. Nanomedicine Heng JB, Aksimentiev A, Ho C,

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

    E-Print Network [OSTI]

    Lingaraju, Gondichatnahalli M.

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

  9. DNA ruler : enhancing nanopore sizing resolution by multiple measurements on the same DNA molecule

    E-Print Network [OSTI]

    Sen, Yi-Heng

    2012-01-01T23:59:59.000Z

    Nanopores are versatile sensors for label-free detection of single molecules and particles that have attracted attention for applications such as DNA sequencing and nanoparticle analysis. Detection of single molecules or ...

  10. Updating SRM 2391c: PCR-Based DNA Profiling Standard

    E-Print Network [OSTI]

    profiling SRM 2391 SRM 2391a SRM 2391b SRM 2391c SRM 2390 DNA profiling 2391 series PCR-based DNA profiling 40 NMDEPARTMENT OF PUBLIC SAFETY 10 DNASI 40 SEROLOGICAL RESEARCH INSTITUTE 11 CHARLOTTE- DNA CRIME LAB 50 SOUTH CAROLINA LAW ENFORCEMENT 20 ILLUMINA INC CARROLL PARK 50 UWA INTERNATIONAL

  11. Design and Characterization of Programmable DNA Nanotubes Supporting Information

    E-Print Network [OSTI]

    Fygenson, Deborah Kuchnir

    . DNA sample preparation: Lyophilized HPLC- or PAGE- purified DNA oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA), resuspended in water, quanti- tated by UV absorbance at 260 nm immersion and 40X/0.75 NA air objectives. Blue light was filtered from a mer- cury arc lamp thro

  12. A Simple and Fast DNA Compressor Giovanni Manzini

    E-Print Network [OSTI]

    Manzini, Giovanni

    A Simple and Fast DNA Compressor Giovanni Manzini Marcella Rastero February 17, 2004 Abstract. For this reason most DNA compressors work by searching and encoding approximate repeats. We depart from to the best DNA compressors. Another important feature of our algorithm is its small space occupancy which

  13. DNA overwinds when stretched , Zev Bryant2,4

    E-Print Network [OSTI]

    Gore, Jeff

    DNA overwinds when stretched Jeff Gore1 , Zev Bryant2,4 , Marcelo No¨llmann2 , Mai U. Le2 , Nicholas R. Cozzarelli2 & Carlos Bustamante1­4 DNA is often modelled as an isotropic rod1­4 , but its coupling between twisting and stretch- ing degrees of freedom. Simple physical intuition predicts that DNA

  14. The DNA binding activity of p53 displays reactiondiffusion kinetics

    E-Print Network [OSTI]

    Hinow, Peter

    The DNA binding activity of p53 displays reaction­diffusion kinetics 26th Southeastern 37240 The DNA binding activity of p53 displays reaction­diffusion kinetics ­ p. 1/2 #12;Collaborators, Vanderbilt University · Emmanuele DiBenedetto, PhD, Department of Mathematics, Vanderbilt University The DNA

  15. DNA methylation and the analysis of CpG Islands

    E-Print Network [OSTI]

    Czygrinow, Andrzej

    DNA methylation and the analysis of CpG Islands in genomes M. F. Wojciechowski MAT 351 25 March 2005 #12;#12;Nucleotides #12;Base pairing * * #12;DNA methylation In mammalian genomes, methylation residues represent a target for covalent modification of DNA Cytosine is one of two bases found commonly

  16. DNA Nanotechnology DOI: 10.1002/anie.201206389

    E-Print Network [OSTI]

    Hone, James

    DNA Nanotechnology DOI: 10.1002/anie.201206389 Assembly of Heterogeneous Functional Nanomaterials on DNA Origami Scaffolds** Risheng Wang,* Colin Nuckolls, and Shalom J. Wind* Hybrid nanomaterial systems;[1] selective growth;[4,9] and DNA-mediated assem- bly,[3,8] including the formation of 3D

  17. DNA IN THE UK By Erica Van Coverden

    E-Print Network [OSTI]

    Goodwin, Kelly D.

    DNA IN THE UK By Erica Van Coverden Dr. Kelly Goodwin, a microbiologist at AOML, finished up. Those proteins then would be sequenced and the amino acid sequence would be used to backtrack to the DNA sequence that codes for that protein. In another approach, total DNA was extracted, digested

  18. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

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

    2006-10-17T23:59:59.000Z

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

  19. Reaction Temperature Constraints in DNA Computing Russell Deaton

    E-Print Network [OSTI]

    Deaton, Russell J.

    Reaction Temperature Constraints in DNA Computing Russell Deaton The Department of Electrical the thermodynamics of DNA melt- ing, a technique is proposed to choose a re- action temperature for the DNA computa the melting temperature, Tm. The melting temperature is determined from curves of UV absorbance versus

  20. Recurrence time statistics: Versatile tools for genomic DNA sequence analysis

    E-Print Network [OSTI]

    Gao, Jianbo

    Recurrence time statistics: Versatile tools for genomic DNA sequence analysis Yinhe Cao1, Wen, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop from DNA sequences. One of the more important structures in a DNA se- quence is repeat-related. Often

  1. Correct and incorrect nucleotide incorporation pathways in DNA polymerase b

    E-Print Network [OSTI]

    Schlick, Tamar

    Correct and incorrect nucleotide incorporation pathways in DNA polymerase b Ravi Radhakrishnan a nucleotide incorporations in the DNA by using a novel protocol involving energy minimizations, dynamics simu- sive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. A large

  2. Structure of the SSB?DNA polymerase III interface and its role in DNA replication

    SciTech Connect (OSTI)

    Marceau, Aimee H.; Bahng, Soon; Massoni, Shawn C.; George, Nicholas P.; Sandler, Steven J.; Marians, Kenneth J.; Keck, James L. (MSKCC); (UMASS, Amherst); (UW-MED)

    2012-05-22T23:59:59.000Z

    Interactions between single-stranded DNA-binding proteins (SSBs) and the DNA replication machinery are found in all organisms, but the roles of these contacts remain poorly defined. In Escherichia coli, SSB's association with the {chi} subunit of the DNA polymerase III holoenzyme has been proposed to confer stability to the replisome and to aid delivery of primers to the lagging-strand DNA polymerase. Here, the SSB-binding site on {chi} is identified crystallographically and biochemical and cellular studies delineate the consequences of destabilizing the {chi}/SSB interface. An essential role for the {chi}/SSB interaction in lagging-strand primer utilization is not supported. However, sequence changes in {chi} that block complex formation with SSB lead to salt-dependent uncoupling of leading- and lagging-strand DNA synthesis and to a surprising obstruction of the leading-strand DNA polymerase in vitro, pointing to roles for the {chi}/SSB complex in replisome establishment and maintenance. Destabilization of the {chi}/SSB complex in vivo produces cells with temperature-dependent cell cycle defects that appear to arise from replisome instability.

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

    E-Print Network [OSTI]

    Peyrard, Michel

    2015-01-01T23:59:59.000Z

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

  4. Mechanical seal assembly

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

    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.

  5. Mechanical seal assembly

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Doering, Tamara

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

  7. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11T23:59:59.000Z

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

  8. Stepped electrophoresis for movement and concentration of DNA

    DOE Patents [OSTI]

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

    2005-03-15T23:59:59.000Z

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

  9. T4 DNA condensation in water-alcohol media

    E-Print Network [OSTI]

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

    2011-07-21T23:59:59.000Z

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

  10. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. (Argonne National Lab., IL (United States) Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology); Vaughan, A.T.M. (Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy)

    1993-01-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  11. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. [Argonne National Lab., IL (United States)]|[Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology; Vaughan, A.T.M. [Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy

    1993-03-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  12. DNA end resection by Dna2Sgs1RPA and its stimulation by Top3Rmi1 and Mre11Rad50Xrs2

    E-Print Network [OSTI]

    Kowalczykowski, Stephen C.

    LETTERS DNA end resection by Dna2­Sgs1­RPA and its stimulation by Top3­Rmi1 and Mre11­Rad50­Xrs2. Campbell3 & Stephen C. Kowalczykowski1,2 The repair of DNA double-strand breaks (DSBs) by homologous to generate a 39-single- stranded DNA (ssDNA) overhang, which becomes a substrate forthe

  13. Long DNA molecule as a pseudoscalar liquid crystal

    E-Print Network [OSTI]

    K. G. Petrosyan; Chin-Kun Hu

    2009-05-13T23:59:59.000Z

    We show that a long DNA molecule can form a novel condensed phase of matter, the pseudoscalar liquid crystal, that consists of aperiodically ordered DNA fragments in right-handed B and left-handed Z forms. We discuss the possibility of transformation of B-DNA into Z-DNA and vice versa via first-order phase transitions as well as transformations from the phase with zero total chirality into pure B- or Z-DNA samples through second-order phase transitions. The presented minimalistic phenomenological model describes the pseudoscalar liquid crystal phase of DNA and the phase transition phenomena. We point out to a possibility that a pseudoscalar liquid nano-crystal can be assembled via DNA-programming.

  14. Hole interactions with molecular vibrations on DNA

    E-Print Network [OSTI]

    A. Omerzu; M. Licer; T. Mertelj; V. V. Kabanov; D. Mihailovic

    2004-05-13T23:59:59.000Z

    We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms, clearly indicating the presence of localization. However, from a quantitative model analysis of the frequency shifts of vibrational modes caused by the PE holes, we find the holevibrational coupling constant to be relatively small, 0.2. This interaction leads to a change in the conformational energy of 0.015 eV, which is too small to cause selftrapping at room temperature. We conclude that, at least in the dry (A) form, DNA is best understood in terms of a double chain of coupled quantum dots arising from the pseudo-random chain sequence of base pairs, in which Anderson localization prevents the formation of a metallic state.

  15. Conditions for positioning of nucleosomes on DNA

    E-Print Network [OSTI]

    Sheinman, Michael

    2015-01-01T23:59:59.000Z

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

  16. Fast DNA Sequencing via Transverse Electronic Transport

    E-Print Network [OSTI]

    Johan Lagerqvist; Michael Zwolak; Massimiliano Di Ventra

    2006-03-01T23:59:59.000Z

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

  17. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Lin, Xi

    operating in microfluidic environment, which can dynamically diverge, collimate and focus surface plasmons in 2012, with a joint appointment in the Department of Mechanical & Industrial Engineering

  18. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Research Center. Currently he is an Assistant Prof. in the Aerospace and Ocean Engineering DepartmentMechanical engineering Department Seminar Cornel Sultan Virginia Tech Design for Control

  19. Determining orientation and direction of DNA sequences

    DOE Patents [OSTI]

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

    2000-01-01T23:59:59.000Z

    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.

  20. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

    SciTech Connect (OSTI)

    Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-05-17T23:59:59.000Z

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  1. MECHANICAL ENGINEERING Program of Study

    E-Print Network [OSTI]

    Thomas, Andrew

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

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

    E-Print Network [OSTI]

    Li, Deyu

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

  3. Yale University Mechanical Engineering

    E-Print Network [OSTI]

    Dollar, Aaron M.

    ) ­ #92474A029 (4x) #12;OpenHand Yale University Mechanical Engineering 3D Printer Requirements · Current · Majority of parts are designed to not require support material · Authors do not know how well alternate 3D printers will produce adequate components #12;OpenHand Yale University Mechanical Engineering Finger

  4. Respiratory Mechanisms of Support

    E-Print Network [OSTI]

    Kay, Mark A.

    Respiratory Mechanisms of Support Nasal Cannula Hi Flow Nasal Cannula CPAP Continuous positive the respiratory system is working to compensate for a metabolic issue so as to normalize the blood pH. HCO3 - 22 uses PIP Mechanical Ventilation: Volume vs. Pressure: Volume Control Pressure Control Cycle Volume Time

  5. Department of Mechanical Engineering

    E-Print Network [OSTI]

    Srivastava, Kumar Vaibhav

    Explore and understand applicable science Create new materials #12;Indian Railways #12;Wheel Impact Load automated system for On-Line estimation of Wheel Impact Loads and detection of Wheel Flats of running trains Detection System (WILD) #12;Derailment Mechanism Laboratory Tests Lab Brake Mechanism Placement of Sensors

  6. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Lin, Xi

    Mechanical engineering Department Seminar Junjie Niu Postdoctoral Associate MIT Engineering Nano nanomaterials in applications of energy storage, biomedicine and chemo-mechanics. In 2007, Dr.Niu received young-structured Materials for Energy Storage 11:00 AM Friday, 14 February 2014 Room 245, 110 Cummington Mall Refreshments

  7. Mechanical and Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical and Aerospace Engineering Abstract Solid materials used in energy conversion and storage Department of Civil & Environmental Engineering, Department of Mechanical Engineering, Northwestern University April 6, 2012 at 2:00pm in SCOB 252 School for Engineering of Matter, Transport & Energy #12;

  8. Mechanical & Aerospace Engineering

    E-Print Network [OSTI]

    Mechanical & Aerospace Engineering The development of high-energy storage devices has been one energy capacity over 500 cycles. Teng Ma received his BS degree in Thermal and Power Engineering from Xi and Technology of China in 2009. He is currently a Ph.D. candidate in Mechanical Engineering at School

  9. periodica polytechnica Mechanical Engineering

    E-Print Network [OSTI]

    Gubicza, Jenő

    structure. Keywords aluminium alloys · nanostructured materials · mechanical characterization · X-thickness texture gradient produced by the different routes of DSR have been studied in Al 1050 aluminium alloy [15 routes on the microstructure and mechanical properties of Al 7075 aluminium alloy. Microstructure

  10. Mechanical code comparator

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  11. 07SCHOOL OF MECHANICAL ENGINEERING

    E-Print Network [OSTI]

    Dimitrova, Vania

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

  12. Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA

    SciTech Connect (OSTI)

    Xia, Shuangluo; Christian, Thomas D.; Wang, Jimin; Konigsberg, William H. (Yale)

    2012-09-17T23:59:59.000Z

    Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10{sup 2}-10{sup 3}-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10{sup 2}-10{sup 3}-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n-2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.

  13. How effective is graphene nanopore geometry on DNA sequencing?

    E-Print Network [OSTI]

    Satarifard, Vahid; Ejtehadi, Mohammad Reza

    2015-01-01T23:59:59.000Z

    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.

  14. Self-assembly of DNA-functionalized Colloids

    E-Print Network [OSTI]

    Panagiotis E. Theodorakis; Nikolaos G. Fytas; Gerhard Kahl; Christoph Dellago

    2015-03-18T23:59:59.000Z

    Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure. Depending on the geometry and the size of the particles, the grafting density of the ssDNA chains, and the length and choice of DNA sequences, a number of different crystalline structures can be fabricated. However, understanding how these factors contribute synergistically to the self-assembly process of DNA-functionalized nano- or micro-sized particles remains an intensive field of research. Moreover, the fabrication of long-range structures due to kinetic bottlenecks in the self-assembly are additional challenges. Here, we discuss the most recent advances from theory and experiment with particular focus put on recent simulation studies.

  15. Introduction The study of DNA repair mechanisms has been aided by the

    E-Print Network [OSTI]

    in the fission yeast Schizosaccharomyces pombe requires microtubule-dependent oscillatory nuclear movements. These events were initially thought to result from gene conversion (GC) accompanied by crossover (Jager and Philippsen, 1989). However, other studies of direct repeat recombination have shown that deletions commonly

  16. Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path

    E-Print Network [OSTI]

    Schlick, Tamar

    of Chemistry and Courant Institute of Mathematical Sciences, 251 Mercer Street, New York University, New York and energetic details of the con- formational change that precedes the chemical reaction of nucle- otide

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our InstagramStructure of All-Polymer Solar Cells Impedes

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solid ... Strengthening aStructure of All-Polymer Solar

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solid ... Strengthening aStructure of All-Polymer SolarStructure

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

    SciTech Connect (OSTI)

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

    2013-05-14T23:59:59.000Z

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

  1. Electronic door locking mechanism

    DOE Patents [OSTI]

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

    1997-10-21T23:59:59.000Z

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

  2. Mechanism of Gravity Impulse

    E-Print Network [OSTI]

    Ning Wu

    2005-10-01T23:59:59.000Z

    It is well-known that energy-momentum is the source of gravitational field. For a long time, it is generally believed that only stars with huge masses can generate strong gravitational field. Based on the unified theory of gravitational interactions and electromagnetic interactions, a new mechanism of the generation of gravitational field is studied. According to this mechanism, in some special conditions, electromagnetic energy can be directly converted into gravitational energy, and strong gravitational field can be generated without massive stars. Gravity impulse found in experiments is generated by this mechanism.

  3. Rotary mechanical latch

    DOE Patents [OSTI]

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

    2012-11-13T23:59:59.000Z

    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.

  4. Isolation of Discrete Nanoparticle-DNA Conjugates for Plasmonic Applications

    SciTech Connect (OSTI)

    Alivisatos, Paul; Claridge, Shelley A.; Liang, Huiyang W.; Basu, Sourav Roger; Frechet, Jean M.J.; Alivisatos, A. Paul

    2008-04-11T23:59:59.000Z

    Discrete DNA-gold nanoparticle conjugates with DNA lengths as short as 15 bases for both 5 nm and 20 nm gold particles have been purified by anion-exchange HPLC. Conjugates comprising short DNA (<40 bases) and large gold particles (>_ 20 nm) are difficult to purify by other means, and are potential substrates for plasmon coupling experiments. Conjugate purity is demonstrated by hybridizing complementary conjugates to form discrete structures, which are visualized by TEM.

  5. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

    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.

  6. DNA Methylation as a Biomarker for Preeclampsia

    SciTech Connect (OSTI)

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

    2014-10-01T23:59:59.000Z

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

  7. Ergonomics in DNA Sequencing: Standing Down to Ergonomics

    E-Print Network [OSTI]

    Naca, Christine

    2009-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2014-09-01T23:59:59.000Z

    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.

  9. Dynamics of extracellular DNA in the marine environment

    SciTech Connect (OSTI)

    Paul, J.H.; Jeffrey, W.H.; DeFlaun, M.F.

    1987-01-01T23:59:59.000Z

    The production and turnover of dissolved DNA in subtropical estuarine and oligotrophic oceanic environments were investigated. Actively growing heterotrophic bacterioplankton (i.e., those capable of (/sup 3/H)thymidine incorporation) were found to produce dissolved DNA, presumably through the processes of death and lysis, grazing by bacteriovores, and excretion. Production of dissolved DNA as determined by (/sup 3/H)thymidine incorporation was less than or equal to4% of the ambient dissolved DNA concentration per day. In turnover studies, the addition of (/sup 3/H)DNA (Escherichia coli chromosomal) to seawater resulted in rapid hydrolysis and uptake of radioactivity by microbial populations. DNA was hydrolyzed by both cell-associated and extracellular nucleases, in both estuarine and offshore environments. Kinetic analysis performed for a eutrophic estuary indicated a turnover time for dissolved DNA as short as 6.5 h. Microautoradiographic studies of bacterial populations in Tampa Bay indicated that filamentous and attached bacteria took up most of the radioactivity from (/sup 3/H)DNA. Dissolved DNA is therefore a dynamic component of the dissolved organic matter in the marine environment, and bacterioplankton play a key role in the cycling of this material.

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

    SciTech Connect (OSTI)

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

    2014-06-09T23:59:59.000Z

    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.

  11. assemble linear dna: Topics by E-print Network

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

    compute? In his early studies of reversible computation, Bennett imagined an enzymatic Turing Machine which modified a hetero-polymer (such as DNA) to perform computation with...

  12. assembly regulate dna: Topics by E-print Network

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

    compute? In his early studies of reversible computation, Bennett imagined an enzymatic Turing Machine which modified a hetero-polymer (such as DNA) to perform computation with...

  13. automated dna extraction: Topics by E-print Network

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

    and Crop Cleaning PCR Products. . Labeling Cleaned... 5 56 57 . . . 57 CHAPTER IV AUTOMATION POTENTIAL . . . . . . . 59 Introduction . . Collecting Field Data . DNA Extraction....

  14. automated dna mutation: Topics by E-print Network

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

    and Crop Cleaning PCR Products. . Labeling Cleaned... 5 56 57 . . . 57 CHAPTER IV AUTOMATION POTENTIAL . . . . . . . 59 Introduction . . Collecting Field Data . DNA Extraction....

  15. Genetic Transformation and Mutagenesis Via Single-Stranded DNA...

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

    Genetic Transformation and Mutagenesis Via Single-Stranded DNA in the Unicellular, Diazotrophic Cyanobacteria of the Genus Genetic Transformation and Mutagenesis Via...

  16. ancient dna analysis: Topics by E-print Network

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

    model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic...

  17. Gel Electrophoresis of Gold-DNA Nano-Conjugates

    E-Print Network [OSTI]

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

    2008-01-01T23:59:59.000Z

    R. A. Sperling 1,# , A. P. Alivisatos 2 , W. J. Parak 1,2,*materials {Mirkin, 1996 #3440; Alivisatos, 1996 #3342}. DNA-

  18. ancient human dna: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  19. ancient dna studies: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  20. Helical Disruptions in Small Loops of DNA

    E-Print Network [OSTI]

    Zoli, Marco

    2015-01-01T23:59:59.000Z

    The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles with $100$ base pairs and appear as a strategy to soften the stress due to the bending and torsion of the helix.

  1. DNA analysis conference in Santa Fe

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract Management Fermi SitePART I SECTION ADMSE ElectronDNA analysis

  2. A DNA tweezer-actuated enzyme nanoreactor

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch >InternshipDepartment ofAugustDecember8threbuildA Comprehensive LookA DNA

  3. Intriguing DNA Editor Has a Structural Trigger

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville PowerCherries 82981-1cnHigh SchoolIn OtherEnergy International Fuel7RadiativeIntriguing DNA

  4. Intriguing DNA Editor Has a Structural Trigger

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville PowerCherries 82981-1cnHigh SchoolIn OtherEnergy InternationalIntriguing DNA Editor Has a

  5. A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota

    SciTech Connect (OSTI)

    Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L. (Cornell); (Vanderbilt); (NCI); (Arkansas)

    2012-10-25T23:59:59.000Z

    Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol{iota}) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol{iota} through use of the fixed-conformation nucleotide North-methanocarba-2{prime}-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol{iota} in complex with DNA containing a template 2{prime}-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol{iota} inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol{iota}. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol{iota} by preventing the Hoogsteen base-pairing mode normally observed for hpol{iota}-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

  6. Ultralight, ultrastiff mechanical metamaterials

    E-Print Network [OSTI]

    Zheng, Xiaoyu

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

  7. Mechanical Compression Heat Pumps 

    E-Print Network [OSTI]

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

    1986-01-01T23:59:59.000Z

    to develop, design and test compressors built to meet the needs of the mechanically demanding industrial heat pump applications which often require high compression ratios and temperatures in excess of 200 degrees F. This paper will review the theoretical...

  8. Renewable Auction Mechanism (RAM)

    Broader source: Energy.gov [DOE]

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

  9. Modeling DNA Interactions in Nucleosome Particles (A Computational Study of DNA Interactions in Nucleosome Particles)

    E-Print Network [OSTI]

    Kansas, University of

    Technology Center, University of Kansas, Lawrence, KS 66045. 2006 Annual Kansas City Area Life Sciences characterize global motions of the histone-DNA complex with respect to energy fluctuations in an assessment of energy differences resulting from the nucleotide substitutions will be presented in the context

  10. Regulation of DNA Repair Fidelity by Molecular Checkpoints: "Gates" in DNA Polymerase 's Substrate Selection

    E-Print Network [OSTI]

    Schlick, Tamar

    Schlick*, Department of Chemistry and Courant Institute of Mathematical Sciences, New York UniVersity, New York, New York 10012, and Laboratory of Structural Biology, National Institute of EnVironmental Health enzymology data. Focusing on DNA polymerase (pol ), we present an emerging view of the geometric, energetic

  11. DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents and Investigations

    E-Print Network [OSTI]

    Ernest, Holly

    1 DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents concolor, bobcat, forensic, genetics, DNA techniques, noninvasive sampling, fecal DNA, prey swab DNA ABSTRACT Using three case studies, we demonstrated the utility of techniques to analyze DNA from trace

  12. Jar mechanism accelerator

    SciTech Connect (OSTI)

    Anderson, E.A.; Webb, D.D.

    1989-07-11T23:59:59.000Z

    This patent describes an accelerator for use with a jar mechanism in a well pipe string to enhance the jarring impact delivered to a stuck object wherein the jar mechanism includes inner and outer members for connection, respectively, between the well pipe string the stuck object. The jar mechanism members are constructed to (1) restrict relative longitudinal movement therebetween to build up energy in the well pipe string and accelerator and then (2) to release the jar mechanism members for unrestrained, free relative longitudinal movement therebetween to engage jarring surfaces on the jar mechanism members for delivering a jarring impact to the stuck object. The accelerator includes: inner and outer telescopically connected members relatively movable longitudinally to accumulate energy in the accelerator; the inner and outer accelerator members each having means for connecting the accelerator in the well pipe string; means associated with the inner and outer members for initially accomodating a predetermined minimum length of unrestrained, free relative longitudinal movement between the inner and outer accelerator members.

  13. Functional Characterization of Kansl2 and Its Role in Mitochondrial DNA Repair and Maintenance

    E-Print Network [OSTI]

    Liau, Wei-Siang

    2012-01-01T23:59:59.000Z

    understanding of the maintenance and repair of the mtDNA,A is necessary for mtDNA maintenance and embryogenesis in1997). Mitochondrial DNA maintenance in vertebrates. Annu

  14. Development of new tools for the production of plasmid DNA biopharmaceuticals

    E-Print Network [OSTI]

    Bower, Diana M. (Diana Morgan)

    2012-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

    Zamudio, Kelly R.

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

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

    SciTech Connect (OSTI)

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

    2009-07-21T23:59:59.000Z

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

  17. Superconducting Nanowires Fabricated Using DNA and Nanotubes as Molecular Templates

    E-Print Network [OSTI]

    Goldbart, Paul M.

    functions of DNA have been demonstrated in recent experiments in which a linear arrangement of nanoparticles acid molecules or suspended single-wall carbon nanotubes as templates for making superconducting Introduction Deoxyribonucleic acid (DNA) contains genetic instructions used in the develop- ment

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

    E-Print Network [OSTI]

    Perkins, Richard A.

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

  19. Conserved and Unconventional Responses to DNA Damage in Tetrahymena 

    E-Print Network [OSTI]

    Sandoval Oporto, Pamela

    2012-07-16T23:59:59.000Z

    characterization of the response to genotoxic agents showed that Tetrahymena is able to activate a G1/S and intra-S phase DNA damage response. The results presented here suggest that a caffeine-dependent checkpoint activator protein modulates the response to DNA...

  20. Yeast Genomic Library Genomic DNA Sau3AI partial digestion

    E-Print Network [OSTI]

    Odorizzi, Greg

    Yeast Genomic Library Concept: Genomic DNA ­ Sau3AI partial digestion Vector DNA ­ BamHI full digestion partial Ligate and transform above products Vector Information: · use centromeric plasmid to avoid of the mcs Preparing Vector: 1) digest 3-4ug of library vector with BamHI for 2-4hrs in a total volume of 20

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

    E-Print Network [OSTI]

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

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

    SciTech Connect (OSTI)

    Quirk, W.A.

    1993-04-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Straight, Aaron

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

  4. cDNA encoding a polypeptide including a hevein sequence

    DOE Patents [OSTI]

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

    1993-02-16T23:59:59.000Z

    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.

  5. Charge Transfer Across the Nanocrystalline-DNA Interface: Probing

    E-Print Network [OSTI]

    Scherer, Norbert F.

    matched DNA. The initial charge separation sequence in these hybrid bioinor- ganic nanocomposites, Illinois 60637 Received February 26, 2004; Revised Manuscript Received March 26, 2004 ABSTRACT Hybrid nanocomposites that electronically link TiO2 nanoparticles to DNA oligonucleotides were developed. The linking

  6. Conformational Manipulation of DNA in Nanochannels Using Hydrodynamics

    E-Print Network [OSTI]

    Qihao He; Hubert Ranchon; Pascal Carrivain; Yannick Viero; Joris Lacroix; Charline Blatché; Emmanuelle Daran; Jean-Marc Victor; Aurélien Bancaud

    2014-09-01T23:59:59.000Z

    The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics, although the physics of soft matter in nanoscale flows has raised considerable interest over the past decade. In this report the migration of DNA is studied in nanochannels of lateral dimension spanning 100 to 500 nm using both actuation principles. We show that the relaxation kinetics are 3-fold slowed down and the extension increases up to 3-fold using hydrodynamics. We propose a model to account for the onset in elongation with the flow, which assumes that DNA response is determined by the shear-driven lift forces mediated by the proximity of the channels' walls. Overall, we suggest that hydrodynamic actuation allows for an improved manipulation of DNA in nanochannels.

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

    SciTech Connect (OSTI)

    Badji, Riad [LPMTM-CNRS- Universite Paris 13, 99, av. J.B. Clement, 93430 Villetaneuse (France)], E-mail: riadbadji1@yahoo.fr; Bouabdallah, Mabrouk [Ecole Nationale Polytechnique, 10, Avenue Hassan Badi, BP 182, El Harrach (Algeria); Bacroix, Brigitte; Kahloun, Charlie [LPMTM-CNRS- Universite Paris 13, 99, av. J.B. Clement, 93430 Villetaneuse (France); Belkessa, Brahim; Maza, Halim [Welding and NDT research Centre, B.P 64, Cheraga (Algeria)

    2008-04-15T23:59:59.000Z

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

  8. The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP) AND DNA BINDING TO NTP

    E-Print Network [OSTI]

    Richardson, Charles C.

    The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP also creates nucleotide-binding sites located at the interfaces of the sub- units. DNA binding of a bound nucleoside 5 -triphosphate. However, in the absence of a nucleotide, Glu-343 changes orientation

  9. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied...

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

    8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with...

  10. Folding of a DNA Hairpin Loop Structure in Explicit SolventUsingRepli...

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

    of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations. Folding of a DNA Hairpin Loop Structure in Explicit Solvent...

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

    DOE Patents [OSTI]

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

    1999-02-16T23:59:59.000Z

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

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

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

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

    2015-03-23T23:59:59.000Z

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

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

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

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

    2015-03-23T23:59:59.000Z

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

  14. Information weights of nucleotides in DNA sequences

    E-Print Network [OSTI]

    M. R. Dudek; S. Cebrat; M. Kowalczuk; P. Mackiewicz; A. Nowicka; D. Mackiewicz; M. Dudkiewicz

    2003-01-21T23:59:59.000Z

    The coding sequence in DNA molecule is considered as a message to be transferred to receiver, the proteins, through a noisy information channel and each nucleotide is assigned a respective information weight. With the help of the nucleotide substitution matrix we estimated the lower bound of the amount of information carried out by nucleotides which is not subject of mutations. We used the calculated weights to reconstruct k-oligomers of genes from the Borrelia burgdorferi genome. We showed, that to this aim there is sufficient a simple rule, that the number of bits of the carried information cannot exceed some threshold value. The method introduced by us is general and applies to every genome.

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

    E-Print Network [OSTI]

    Utrecht, Universiteit

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

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

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    ice) for 20 min. 7. Spin tubes at 13K rpm for 20 min in a Sorval centrifuge with the SA-600 rotor (~25 at 12K rpm for 15 min in a Sorval centrifuge with the SA-600 rotor (~20,000 x g). 11. Gently pour off. The most efficient number of samples for Dellaporta DNA Isolation is 12 each time due to centrifuge rotor

  17. Hybridization and Selective Release of DNA Microarrays

    SciTech Connect (OSTI)

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

    2011-11-29T23:59:59.000Z

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

  18. Mechanical & Industrial Engineering

    E-Print Network [OSTI]

    Mountziaris, T. J.

    on the PI's current research on energy harvesting nanowires, Li-ion batteries, and PEM fuel cells. In energy nanowires from both modeling and in-situ quantitative microscopy perspectives. In Li-ion battery work, we-ion intercalation into nanowires. The last, electro-mechanical characterization of degraded and fresh electrode

  19. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Mechanical engineering Department Seminar Wynter J. Duncanson Department of Aerospace and Ocean Engineering Virginia Tech Smart' Bubbles for Acoustic Contrast in Oil Reservoirs 11:00 AM Friday, 19 April engineering from Boston University. Her doctoral research was devoted to designing surface architectures

  20. Mechanical engineering Department Seminar

    E-Print Network [OSTI]

    Lin, Xi

    -electronics, soft robotics, and bio-integrated systems. Host: Basu #12;, Urbana-Champaign Mechanical Design and Fabrication Techniques for Bio-Electronic Systems 11:00 AM Friday, 7 February 2014 Room 245, 110 Cummington Mall Refreshments served at 10:45 AM Biological systems