Sample records for dna double strand

  1. 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 ...

  2. Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid "Invasion"

    SciTech Connect (OSTI)

    Stadler, A.L.; van der Lelie, D.; Sun, D.; Maye, M. M.; Gang, O.

    2011-04-01T23:59:59.000Z

    We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

  3. Induction of linear tracks of DNA double-strand breaks by -particle irradiation of

    E-Print Network [OSTI]

    Cai, Long

    Induction of linear tracks of DNA double- strand breaks by -particle irradiation of cells Jan Stap1,4, Przemek M Krawczyk1,4, Carel H Van Oven1, Gerrit W Barendsen2, Jeroen Essers3, Roland Kanaar3 & Jacob describe a procedure for induction of easily recognizable linear arrays of DSBs in nuclei of adherent

  4. A MICROBEAM STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS

    E-Print Network [OSTI]

    stained with different dyes. Directly irradiated cells have exhibited the expected early and linear dose by assessing DNA double-strand break (DSB) formation in situ with the rapid and sensitive c-H2AX focus formation assay. Utilising the Columbia University single-cell microbeam system to deliver 2 or 20

  5. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23T23:59:59.000Z

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  6. 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.

  7. Sequence-Enabled Reassembly of -Lactamase (SEER-LAC): A Sensitive Method for the Detection of Double-Stranded DNA

    E-Print Network [OSTI]

    Ghosh, Indraneel

    Sequence-Enabled Reassembly of -Lactamase (SEER-LAC): A Sensitive Method for the Detection the development of a new methodology for the detection of specific double- stranded DNA sequences. We previously of a predefined DNA sequence. This system, designated sequence-enabled reassembly (SEER), was demonstrated

  8. 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 ...

  9. 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.

  10. 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.

  11. Probability of double-strand breaks in genome-sized DNA by {gamma}-ray decreases markedly as the DNA concentration increases

    SciTech Connect (OSTI)

    Shimobayashi, Shunsuke F. [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Iwaki, Takafumi [Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103 (Japan); Mori, Toshiaki [Radiation Research Center, Osaka Prefecture University, Sakai 599-8570 (Japan); Yoshikawa, Kenichi [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394 (Japan)

    2013-05-07T23:59:59.000Z

    By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by {gamma}-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P{sub 1}, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.

  12. 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.

  13. Intense photoluminescence from dried double-stranded DNA and single-walled carbon nanotube hybrid

    SciTech Connect (OSTI)

    Ito, M.; Kobayashi, T.; Ito, Y.; Hayashida, T.; Nii, D.; Umemura, K.; Homma, Y. [Department of Physics, Tokyo University of Science, Tokyo 162-8601 (Japan)

    2014-01-27T23:59:59.000Z

    Semiconducting single-walled carbon nanotubes (SWNTs) show near-infrared photoluminescence (PL) when they are individually isolated. This was an obstacle to use photonic properties of SWNTs on a solid surface. We show that SWNTs wrapped with DNA maintain intense PL under the dry conditions. SWNTs are well isolated individually by DNA even when the DNA-SWNT hybrids are agglomerated. This finding opens up application of SWNTs to photonic devices.

  14. Comment on "Monomer Dynamics in Double- and Single-Stranded DNA Polymers"

    E-Print Network [OSTI]

    J. Tothova; B. Brutovsky; V. Lisy

    2005-09-15T23:59:59.000Z

    It is discussed that the kinetics observed by Shusterman et al. [Phys. Rev. Lett. 92, 048303] for long dsDNA is not the Rouse one and, in fact, the macromolecule behaves (approximately) as the Zimm polymer.

  15. auger electron-induced double-strand: 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...

  16. Homologous recombination contributes to the repair of DNA double-strand breaks induced by high-energy iron ions

    SciTech Connect (OSTI)

    Zafar, Faria; Seidler, Sara B.; Kronenberg, Amy; Schild, David; Wiese, Claudia

    2010-06-29T23:59:59.000Z

    To test the contribution of homologous recombinational repair (HRR) in repairing DNA damaged sites induced by high-energy iron ions, we used: (1) HRR-deficient rodent cells carrying a deletion in the RAD51D gene and (2) syngeneic human cells impaired for HRR by RAD51D or RAD51 knockdown using RNA interference. We show that in response to iron ions, HRR contributes to cell survival in rodent cells, and that HRR-deficiency abrogates RAD51 foci formation. Complementation of the HRR defect by human RAD51D rescues both enhanced cytotoxicity and RAD51 foci formation. For human cells irradiated with iron ions, cell survival is decreased, and, in p53 mutant cells, the levels of mutagenesis are increased when HRR is impaired. Human cells synchronized in S phase exhibit more pronounced resistance to iron ions as compared with cells in G1 phase, and this increase in radioresistance is diminished by RAD51 knockdown. These results implicate a role for RAD51-mediated DNA repair (i.e. HRR) in removing a fraction of clustered lesions induced by charged particle irradiation. Our results are the first to directly show the requirement for an intact HRR pathway in human cells in ensuring DNA repair and cell survival in response to high-energy high LET radiation.

  17. The Impact of Individual In Vivo Repair of DNA Double-Strand Breaks on Oral Mucositis in Adjuvant Radiotherapy of Head-and-Neck Cancer

    SciTech Connect (OSTI)

    Fleckenstein, Jochen, E-mail: rajfle@uks.eu [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany); Kuehne, Martin; Seegmueller, Katharina; Derschang, Sarah; Melchior, Patrick [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany); Graeber, Stefan [Institute for Medical Biometry, Epidemiology und Medical Informatics (IMBEI), Saarland University Medical School, Homburg (Germany); Fricke, Andreas; Ruebe, Claudia E.; Ruebe, Christian [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany)

    2011-12-01T23:59:59.000Z

    Purpose: To evaluate the impact of individual in vivo DNA double-strand break (DSB) repair capacity on the incidence of severe oral mucositis in patients with head-and-neck cancer undergoing adjuvant radiotherapy (RT) or radiochemotherapy (RCT). Patients and Methods: Thirty-one patients with resected head-and-neck cancer undergoing adjuvant RT or RCT were examined. Patients underwent RT of the primary tumor site and locoregional lymph nodes with a total dose of 60-66 Gy (single dose 2 Gy, five fractions per week). Chemotherapy consisted of two cycles of cisplatin and 5-fluorouracil. To assess DSB repair, {gamma}-H2AX foci in blood lymphocytes were quantified before and 0.5 h, 2.5 h, 5 h, and 24 h after in vivo radiation exposure (the first fraction of RT). World Health Organization scores for oral mucositis were documented weekly and correlated with DSB repair. Results: Sixteen patients received RT alone; 15 patients received RCT. In patients who developed Grade {>=} 3 mucositis (n = 18) the amount of unrepaired DSBs 24 h after radiation exposure and DSB repair half-times did not differ significantly from patients with Grade {<=}2 mucositis (n = 13). Patients with a proportion of unrepaired DSBs after 24 h higher than the mean value + one standard deviation had an increased incidence of severe oral mucositis. Conclusions: Evaluation of in vivo DSB repair by determination of {gamma}-H2AX foci loss is feasible in clinical practice and allows identification of patients with impaired DSB repair. The incidence of oral mucositis is not closely correlated with DSB repair under the evaluated conditions.

  18. 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 ...

  19. 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...

  20. 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

  1. The DNA Single-Strand Break Repair Machinery Facilitates CAF-1-Mediated Histone Deposition at Oxidative DNA Strand Breaks

    E-Print Network [OSTI]

    Arman Nabatiyan; Zhihong Zeng; Keith W. Caldecott

    2012-02-01T23:59:59.000Z

    Oxidative DNA single strand breaks arise continuously in cells and defects in their repair have been implicated in neurological disease. While much progress has been made in understanding how chromosomal single strand breaks are repaired little is known about the changes chromatin structure that accompany this process. Here, we show that nascent recombinant histone H3.1 protein accumulates and is deposited into chromatin at sites of DNA strand breakage in quiescent human cells following oxidative stress, and that core components of the single-strand break repair machinery are required for this process. We show that the SSBR sensor and scaffold proteins poly (ADP-ribose) polymerase and XRCC1 facilitate accumulation of chromatin assembly factor-1 (CAF-1) at sites of oxidative DNA strand breakage, which in turn mediates the deposition of Histone H3.1. We also demonstrate that depletion of CAF-1 slows global rates of DNA strand break repair in quiescent cells following oxidative stress, demonstrating that single-strand break repair and histone deposition are tightly coordinated processes. These data describe a novel role for the DNA singlestrand break repair machinery and implicate histone turnover as a core component of the cellular response of quiescent cells to oxidative damage.

  2. Creating Directed Double-strand Breaks with the Ref Protein A NOVEL RecA-DEPENDENT NUCLEASE FROM BACTERIOPHAGE P1*S

    E-Print Network [OSTI]

    Cox, Michael M.

    tar- geted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required

  3. aluminum strand coating: 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 by assessing DNA double-strand break (DSB) formation in situ with the rapid and...

  4. 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.

  5. 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.

  6. A novel high-throughput in-cell Western assay for the quantitative measurement of signaling dynamics in DNA damage signaling networks : cell decision processes in response to DNA double strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2006-01-01T23:59:59.000Z

    Following exposure to DNA damage, cells initiate a stress response involving multiple protein kinase signaling cascades. The DNA damage response results in one of several possible cell-fate decisions, or cellular responses: ...

  7. DNA Strand Damage Product Analysis Provides Evidence That the Tumor Cell-Specific Cytotoxin Tirapazamine

    E-Print Network [OSTI]

    Gates, Kent. S.

    DNA Strand Damage Product Analysis Provides Evidence That the Tumor Cell-Specific Cytotoxin DNA strand damage that is initiated by the abstraction of hydrogen atoms from the deoxyribose damage. We find that the action of TPZ on duplex DNA under hypoxic conditions generates 5-methylene-2

  8. 1 Plasmodium falciparum SSB Tetramer Wraps 2 Single-Stranded DNA with Similar Topology but

    E-Print Network [OSTI]

    Lohman, Timothy M.

    1 Plasmodium falciparum SSB Tetramer Wraps 2 Single-Stranded DNA with Similar Topology but 3 methods, we show that Pf-SSB forms a stable homo-tetramer 32 alone and when bound to single-stranded DNA (ssDNA). We also present a 33 crystal structure at 2.1 Ĺ resolution of the Pf-SSB tetramer bound

  9. 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

  10. Asymmetric quantum transport in a double-stranded Kronig-Penney model

    E-Print Network [OSTI]

    Taksu Cheon; Sergey S. Poghosyan

    2015-03-03T23:59:59.000Z

    We introduce a double-stranded Kronig-Penney model and analyze its transport properties. The asymmetric fluxes between two strands with suddenly alternating localization patterns are found as the energy is varied. The zero-size limit of the internal lines connecting two strands is examined using quantum graph vertices with four edges. We also consider a two-dimensional Kronig-Penney lattice with two types of alternating layers with $\\delta$ and $\\delta'$ connections, and show that the existence of energy bands in which the quantum flux can flow only in selected directions.

  11. adducts strand breaks: 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...

  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

    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

  13. 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

  14. Efimov like phase of a three stranded DNA (Efimov-DNA) and the renormalization group limit cycle

    E-Print Network [OSTI]

    Tanmoy Pal; Poulomi Sadhukhan; Somendra M. Bhattacharjee

    2015-04-10T23:59:59.000Z

    A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three chain bound state at the two chain melting point where no two are bound. By using a non-perturbative renormalization group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three dimensional parameter space of the two-chain coupling and a complex three chain interaction.

  15. Single-strand DNA translation initiation step analyzed by Isothermal Titration Calorimetry

    SciTech Connect (OSTI)

    Damian, Luminita, E-mail: luminitadamian@microcal.eu.com [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France) [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS, F-31077 Toulouse (France); IUB, School of Engineering and Science, D-28727 Bremen (Germany); Marty-Detraves, Claire, E-mail: claire.detraves@free.fr [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France) [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS, F-31077 Toulouse (France); Winterhalter, Mathias [IUB, School of Engineering and Science, D-28727 Bremen (Germany)] [IUB, School of Engineering and Science, D-28727 Bremen (Germany); Fournier, Didier, E-mail: Didier.Fournier@ipbs.fr [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France) [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS, F-31077 Toulouse (France); Paquereau, Laurent, E-mail: Laurent.Paquereau@ipbs.fr [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France) [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS, F-31077 Toulouse (France)

    2009-07-31T23:59:59.000Z

    Is single-strand DNA translatable? Since the 60s, the question still remains whether or not DNA could be directly translated into protein. Some discrepancies in the results were reported about functional translation of single-strand DNA but all results converged on a similar behavior of RNA and ssDNA in the initiation step. Isothermal Titration Calorimetry method was used to determine thermodynamic constants of interaction between single-strand DNA and S30 extract of Escherichia coli. Our results showed that the binding was not affected by the nature of the template tested and the dissociation constants were in the same range when ssDNA (K{sub d} = 3.62 {+-} 2.1 x 10{sup -8} M) or the RNA corresponding sequence (K{sub d} = 2.7 {+-} 0.82 x 10{sup -8} M) bearing SD/ATG sequences were used. The binding specificity was confirmed by antibiotic interferences which block the initiation complex formation. These results suggest that the limiting step in translation of ssDNA is the elongation process.

  16. The adsorption of short single-stranded DNA oligomers to mineral surfaces H. James Cleaves II a,

    E-Print Network [OSTI]

    Sverjensky, Dimitri A.

    The adsorption of short single-stranded DNA oligomers to mineral surfaces H. James Cleaves II a 12 February 2011 Keywords: DNA Mineral surface adsorption Nucleic acids in the environment Origin of life a b s t r a c t We studied the adsorption of short single-stranded deoxyribonucleic acid (ss

  17. Method for producing labeled single-stranded nucleic acid probes

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-10-19T23:59:59.000Z

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  18. 1 Plasmodium falciparum SSB Tetramer Binds 2 Single-Stranded DNA Only in a Fully Wrapped Mode

    E-Print Network [OSTI]

    Lohman, Timothy M.

    1 Plasmodium falciparum SSB Tetramer Binds 2 Single-Stranded DNA Only in a Fully Wrapped Mode 3 with numerous DNA repair and replication proteins. Ec- 24 SSB tetramers can bind ssDNA in multiple DNA binding in fully wrapped complexes with site sizes of 30 52­65 nt/tetramer. Pf-SSB does not transition to the more

  19. 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

  20. Template strand scrunching during DNA gap repair synthesis by human polymerase [lamda

    SciTech Connect (OSTI)

    Garcia-Diaz, Miguel; Bebenek, Katarzyna; Larrea, Andres A.; Havener, Jody M.; Perera, Lalith; Krahn, Joseph M.; Pedersen, Lars C.; Ramsden, Dale A.; Kunkel, Thomas A.; (NIH); (UNC)

    2009-09-25T23:59:59.000Z

    Family X polymerases such as DNA polymerase {lambda}(Pol {lambda}) are well suited for filling short gaps during DNA repair because they simultaneously bind both the 5{prime} and 3{prime} ends of short gaps. DNA binding and gap filling are well characterized for 1-nucleotide (nt) gaps, but the location of yet-to-be-copied template nucleotides in longer gaps is unknown. Here we present crystal structures revealing that, when bound to a 2-nt gap, Pol {lambda} scrunches the template strand and binds the additional uncopied template base in an extrahelical position within a binding pocket that comprises three conserved amino acids. Replacing these amino acids with alanine results in less processive gap filling and less efficient NHEJ when 2-nt gaps are involved. Thus, akin to scrunching by RNA polymerase during transcription initiation, scrunching occurs during gap filling DNA synthesis associated with DNA repair.

  1. 8DNA can be modeled as two parallel polymer strands with links between the strands called base pairs. Each base pair can be in a closed state with energy 0 or in an open state with energy .

    E-Print Network [OSTI]

    Gilbert, Matthew

    B-9 8DNA can be modeled as two parallel polymer strands with links between the strands called base a DNA molecule with N base pairs in thermal equilibrium at temperature T, as shown below. Thermal your expression separately in the limits that , and that . Next, consider the same DNA molecule now

  2. Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5

    E-Print Network [OSTI]

    Strong, Roland K.

    Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5 Xiaojun Li online 14 June 2009 Keywords: Innate immunity Nucleic acid receptor MDA5 CTD Crystal structure a b s t r a c t RIG-I, MDA5 and LGP2 are cytosolic pattern recognition receptors detecting single

  3. 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.

  4. C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices

    E-Print Network [OSTI]

    Bansal, Manju

    C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices Anirban Ghosh and Manju-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within leads to a narrow minor groove in these regions. # 1999 Academic Press Keywords: C-H..O hydrogen bonds

  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

    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,

  6. 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...

  7. 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...

  8. Activation of double-stranded RNA-dependent protein kinase inhibits proliferation of pancreatic ?-cells

    SciTech Connect (OSTI)

    Chen, Shan-Shan [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Jiang, Teng [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Wang, Yi; Gu, Li-Ze [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Wu, Hui-Wen [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China)] [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China); Tan, Lan [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Guo, Jun, E-mail: Guoj@njmu.edu.cn [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China)

    2014-01-17T23:59:59.000Z

    Highlights: •PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in ?-cells. •Activated PKR inhibited ?-cell proliferation by arresting cell cycle at G1 phase. •Activated PKR fully abrogated the pro-proliferative effects of IGF-I on ?-cells. -- Abstract: Double-stranded RNA-dependent protein kinase (PKR) is revealed to participate in the development of insulin resistance in peripheral tissues in type 2 diabetes (T2DM). Meanwhile, PKR is also characterized as a critical regulator of cell proliferation. To date, no study has focused on the impact of PKR on the proliferation of pancreatic ?-cells. Here, we adopted insulinoma cell lines and mice islet ?-cells to investigate: (1) the effects of glucolipotoxicity and pro-inflammatory cytokines on PKR activation; (2) the effects of PKR on proliferation of pancreatic ?-cells and its underlying mechanisms; (3) the actions of PKR on pro-proliferative effects of IGF-I and its underlying pathway. Our results provided the first evidence that PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in pancreatic ?-cells, and activated PKR significantly inhibited cell proliferation by arresting cell cycle at G1 phase. Reductions in cyclin D1 and D2 as well as increases in p27 and p53 were associated with the anti-proliferative effects of PKR, and proteasome-dependent degradation took part in the reduction of cyclin D1 and D2. Besides, PKR activation abrogated the pro-proliferative effects of IGF-I by activating JNK and disrupting IRS1/PI3K/Akt signaling pathway. These findings indicate that the anti-proliferative actions of PKR on pancreatic ?-cells may contribute to the pathogenesis of T2DM.

  9. 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

  10. 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

  11. Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand

    E-Print Network [OSTI]

    Cox, Michael M.

    : This project is supported by National Science Council of Taiwan to HWL and the United States National information is crucial for cell survival. RecA-mediated homologous recombination repairs double-stranded (ds ssDNA and the dsDNA, with the ejection of the displaced strand, and (v) depolymerization of RecA from

  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. Rolling-circle replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro

    SciTech Connect (OSTI)

    Shavitt, O.; Livneh, Z.

    1989-06-01T23:59:59.000Z

    Cloning of the phi X174 viral origin of replication into phage M13mp8 produced an M13-phi X174 chimera, the DNA of which directed efficient replicative-form----single-strand rolling-circle replication in vitro. This replication assay was performed with purified phi X174-encoded gene A protein, Escherichia coli rep helicase, single-stranded DNA-binding protein, and DNA polymerase III holoenzyme. The nicking of replicative-form I (RFI) DNA by gene A protein was essentially unaffected by the presence of UV lesions in the DNA. However, unwinding of UV-irradiated DNA by the rep helicase was inhibited twofold as compared with unwinding of the unirradiated substrate. UV irradiation of the substrate DNA caused a strong inhibition in its ability to direct DNA synthesis. However, even DNA preparations that contained as many as 10 photodimers per molecule still supported the synthesis of progeny full-length single-stranded DNA. The appearance of full-length radiolabeled products implied at least two full rounds of replication, since the first round released the unlabeled plus viral strand of the duplex DNA. Pretreatment of the UV-irradiated DNA substrate with purified pyrimidine dimer endonuclease from Micrococcus luteus, which converted photodimer-containing supercoiled RFI DNA into relaxed, nicked RFII DNA and thus prevented its replication, reduced DNA synthesis by 70%. Analysis of radiolabeled replication products by agarose gel electrophoresis followed by autoradiography revealed that this decrease was due to a reduction in the synthesis of progeny full-length single-stranded DNA. This implies that 70 to 80% of the full-length DNA products produced in this system were synthesized on molecules that carried photodimers.

  14. SOLVING LARGE DOUBLE DIGESTION PROBLEMS FOR DNA RESTRICTION MAPPING BY USING

    E-Print Network [OSTI]

    SOLVING LARGE DOUBLE DIGESTION PROBLEMS FOR DNA RESTRICTION MAPPING BY USING BRANCH;Solving Large Double Digestion Problems for DNA Restriction Mapping by Using Branch-and-Bound Integer.S.A. Abstract. The double digestion problem for DNA restriction mapping has been proved to be NP

  15. Effects of Monovalent Anions on a Temperature-Dependent Heat Capacity Change for Escherichia coli SSB Tetramer Binding to Single-Stranded DNA

    E-Print Network [OSTI]

    Lohman, Timothy M.

    SSB Tetramer Binding to Single-Stranded DNA Alexander G. Kozlov and Timothy M. Lohman* Department, where the subscript denotes the average number of ssDNA nucleotides occluded by each bound tetramer cooperat- ivity (SSB)65 mode in which ssDNA interacts with all four subunits and wraps around the tetramer

  16. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, Charles R. (Boston, MA); Ito, Takashi (Chiba, JP); Smith, Cassandra L. (Boston, MA)

    1996-01-01T23:59:59.000Z

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel.

  17. Extreme bendability of DNA double helix due to bending asymmetry

    E-Print Network [OSTI]

    Salari, Hossein; Naderi, M S; Ejtehadi, M R

    2015-01-01T23:59:59.000Z

    Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model w...

  18. 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, ...

  19. Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

    SciTech Connect (OSTI)

    Prins, Kathleen C.; Delpeut, Sebastien; Leung, Daisy W.; Reynard, Olivier; Volchkova, Valentina A.; Reid, St. Patrick; Ramanan, Parameshwaran; Cárdenas, Washington B.; Amarasinghe, Gaya K.; Volchkov, Viktor E.; Basler, Christopher F. (CNRS-INSERM); (Mount Sinai Hospital); (LB-Ecuador); (Iowa State)

    2010-10-11T23:59:59.000Z

    Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that loss of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.

  20. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.

  1. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

    Soares, M.B.; Fatima Bonaldo, M. de

    1998-12-08T23:59:59.000Z

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

  2. Three-dimensional Reconstruction of Agrobacterium VirE2 Protein with Single-stranded DNA*

    E-Print Network [OSTI]

    Citovsky, Vitaly

    for publication, February 18, 2004, and in revised form, March 29, 2004 Published, JBC Papers in Press, March 30 ("telephone coil") organization of the VirE2- DNA complex. Here we report a three-dimensional re- construction breeding (16­18). Upon induction of the vir region by detection of plant-specific wound signals, the VirD1

  3. ORIGINAL PAPER Ionizing radiation induces DNA double-strand breaks in bystander primary

    E-Print Network [OSTI]

    fibroblasts Mykyta V Sokolov1,2 , Lubomir B Smilenov3 , Eric J Hall3 , Igor G Panyutin1 , William M Bonner*,4

  4. Screening Tool for Providers of Double-Stranded DNA - Energy Innovation

    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's PossibleRadiationImplementingnpitcheResearchPhysics LabwildfiresScott Taylor,

  5. Collection, focusing, and metering of DNA in microchannels using addressable electrode arrays for portable low-power bioanalysis

    E-Print Network [OSTI]

    Shaikh, Faisal

    2008-10-10T23:59:59.000Z

    the funding for this work. vii NOMENCLATURE DNA Deoxyribonucleic Acid dsDNA Double Stranded DNA ssDNA Single Stranded DNA EDTA Ethylene Diamine Tetracetic Acid TBE Tris-Borate EDTA BME Beta Mercapto Ethanol PCB Printed Circuit Board DI Deionized... through a USB cable using a Personal Computer........................................................................................ 66 Figure 27 Top level block diagram of the FPGA based portable analysis device showing flow of information...

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

    E-Print Network [OSTI]

    Giunta, Simona

    2010-11-16T23:59:59.000Z

    During my PhD, I have investigated aspects of the DNA damage response (DDR) in the context of three different cellular scenarios: DNA damage signalling in response to double-strand breaks during mitosis, coordination of DNA replication with DNA...

  7. 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

  8. How Do Low-Energy (0.1-2 eV) Electrons Cause DNA-Strand

    E-Print Network [OSTI]

    Simons, Jack

    by which very low-energy (0.1-2 eV) free electrons attach to DNA and cause strong (ca. 4 eV) covalent bonds. The free electrons generated when water or DNA is ionized have a wide range of energies (1-20 eV), but they lose energy through collisions and can eventually yield solvated electrons. As these free electrons

  9. 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

  10. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOE Patents [OSTI]

    Ji, Huamin (4817 Sheboygan Ave., Madison, WI 53705); Smith, Lloyd M. (1115 Amherst Dr., Madison, WI 53705)

    1997-01-01T23:59:59.000Z

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support.

  11. DNA Double-Strand Breaks Form in Bystander Cells after Microbeam Irradiation of Three-dimensional Human Tissue Models

    E-Print Network [OSTI]

    Brenner, David Jonathan

    Research Accelerator Facility, Center for Radiological Research, College of Physicians and Surgeons Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada; and 3 Radiological implications for cancer radiother- apy and diagnostic radiology as well as for human health in general

  12. Double-strand DNA-templated formation of copper nanoparticles as fluorescent probe for label free nuclease enzyme detection

    E-Print Network [OSTI]

    Tan, Weihong

    cleavage activity. Thus, a label-free strategy for sensitive detection of nuclease has been developed B.V. All rights reserved. 1. Introduction As promising substitutes for organic dyes and quantum dots epithelial cervical cancer cells (HeLa cells) using fluorescent gold nanoparticles which emitted a stable

  13. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair

    E-Print Network [OSTI]

    Ochi, Takashi; Blackford, Andrew N.; Coates, Julia; Jhujh, Satpal; Mehmood, Shahid; Tamura, Naoka; Travers, Jon; Wu, Qian; Draviam, Viji M.; Robinson, Carol V.; Blundell, Tom L.; Jackson, Stephen P.

    2015-01-09T23:59:59.000Z

    ) for 2 hours with end-to-end mixing at 4 °C. Beads were washed five times in IP buffer before resuspension in 2x SDS loading buffer. 5% input lysate was loaded alongside unless otherwise stated. Surface plasmon resonance SPR experiments were performed...

  14. Polymorphisms in genes involved in DNA double-strand break repair pathway and susceptibility to benzene-induced hematotoxicity

    E-Print Network [OSTI]

    California at Berkeley, University of

    to benzene-induced hematotoxicity Min Shen1,Ă, Qing Lan1 , Luoping Zhang2 , Stephen Chanock1,3 , Guilan Li4; Email: shenmi@mail.nih.gov Benzene is a recognized hematotoxicant and carcinogen that produces genotoxic and indirectly by benzene metabolites. DSB may lead to chromosome aberrations, apoptosis and hematopoietic

  15. PM2 DNA, Forms I and I: a quantitative comparison of strand breakage induced by ionizing radiation

    E-Print Network [OSTI]

    Myers, Peter Hall

    1981-01-01T23:59:59.000Z

    precedant to success. All the Health Physics students with whom I have shared classes and from whom I have learned much. Mrs Debbie Adkins for her smiles and earnest interest. vs1 TABIE OF CONTENTS INTRODUCTION STATUS OF 1HE QUESTION MATERIALS... second function of DNA, that of orchestr-tion of protein synthesis, prompted intensified ef'forts in the 1960s. Researchers like Marshall Nirenberg and his associates at the National Institutes of' Health were able to decipher the gene- tic code...

  16. 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

  17. Derivatized versions of ligase enzymes for constructing DNA sequences

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Effects of Sequence Disorder on DNA Looping and Cyclization

    E-Print Network [OSTI]

    Yuri O. Popov; Alexei V. Tkachenko

    2007-06-08T23:59:59.000Z

    Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.

  3. 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.

  4. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, Barry L. (Newton, MA); Thilly, William G. (Winchester, MA); Foret, Frantisek (Malden, MA); Khrapko, Konstaintin (Brookline, MA); Koehavong, Phouthone (Pittsburgh, PA); Cohen, Aharon S. (Newton, MA); Giese, Roger W. (Quincy, MA)

    1997-01-01T23:59:59.000Z

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability.

  5. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, B.L.; Thilly, W.G.; Foret, F.; Khrapko, K.; Koehavong, P.; Cohen, A.S.; Giese, R.W.

    1997-05-27T23:59:59.000Z

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability. 18 figs.

  6. 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.

  7. 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

  8. In vivo evidence of alternative loop geometries in DNA-protein complexes

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-02-10T23:59:59.000Z

    The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an oscillatory component of about half the helical period and oscillates asymmetrically with an amplitude significantly smaller than predicted by current theories. Here, we show that the in vivo behavior is accurately accounted for by the simultaneous presence of two distinct conformations of looped DNA. Our analysis reveals that these two conformations have different optimal free energies and phases and that they behave distinctly in the presence of key architectural proteins.

  9. Stopped-Flow Studies of the Kinetics of Single-Stranded DNA Binding and Wrapping around the Escherichia coli SSB Tetramer

    E-Print Network [OSTI]

    Lohman, Timothy M.

    the Escherichia coli SSB Tetramer Alexander G. Kozlov and Timothy M. Lohman* Department of Biochemistry in which either one molecule of (dT)70 or two molecules of (dT)35 bind per tetramer. Stopped-flow studies. Our results indicate that initial ssDNA binding to the tetramer is very rapid, with a bimolecular rate

  10. Theory of DNA translocation through narrow ion channels and nanopores with charged walls

    E-Print Network [OSTI]

    Tao Hu; B. I. Shklovskii

    2008-06-20T23:59:59.000Z

    Translocation of a single stranded DNA through genetically engineered $\\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild type $\\alpha$-hemolysin channel. We assume that the wall charges compensate the fraction $x$ of the bare charge $q_{b}$ of the DNA piece residing in the channel. Our prediction are as follows (i) At small concentration of salt the blocked ion current decreases with $x$. (ii) The effective charge $q$ of DNA piece, which is very small at $x = 0$ (neutral channel) grows with $x$ and at $x=1$ reaches $q_{b}$. (iii) The rate of DNA capture by the channel exponentially grows with $x$. Our theory is also applicable to translocation of a double stranded DNA in narrow solid state nanopores with positively charged walls.

  11. RESEARCH ARTICLE Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the

    E-Print Network [OSTI]

    Arndt, Peter

    if the enrichment of CGIs at ORIs occurs at genome-wide scale. However, a recent large-scale survey could expand by the Okazaki frag- ments increases the frequency in which the template of the lagging strand is in single-strand (ss) DNA conformation relative to the template of the leading strand, which is rep- licated

  12. 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...

  13. 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-

  14. 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-

  15. Absence of zero-temperature transmission rate of a double-chain tight-binding model for DNA with random sequence of nucleotides in thermodynamic limit

    E-Print Network [OSTI]

    Gang Xiong; X. R. Wang

    2005-12-16T23:59:59.000Z

    The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While the whole spectrum tends to zero in thermodynamic limit, regardless of the strength of inter-chain coupling. It is also shown that a more faithful model for real DNA with periodic sugar-phosphate chains in backbone structures can be mapped into the above simple double-chain tight-binding model. Combined with above results, the transmission rate of real DNA with long random sequence of nucleotides is expected to be poor.

  16. 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

  17. Identification, Exploitation and Manipulation of BRCA1-Dependent DNA Double-Strand Break and Interstrand Crosslink Repair in Breast and Ovarian Cancer Therapy

    E-Print Network [OSTI]

    Stecklein, Shane Richard

    2012-05-12T23:59:59.000Z

    required by my academic journey. Your encouragement, support and love will always be the greatest treasures of my life. vi Acknowledgements To my mentor, Dr. Roy Jensen, I can never fully express my gratitude... hope to continue working in this discipline for the rest of my life. To my co-mentor, Dr. Fariba Behbod, I thank you for your unwavering support and enthusiasm throughout my graduate career. Your decision to come to KUMC has truly been a blessing...

  18. Dose-dependent misrejoining of radiation-induced DNA double-strand breaks in human fibroblasts: Experimental and theoretical study for high and low LET radiation

    E-Print Network [OSTI]

    Rydberg, Bjorn; Cooper, Brian; Cooper, Priscilla K.; Holley, William; Chatterjee, Aloke

    2004-01-01T23:59:59.000Z

    S. Kim, and R. M. Myers. Radiation hybrid mapping: a somaticformulation of dual radiation action. Radiat. Res. 75: 471-High-Linear Energy Transfer Radiation in Human Fibroblasts.

  19. ESI/TOF Measurements of a Noncovalent Complex between Lactose Repressor Protein (LacI) and Double-Stranded DNA Containing its Specific Operator Sequence

    E-Print Network [OSTI]

    Ens, Werner

    M buffer solution. Initial attempts to observe the protein tetramer were unsuccessful (as in the case rather broad peaks for both dimer and tetramer. The tetramer appears in two separate envelopes, suggesting that the the charge states 20 to 22 between m/z 7000 and 8000 represent the native tetramer

  20. 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

  1. 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

  2. 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

  3. CtIP tetramer assembly is required for DNA-end resection and repair

    E-Print Network [OSTI]

    Davies, Owen R.; Forment, Josep V.; Sun, Meidai; Belotserkovskaya, Rimma; Coates, Julia; Galanty, Yaron; Demir, Mukerrem; Morton, Christopher; Rzechorzek, Neil; Jackson, Stephen P.; Pellegrini, Luca

    2015-01-05T23:59:59.000Z

    1     CtIP tetramer assembly is required for DNA-end resection and repair Owen R. Davies1,4*, Josep V. Forment1,2,3*, Meidai Sun1, Rimma Belotserkovskaya1,2, Julia Coates1,2, Yaron Galanty1,2, Mukerrem Demir1,2, Christopher Morton1... that a CtIP tetramer architecture is essential for effective DSB repair by homologous recombination. Keywords CtIP/RBBP8, double-strand DNA break repair, DNA-end resection, gene conversion, homologous recombination. 3...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Less Haste, Less Waste: On Recycling and its Limits in Strand Displacement Systems

    E-Print Network [OSTI]

    Condon, Anne

    Less Haste, Less Waste: On Recycling and its Limits in Strand Displacement Systems Anne Condon Columbia, Vancouver, British Columbia, V6T 1Z4 Abstract. We study the potential for molecule recycling in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product

  12. 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.

  13. Design and Construction of Double-Decker Tile as a Route to Three-Dimensional Periodic Assembly of DNA

    E-Print Network [OSTI]

    Reif, John H.

    of DNA Urmi Majumder§ , Abhijit Rangnekar§|| , Kurt V Gothelf || , John H Reif§* and Thomas H LaBean water and letting it cool down slowly in an insulated (styrofoam) box over 16 hours, followed

  14. DNA heats up : Energetics of genome ejection from phage revealed by isothermal titration calorimetry

    E-Print Network [OSTI]

    Meerim Jeembaeva; B. Jönsson; Martin Castelnovo; Alex Evilevitch

    2010-01-06T23:59:59.000Z

    Most bacteriophages are known to inject their double-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released DNA is made possible by the energy stored during active packaging of the genome into the capsid. Only indirect measurements of this energy have been available until now using either single-molecule or osmotic suppression techniques. In this paper, we describe for the first time the use of isothermal titration calorimetry to directly measure the heat released (or equivalently the enthalpy) during DNA ejection from phage lambda, triggered in solution by a solubilized receptor. Quantitative analyses of the results lead to the identification of thermodynamic determinants associated with DNA ejection. The values obtained were found to be consistent with those previously predicted by analytical models and numerical simulations. Moreover, the results confirm the role of DNA hydration in the energetics of genome confinement in viral capsids.

  15. 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...

  16. 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...

  17. 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

  18. 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

  19. Melatonin Protects Human Cells from Clustered DNA Damages, Killing and Acquisition of Soft Agar Growth Induced by X-rays or 970 MeV/n Fe ions

    SciTech Connect (OSTI)

    Das, B.; Sutherland, B.; Bennett, P. V.; Cutter, N. C.; Sutherland, J. C.

    2011-06-01T23:59:59.000Z

    We tested the ability of melatonin (N-acetyl-5 methoxytryptamine), a highly effective radical scavenger and human hormone, to protect DNA in solution and in human cells against induction of complex DNA clusters and biological damage induced by low or high linear energy transfer radiation (100 kVp X-rays, 970 MeV/nucleon Fe ions). Plasmid DNA in solution was treated with increasing concentrations of melatonin (0.0-3.5 mM) and were irradiated with X-rays. Human cells (28SC monocytes) were also irradiated with X-rays and Fe ions with and without 2 mM melatonin. Agarose plugs containing genomic DNA were subjected to Contour Clamped Homogeneous Electrophoretic Field (CHEF) followed by imaging and clustered DNA damages were measured by using Number Average length analysis. Transformation experiments on human primary fibroblast cells using soft agar colony assay were carried out which were irradiated with Fe ions with or without 2 mM melatonin. In plasmid DNA in solution, melatonin reduced the induction of single- and double-strand breaks. Pretreatment of human 28SC cells for 24 h before irradiation with 2 mM melatonin reduced the level of X-ray induced double-strand breaks by {approx}50%, of abasic clustered damages about 40%, and of Fe ion-induced double-strand breaks (41% reduction) and abasic clusters (34% reduction). It decreased transformation to soft agar growth of human primary cells by a factor of 10, but reduced killing by Fe ions only by 20-40%. Melatonin's effective reduction of radiation-induced critical DNA damages, cell killing, and striking decrease of transformation suggest that it is an excellent candidate as a countermeasure against radiation exposure, including radiation exposure to astronaut crews in space travel.

  20. 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.

  1. DNA Repair Alterations in Children With Pediatric Malignancies: Novel Opportunities to Identify Patients at Risk for High-Grade Toxicities

    SciTech Connect (OSTI)

    Ruebe, Claudia E., E-mail: claudia.ruebe@uks.e [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Fricke, Andreas; Schneider, Ruth; Simon, Karin; Kuehne, Martin; Fleckenstein, Jochen [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Graeber, Stefan [Institute of Medical Biometrics, Epidemiology and Medical Informatics, Saarland University, Homburg/Saar (Germany); Graf, Norbert [Department of Pediatric Hematology and Oncology, Saarland University, Homburg/Saar (Germany); Ruebe, Christian [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany)

    2010-10-01T23:59:59.000Z

    Purpose: To evaluate, in a pilot study, the phosphorylated H2AX ({gamma}H2AX) foci approach for identifying patients with double-strand break (DSB) repair deficiencies, who may overreact to DNA-damaging cancer therapy. Methods and Materials: The DSB repair capacity of children with solid cancers was analyzed compared with that of age-matched control children and correlated with treatment-related normal-tissue responses (n = 47). Double-strand break repair was investigated by counting {gamma}H2AX foci in blood lymphocytes at defined time points after irradiation of blood samples. Results: Whereas all healthy control children exhibited proficient DSB repair, 3 children with tumors revealed clearly impaired DSB repair capacities, and 2 of these repair-deficient children developed life-threatening or even lethal normal-tissue toxicities. The underlying mutations affecting regulatory factors involved in DNA repair pathways were identified. Moreover, significant differences in mean DSB repair capacity were observed between children with tumors and control children, suggesting that childhood cancer is based on genetic alterations affecting DSB repair function. Conclusions: Double-strand break repair alteration in children may predispose to cancer formation and may affect children's susceptibility to normal-tissue toxicities. Phosphorylated H2AX analysis of blood samples allows one to detect DSB repair deficiencies and thus enables identification of children at risk for high-grade toxicities.

  2. 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.

  3. ExpandplusCrystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA

    SciTech Connect (OSTI)

    M Langelier; J Planck; S Roy; J Pascal

    2011-12-31T23:59:59.000Z

    Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

  4. 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.

  5. A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4, 2003, and in revised form, October 3, 2003

    E-Print Network [OSTI]

    Cox, Michael M.

    A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4A proteins of Escherichia coli (Ec) and Deino- coccus radiodurans (Dr) both promote a DNA strand exchange- stranded DNA-binding protein (SSB). In the absence of SSB, the initiation of strand exchange is greatly en

  6. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

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

  7. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

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

    1997-12-30T23:59:59.000Z

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

  8. 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

  9. 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 ...

  10. 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...

  11. Force-induced rupture of a DNA duplex

    E-Print Network [OSTI]

    Mosayebi, Majid; Doye, Jonathan P K; Ouldridge, Thomas E

    2015-01-01T23:59:59.000Z

    The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex within a given experiment depends strongly on the time scale of observation. We use simple models of DNA to demonstrate that this approach naturally captures the experimentally observed dependence of the critical force on duplex length for a given observation time. In particular, the critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence o...

  12. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

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

    1996-01-01T23:59:59.000Z

    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.

  13. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1996-01-09T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2009-06-08T23:59:59.000Z

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

  15. . 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

  16. DNA Extraction 5th Grade Physical Science Standard 1.1

    E-Print Network [OSTI]

    DNA Extraction 5th Grade Physical Science Standard 1.1 Concepts and Skills: Mixtures of matter can don't mix. 5. Gently pull DNA strands from the bottom solution into the isopropanol with a stir rod. DNA should precipitate into fine white strands that look like cotton candy. What is happening? Mashing

  17. 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.

  18. Analysis of Two Widespread Versions of a Bacterial Replicative DNA Polymerase

    E-Print Network [OSTI]

    Guenther, Joel Michael

    2010-01-01T23:59:59.000Z

    helical geometry. To permit this relaxation without haltingthe DNA primer strand to permit mismatch removal, either byresulting crosslink permits the storage and crystallization

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

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06T23:59:59.000Z

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

  20. Recognition of the unique structure of DNA:RNA hybrids Nicholas N. Shaw, Dev P. Arya*

    E-Print Network [OSTI]

    Stuart, Steven J.

    their therapeutic potential. Surprisingly, a survey of the literature reveals only a handful of ligands that bind template strand and a newly formed RNA strand, was also hypothesized. Experimental data supported simultaneously, reported the use of reverse transcriptase in the synthesis of a new DNA strand, via RNA template

  1. 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...

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

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

    DNA, so that the polymerase can move at high speed. As it sequentially copies the nucleotides that make up the DNA strand, synthesis can occur as fast as 1000 nucleotides per...

  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. Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

    SciTech Connect (OSTI)

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun-Joo (BU-M); (Florida); (Texas)

    2012-10-16T23:59:59.000Z

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 {angstrom} resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  5. 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).

  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. Neural network computation with DNA strand displacement cascades

    E-Print Network [OSTI]

    Bruck, Jehoshua (Shuki)

    is Alan Turing (1 1 1 1). ? ? 0 ? 1 0 0 0 Human: The scientist I am thinking of was not born in the 20th Alan Turing 0 0 1 1 Claude Shannon 1 0 0 0 Santiago Ramon y Cajal A "read your mind" game Figure S1

  8. Control of DNA Strand Displacement Kinetics Using Toehold Exchange

    E-Print Network [OSTI]

    Zhang, David Yu

    . A. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15275. (7) Pei, R.; Taylor, S. K.; Stefanovic, D) Kallenbach, N. R.; Ma, R. I.; Seeman, N. C. Nature 1983, 305, 829. (2) Rothemund, P. Nature 2006, 440, 297. J.; Mills, A. P.; Simmel, F. C.; Neumann, J. L. Nature 2000, 406, 605. (6) Dirks, R. M.; Pierce, N

  9. Unidirectional Scaffold-Strand Arrangement in DNA Origami

    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 aTurbulence mayUndergraduate ProgramCenter |Solar

  10. 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...

  11. The DNA Binding Properties of Saccharomyces cerevisiae Rad51 (Received for publication, June 12, 1998, and in revised form, November 16, 1998)

    E-Print Network [OSTI]

    Kowalczykowski, Stephen C.

    The DNA Binding Properties of Saccharomyces cerevisiae Rad51 Protein* (Received for publication Rad51 protein is the para- digm for eukaryotic ATP-dependent DNA strand ex- change proteins. To explain some of the unique charac- teristics of DNA strand exchange promoted by Rad51 protein, when

  12. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1998-11-03T23:59:59.000Z

    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 appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.

  13. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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 appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

  14. 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.

  15. 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.

  16. Solving the Double Digestion Problem as a MixedInteger Linear Program \\Lambda

    E-Print Network [OSTI]

    Zhang, Yin

    Solving the Double Digestion Problem as a Mixed­Integer Linear Program \\Lambda Zhijun Wu y and Yin Zhang z August, 2001 Abstract. The double digestion problem for DNA restriction mapping is known­scale double digestion problems. Key Words. DNA sequencing, restriction mapping, double digestion, NP

  17. DNA Assisted Assembly of Multisegmented Nanowires Aijun A. Wang,b

    E-Print Network [OSTI]

    Chen, Wilfred

    for the assembly of Au nanoparticles functionalized with thiolated single-stranded DNA (ssDNA) onto a prepatterned is an attractive method to assem- ble nanostructures into functional devices because of the highly specific nature offered by biomolecules such as proteins and deoxyribonucleic acid (DNA). DNA is partic- ularly attractive

  18. Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities

    SciTech Connect (OSTI)

    Langland, Gregory T.; Yannone, Steven M.; Langland, Rachel A.; Nakao, Aki; Guan, Yinghui; Long, Sydney B.T.; Vonguyen, Lien; Chen, David J.; Gray, Joe W; Chen, Fanqing

    2009-09-07T23:59:59.000Z

    The variability of radiation responses in ovarian tumors and tumor-derived cell lines is poorly understood. Since both DNA repair capacity and p53 status can significantly alter radiation sensitivity, we evaluated these factors along with radiation sensitivity in a panel of sporadic human ovarian carcinoma cell lines. We observed a gradation of radiation sensitivity among these sixteen lines, with a five-fold difference in the LD50 between the most radiosensitive and the most radioresistant cells. The DNA-dependent protein kinase (DNA-PK) is essential for the repair of radiation induced DNA double-strand breaks in human somatic cells. Therefore, we measured gene copy number, expression levels, protein abundance, genomic copy and kinase activity for DNA-PK in all of our cell lines. While there were detectable differences in DNA-PK between the cell lines, there was no clear correlation with any of these differences and radiation sensitivity. In contrast, p53 function as determined by two independent methods, correlated well with radiation sensitivity, indicating p53 mutant ovarian cancer cells are typically radioresistant relative to p53 wild-type lines. These data suggest that the activity of regulatory molecules such as p53 may be better indicators of radiation sensitivity than DNA repair enzymes such as DNAPK in ovarian cancer.

  19. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  20. DNA Functionalized Single-Walled Carbon Nanotubes for Electrochemical Detection Chenguo Hu,, Yiyi Zhang, Gang Bao, Yuelan Zhang, Meilin Liu, and Zhong Lin Wang*,

    E-Print Network [OSTI]

    Wang, Zhong L.

    DNA Functionalized Single-Walled Carbon Nanotubes for Electrochemical Detection Chenguo Hu,, Yiyi dispersed and functionalized by wrapping with single-stranded DNA (ssDNA). The ssDNA-SWNTs attach strongly responses, and quick electron transfer for a Fe(CN)6 3- /Fe(CN)6 4 system, indicating that the ssDNA

  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. BOND PROPERTIES OF CFCC PRESTRESSING STRANDS IN PRETENSIONED CONCRETE BEAMS

    E-Print Network [OSTI]

    BOND PROPERTIES OF CFCC PRESTRESSING STRANDS IN PRETENSIONED CONCRETE BEAMS by Nolan G. Domenico plastic prestressing strands (CFCC) in pretensioned concrete beams. The bond characteristics are examined for 15.2 mm diameter and 12.5 mm diameter seven-wire CFCC strands. Ten prestressed concrete beams

  3. 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.

  4. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    SciTech Connect (OSTI)

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01T23:59:59.000Z

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

  5. 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.

  6. 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

  7. Development of affinity technology for isolating individual human chromosomes by third strand binding

    SciTech Connect (OSTI)

    Fresco, Jacques R.

    2003-06-01T23:59:59.000Z

    The overall goal was to explore whether nucleic acid third strands could be used to bind with very high specificity to specific targets within whole genomes. Towards this end conditions had to be found to keep erroneous binding to an absolute minimum. The goal to use third strands (linked to magnetic beads) to ''capture'' large particles such as plasmids, cosmids, and whole chromosomes from complex mixtures was partially met; their use to serve as cytogenetic probes of metaphase chromosomes and to deliver reactive reagents to unique target sites on chromosomes in vivo for the purpose of mutagenizing specific base pairs was fully met; and their use as cytogenetic probes of chromosomal DNA in sections of formalin-fixed, paraffin-embedded tissue has been met since the DOE support was terminated.

  8. 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

  9. Study of DNA coated nanoparticles as possible programmable self-assembly building blocks

    E-Print Network [OSTI]

    Högberg, Björn

    Author's personal copy Study of DNA coated nanoparticles as possible programmable self Available online 3 April 2006 Abstract Nanoparticles coated with single stranded DNA have been shown (or algorithmic) self-assembly to build nanoparticle structures. However, we argue that a DNA coated

  10. DNA heats up: Energetics of genome ejection from phage revealed by isothermal titration calorimetry.

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 DNA heats up: Energetics of genome ejection from phage revealed by isothermal titration-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released DNA is made possible

  11. 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

  12. Stranded Wire With Uninsulated Strands as a Low-Cost Alternative to Litz Wire

    E-Print Network [OSTI]

    the power loss, is measured experimen- tally. The analytical model is solved to get an optimal pitch, which to 100 kHz. Compared with the same transformer using a solid wire winding, about 67 percent less power loss at 100 kHz is achieved using stranded wire. Using the loss-prediction model provided in this paper

  13. Erasmus Mundus Action 2 Strand 1 / Strand 2 (delete as appropriate) PROJECT SUMMARY SHEET

    E-Print Network [OSTI]

    Schenato, Luca

    ____________________________________ Title of proposal EM A2 Strand 1 Lot 1:Algeria, Morocco, Tunisia, Egypt and Libya (EM A2 LOT 1 Al- Fihri Partner 18 Libyan International Medical University Libya Partner 19 Omar Muhktar University Libya TC, Morocco, Tunisia, Egypt and Libya Project duration (months) 48 months #12;Amount requested (EUR) 4

  14. 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.

  15. 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.

  16. 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

  17. Coding properties of DNA languages \\Lambda\\Lambda Salah Hussini \\Lambda , Lila Kari y , Stavros Konstantinidis \\Lambda

    E-Print Network [OSTI]

    cellular organism as the storage medium for genetic information. It is composed of units called nucleotides to the nucleotides that contain them.) Single nucleotides are linked together end--to--end to form DNA strands. A short single­stranded polynucleotide chain, usually less than 30 nucleotides long, is called

  18. Stomach contents of cetaceans stranded in the Canary Islands 19962006

    E-Print Network [OSTI]

    Pierce, Graham

    Stomach contents of cetaceans stranded in the Canary Islands 1996­2006 r. fernandez1 , m.b. santos2, Kogiidae and Ziphiidae, stranded between 1996 and 2006 in the Canary Islands. Cephalopod mandibles (beaks teuthophagous whales. Keywords: feeding, Canary Islands, cetaceans, cephalopods, plastic Submitted 5 August 2008

  19. Sturdier DNA Nanotubes via Ligation Patrick O'Neill, Paul W. K. Rothemund, Ashish Kumar, and D. K. Fygenson*,,

    E-Print Network [OSTI]

    Winfree, Erik

    -stranded DNA (dsDNA), DNA nanotubes combine the binding specificity of nucleic acids with a rigid, linear interesting for applications. For example, they might be metallized or functionalized by surface attachment of bio- molecules or nanoparticles and so serve as interconnects in self-assembled networks.4

  20. Genetic variation in the 16s mitochondrial rDNA gene from Texas and Oklahoma populations of Amblyomma maculatum

    E-Print Network [OSTI]

    Lostak, Tracy Karon

    2009-05-15T23:59:59.000Z

    Single-strand conformation polymorphism was used to detect different haplotypes of the 16S mitochondrial rDNA gene within samples of Gulf Coast ticks, Amblyomma maculatum Koch, collected from Payne County, Oklahoma and Brazos and Refugio Counties...

  1. Use of 2-Aminopurine Fluorescence as a probe of DNA and computational studies of a new class of base analogues 

    E-Print Network [OSTI]

    Wu, Xiaohua

    2012-06-22T23:59:59.000Z

    The steady-state and time-resolved fluorescence of 2-aminopurine (2AP) have been used to monitor base dynamics and base stacking interactions in DNA single strands and dinucleotides, and to investigate the interactions ...

  2. Z:\\Payroll Related\\Misc Payroll Information\\Strand Union Employment Application.doc STRAND UNION EMPLOYMENT APPLICATION

    E-Print Network [OSTI]

    Maxwell, Bruce D.

    Z:\\Payroll Related\\Misc Payroll Information\\Strand Union Employment Application.doc STRAND UNION EMPLOYMENT APPLICATION Complete both sides of this application form and return it to The Ask Us Desk OR Room ____Manager Ask Us Desk ____Instructor ____Desk Attendant ____Manager Have you been previously employed

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Method for detecting point mutations in DNA utilizing fluorescence energy transfer

    DOE Patents [OSTI]

    Parkhurst, Lawrence J. (Lincoln, NE); Parkhurst, Kay M. (Lincoln, NE); Middendorf, Lyle (Lincoln, NE)

    2001-01-01T23:59:59.000Z

    A method for detecting point mutations in DNA using a fluorescently labeled oligomeric probe and Forster resonance energy transfer (FRET) is disclosed. The selected probe is initially labeled at each end with a fluorescence dye, which act together as a donor/acceptor pair for FRET. The fluorescence emission from the dyes changes dramatically from the duplex stage, wherein the probe is hybridized to the complementary strand of DNA, to the single strand stage, when the probe is melted to become detached from the DNA. The change in fluorescence is caused by the dyes coming into closer proximity after melting occurs and the probe becomes detached from the DNA strand. The change in fluorescence emission as a function of temperature is used to calculate the melting temperature of the complex or T.sub.m. In the case where there is a base mismatch between the probe and the DNA strand, indicating a point mutation, the T.sub.m has been found to be significantly lower than the T.sub.m for a perfectly match probelstand duplex. The present invention allows for the detection of the existence and magnitude of T.sub.m, which allows for the quick and accurate detection of a point mutation in the DNA strand and, in some applications, the determination of the approximate location of the mutation within the sequence.

  8. 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.

  9. Methods for sequencing GC-rich and CCT repeat DNA templates

    DOE Patents [OSTI]

    Robinson, Donna L.

    2007-02-20T23:59:59.000Z

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  10. Self-avoiding worm-like chain model for dsDNA loop formation

    E-Print Network [OSTI]

    Yaroslav Pollak; Sarah Goldberg; Roee Amit

    2014-11-06T23:59:59.000Z

    We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used to compute the J-factor for varying lengthscales. In the entropic regime, we confirm the scaling-theory prediction of a power-law drop off of -1.92, which is significantly stronger than the -1.5 power-law predicted by the non-self-avoiding worm-like chain model. In the elastic regime, we find that the angle-independent end-to-end chain distribution is highly anisotropic. This anisotropy, combined with the excluded volume constraints, lead to an increase in the J-factor of the self-avoiding worm-like chain by about half an order of magnitude relative to its non-self-avoiding counterpart. This increase could partially explain the anomalous results of recent cyclization experiments, in which short dsDNA molecules were found to have an increased propensity to form a loop.

  11. Radiation induced strand breakage analyzed by tunel technique 

    E-Print Network [OSTI]

    Reynolds, Marissa Dawn

    2003-01-01T23:59:59.000Z

    The objective of this research is to fully characterize the effectiveness and limits of using the terminal deoxynucleotidyl transferase mediated biotin-dUTP nick end labeling (TUNEL) technique for analysis of radiation induced strand breakage...

  12. Characterization of Nb?Sn superconducting strand under pure bending

    E-Print Network [OSTI]

    Harris, David L., S.M. Massachusetts Institute of Technology

    2005-01-01T23:59:59.000Z

    Characterizing the strain-dependent behavior of technological Nb?Sn superconducting strand has been an important subject of research for the past 25 years. Most of the effort has focused on understanding the uniaxial tension ...

  13. Radiation induced strand breakage analyzed by tunel technique

    E-Print Network [OSTI]

    Reynolds, Marissa Dawn

    2003-01-01T23:59:59.000Z

    The objective of this research is to fully characterize the effectiveness and limits of using the terminal deoxynucleotidyl transferase mediated biotin-dUTP nick end labeling (TUNEL) technique for analysis of radiation induced strand breakage...

  14. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis

    SciTech Connect (OSTI)

    Pozo-Yauner, Luis del, E-mail: ldelpozo@inmegen.gob.mx [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Wall, Jonathan S. [Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN (United States)] [Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN (United States); González Andrade, Martín [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico)] [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); Sánchez-López, Rosana [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210 (Mexico)] [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210 (Mexico); Rodríguez-Ambriz, Sandra L. [Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731 (Mexico)] [Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731 (Mexico); Pérez Carreón, Julio I. [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico)] [Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610 (Mexico); and others

    2014-01-10T23:59:59.000Z

    Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.

  15. Efficient Turing-Universal Computation with DNA Polymers

    E-Print Network [OSTI]

    Winfree, Erik

    of stack machines -- a Turing-universal model of computation similar to Turing machines -- using DNA strand to logically reversible computation, and arbitrarily little energy per computation step is required. Further computation is significantly more efficient than geometry-free chemical reaction networks. 1 Introduction

  16. A DNA Nanotransport Device Powered by Polymerase 29: Supporting Information

    E-Print Network [OSTI]

    Reif, John H.

    H. LaBean1,2 , and John H. Reif1 1 Department of Computer Science, Box 90129, Duke University solutions were prepared at a concentration of 30µM in ultra pure water. Concentrations of DNA strands were (from Apex Bioresearch) in 200 ml distilled water for 20-25 minutes. The gel was then viewed under UV

  17. Sustainability Double Degree Double Degree Info

    E-Print Network [OSTI]

    Grünwald, Niklaus J.

    Sustainability Double Degree Double Degree Info: · 36 credits in B for graduation. Sustainability Core: Take each course below for a total of 17 -20 credits. Term/Grade Course _____ ____ *NR 350 (4) Sustainable

  18. 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...

  19. 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.

  20. 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...

  1. 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 ...

  2. 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.

  3. Apparatus and method for fabricating multi-strand superconducting cable

    DOE Patents [OSTI]

    Borden, Albert R. (El Cerrito, CA)

    1986-01-01T23:59:59.000Z

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet is fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  4. Method for fabricating multi-strand superconducting cable

    DOE Patents [OSTI]

    Borden, A.R.

    1985-04-01T23:59:59.000Z

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet are fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  5. Stretching chimeric DNA: A test for the putative S-form Stephen Whitelam,1,2,3,a

    E-Print Network [OSTI]

    Geissler, Phillip

    with parameters such as temperature and salt concentration,13­15 both of which are known to change the melting to render B-DNA single-stranded or "molten"14 suggests that overstretching is melting, induced by a pulling force. However, some authors8 charge that molten DNA, in the sense of two parallel but noninteracting

  6. 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

  7. The structural basis for partitioning of the XRCC1/DNA ligase III-[alpha] BRCT-mediated dimer complexes

    SciTech Connect (OSTI)

    Cuneo, Matthew J.; Gabel, Scott A.; Krahn, Joseph M.; Ricker, Melissa A.; London, Robert E. (NIH)

    2011-11-17T23:59:59.000Z

    The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-{alpha}. For efficient ligation, ligase III-{alpha} is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-{alpha} BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.

  8. The Structural Basis for Partitioning of the XRCC1/DNA Ligase III-alpha BRCT-mediated Dimer Complexes

    SciTech Connect (OSTI)

    M Cuneo; S Gabel; J Krahn; M Ricker; R London

    2011-12-31T23:59:59.000Z

    The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-{alpha}. For efficient ligation, ligase III-{alpha} is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-{alpha} BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.

  9. Dynamic change of histone H2AX phosphorylation independent of ATM and DNA-PK in mouse skin in situ

    SciTech Connect (OSTI)

    Koike, Manabu [DNA Repair Gene Research, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)], E-mail: m_koike@nirs.go.jp; Mashino, Minako; Sugasawa, Jun; Koike, Aki [DNA Repair Gene Research, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

    2007-11-30T23:59:59.000Z

    Histone H2AX undergoes phosphorylation on Ser 139 ({gamma}-H2AX) rapidly in response to DNA double-strand breaks induced by exogenous stimuli, such as ionizing radiation. However, the endogenous phosphorylation pattern and modifier of H2AX remain unclear. Here we show that H2AX is regulated physically at the level of phosphorylation at Ser139 during a hair cycle in the mouse skin. In anagen hair follicles, {gamma}-H2AX-positive cells were observed in the outer root sheath (ORS) and hair bulb in a cycling inferior region but not in a permanent superficial region. In telogen hair follicles, {gamma}-H2AX-positive cells were only detected around the germ cell cap. In contrast, following X-irradiation, {gamma}-H2AX was observed in various cell types including the ORS cells in the permanent superficial region. Furthermore, {gamma}-H2AX-positive cells were detected in the skin of mice lacking either ATM or DNA-PK, suggesting that these kinases are not essential for phosphorylation in vivo.

  10. Solvatochromism and time-resolved fluorescence of the antitumor agent mitoxantrone and its analogues in solution and in DNA

    SciTech Connect (OSTI)

    Su Lin; Struve, W.S. (Ames Lab., IA (United States))

    1991-03-21T23:59:59.000Z

    The electronic spectroscopy and fluorescence kinetics of 1,4-dihydroxy-5,8-(2-(2-((2-hydroxyethyl)amino)ethyl)amino)-9,10-anthracenedione (mitoxantrone) and three closely related analogues have been studied in several solvents. The small solvatochromic blue shifts of their visible charge-transfer absorption bands in protic solvents are dominated by interactions with a solvent H-bonding donor, rather than by dipole-dielectric solute-solvent electrostatics. These interactions are unrelated to the phenolic hydroxy groups or the distal N atoms on the side chains but must be localized to the carbonyl groups. The fluorescence decays of all four anthraquinones are controlled by subnanosecond nonradiative relaxation in all solvents studied. At least two decay mechanisms contribute to the observed fluorescence kinetics in solution: (a) subnanosecond internal conversion that is accelerated relative to that in 1,4-diaminoanthraquinone by the presence of the flexible 1,4-side chains in mitoxantrone and its analogues; (b) an additional decay mode that is accentuated in H-bonding solvents. A substantial normal isotope effect occurs in the fluorescence lifetimes of mitoxantrone in perdeuterated water and methanol but not in aprotic solvents. When bound to double-stranded calf thymus DNA, mitoxantrone displays a fluorescence lifetime similar to that in aprotic solvents, suggesting that H-bonding interactions with water are precluded by chromophore intercalation. DNA-bound ametantrone exhibits a lifetime longer than that in either H-bonding or aprotic solvents, indicating that immobilization of the side chains through binding of the distal N atoms to the DNA backbone may influence the decay kinetics. This technique therefore shows potential for elucidating the DNA binding modes for a large class of intercalative drugs.

  11. advanced materials strands: Topics by E-print Network

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

    materials strands First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Department of Advanced Materials...

  12. Mobile linkers on DNA-coated colloids: valency without patches

    E-Print Network [OSTI]

    Stefano Angioletti-Uberti; Patrick Varilly; Bortolo M. Mognetti; Daan Frenkel

    2014-08-27T23:59:59.000Z

    Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal `molecules'. However, in order to design DNACC-based molecules, we must be able to control the valency of the colloids, i.e. the number of partners to which a given DNACC can bind. One obvious, but not very simple approach is to decorate the colloidal surface with patches of single-stranded DNA that selectively bind those on other colloids. Here we propose a design principle that exploits many-body effects to control the valency of otherwise isotropic colloids. Using a combination of theory and simulation, we show that we can tune the valency of colloids coated with mobile ssDNA, simply by tuning the non-specific repulsion between the particles. Our simulations show that the resulting effective interactions lead to low-valency colloids self-assembling in peculiar open structures, very different from those observed in DNACCs with immobile DNA linkers.

  13. DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction

    SciTech Connect (OSTI)

    Zheng Yi; Wagner, J. Richard; Sanche, Leon [Groupe de Recherche en Sciences des Radiations, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QC J1H 5N4 (Canada)

    2006-05-26T23:59:59.000Z

    Thin films of the short single strand of DNA, GCAT, in which guanine (G) or adenine (A) have been removed, were bombarded under vacuum by 4 to 15 eV electrons. The fragments corresponding to base release and strand breaks (SB) were analyzed by high performance liquid chromatography and their yields compared with those obtained from unmodified GCAT. From such a comparison, it is shown that, using GCAT as a model system (1) most SB result from electron capture by DNA bases followed by electron transfer to the phosphate group and (2) the initial capture probability depends on the coherence of the electron wave within the tetramer.

  14. Chromosome doubling method

    DOE Patents [OSTI]

    Kato, Akio

    2006-11-14T23:59:59.000Z

    The invention provides methods for chromosome doubling in plants. The technique overcomes the low yields of doubled progeny associated with the use of prior techniques for doubling chromosomes in plants such as grasses. The technique can be used in large scale applications and has been demonstrated to be highly effective in maize. Following treatment in accordance with the invention, plants remain amenable to self fertilization, thereby allowing the efficient isolation of doubled progeny plants.

  15. Optimal Choice for Number of Strands in a Litz-Wire Transformer Winding

    E-Print Network [OSTI]

    Optimal Choice for Number of Strands in a Litz-Wire Transformer Winding C. R. Sullivan Found Choice for Number of Strands in a Litz-Wire Transformer Winding Charles R. Sullivan Thayer School/inductor Abstract -- The number of strands to minimize loss in a litz-wire transformer winding is determined

  16. 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

  17. 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

  18. FIRST ATTEMPTS AT PREDICTION OF DNA STRAND-BREAK YIELDS USING NANODOSIMETRIC DATA

    E-Print Network [OSTI]

    an ion-cluster size distribution. This approach is the only one possible in case of unknown radiation data consist of ion-cluster size distributions [f(nion)], providing the absolute freq- uency of ion projectile particle. The SV can be approximated by a cylinder of 1.6 mm diam. (in 120 Pa propane gas) whose

  19. Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold

    E-Print Network [OSTI]

    Himpsel, Franz J.

    infrared (FTIR), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopies. XPS reveals core, T25-SH). IR reflection absorption spectra were measured under a dry nitrogen purge using a p

  20. Improvements in strand feeding and its effect of sintering performance

    SciTech Connect (OSTI)

    Beer, H.; Kersting, K.; Werner, P. [Thyssen Stahl AG, Duisburg (Germany)

    1995-12-01T23:59:59.000Z

    Sintering may be considered a rather simple, counter current gas-solid process. A bed of granular solids is moved horizontally on a strand of pallets and suction is applied beneath the grate. Shortly after the sinter mix is fed onto the strand the incorporated solid fuel is ignited in the surface layer and the hot gases are drawn into the bed. The temperature of the top layer is raised high enough to burn the fuel particles while air is sucked down through it. Passing the upper, already sintered part of the bed the air is first preheated then sustains the combustion reaction. The hot, still oxygen-rich combustion gases leave the sintering zone and transfer its heat to the charge below. While the solids are preheated, carbonates, combined water, and moisture are driven off, rapidly cooling the gas. Thus, a flame front propagates through the traveling bed, generating at peak temperatures enough heat to agglomerate the bed of quasi-particles into a sinter cake. The strand speed is adjusted so that the burning through of the combustion zone coincides with the end of the suction area. To ensure stable operation this cross stream reactor has to be kept in a steady state.

  1. ageing human fibroblasts: 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...

  2. ataxia telangiectasia fibroblasts: 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...

  3. acidic fibroblast growth: 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...

  4. adult-onset primary open-angle: 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...

  5. angiogenic gene-modified fibroblasts: 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...

  6. acid-induced fibroblast cell: 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...

  7. asymptomatic primary hyperparathyroidism: 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...

  8. aliphatic primary diamines: 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...

  9. autologous fibroblast metabolism: 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...

  10. acid induces human: 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...

  11. arthritis synovial fibroblasts: 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...

  12. 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.

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

    SciTech Connect (OSTI)

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

    2013-01-17T23:59:59.000Z

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

  14. (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

  15. Control of Strand Scission by Type IIA Topoisomerases

    E-Print Network [OSTI]

    Schmidt, Bryan Harris

    2012-01-01T23:59:59.000Z

    DNA synthesizer Oligo resuspension and annealing for use intag. As such, after resuspension in Buffer A (withoutFollowing a column wash in resuspension buffer, tagged topo

  16. RADIATION SENSITIVITY & PROCESSING OF DNA DAMAGE FOLLOWING LOW DOSES OF GAMMA-RAY ALPHA PARTICLES & HZE IRRADIATION OF NORMAL DSB REPAIR DEFICIENT CELLS

    SciTech Connect (OSTI)

    O'Neil, Peter

    2009-05-15T23:59:59.000Z

    Non-homologous end joining (NHEJ) predominates in the repair of DNA double strand breaks (DSB) over homologous recombination (HR). NHEJ occurs throughout the cell cycle whereas HR occurs in late S/G2 due to the requirement of a sister chromatid (Rothkamm et al, Mol Cell Biol 23 5706-15 [2003]). To date evidence obtained with DSB repair deficient cells using pulsed-field gel electrophoresis has revealed the major pathway throughout all phases of the cell cycle for processing high dose induced DSBs is NHEJ (Wang et al, Oncogene 20 2212-24 (2001); Pluth et al, Cancer Res. 61 2649-55 [2001]). These findings however were obtained at high doses when on average >> 20-30 DSBs are formed per cell. The contribution of the repair pathways (NHEJ and HR) induced in response to DNA damage during the various phases of the cell cycle may depend upon the dose (the level of initial DSBs) especially since low levels of DSBs are induced at low dose. To date, low dose studies using NHEJ and HR deficient mutants have not been carried out to address this important question with radiations of different quality. The work presented here leads us to suggest that HR plays a relatively minor role in the repair of radiation-induced prompt DSBs. SSBs lead to the induction of DSBs which are associated specifically with S-phase cells consistent with the idea that they are formed at stalled replication forks in which HR plays a major role in repair. That DNA-PKcs is in some way involved in the repair of the precursors to replication-induced DSB remains an open question. Persistent non-DSB oxidative damage also leads to an increase in RAD51 positive DSBs. Both simple and complex non-DSB DNA damage may therefore contribute to indirect DSBs induced by ionising radiation at replication forks.

  17. Double Beta Decay: Scintillators

    E-Print Network [OSTI]

    Mark C. Chen

    2008-10-20T23:59:59.000Z

    Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into scintillators or can be loaded into scintillators. Experimental programs developing liquid xenon, inorganic crystals, and Nd-loaded liquid scintillator are described in this review. Experiments with 48Ca and 150Nd benefit from their high endpoint which places the neutrinoless double beta decay signal above most backgrounds from natural radioactivity.

  18. The role of histones and histone modifying enzymes in ribosomal dna silencing in saccharomyces cerevisiae

    E-Print Network [OSTI]

    Li, Chonghua

    2009-05-15T23:59:59.000Z

    DNA silencing. We found that, unlike Sir2 that represses both Pol II transcription and recombination, histone H1 only represses recombination at the rDNA. The hyperrecombination defect at the rDNA is more severe in sir2? hho1? double mutant than in either single...

  19. Mutagenic processing and strand-specific repair of solar light-induced dipyrimidine photoproducts in rodent cells

    SciTech Connect (OSTI)

    Drobetsky, E.A. [Hopital Maisonneuve-Rosemont, Montreal (Canada); Sage, E. [Institut Curie, Paris (France)

    1994-12-31T23:59:59.000Z

    Although mutations induced by {open_quotes}UVC-like{close_quotes} dipyrimidine photoproducts during sunlight exposure have been directly implicated in multistage photocarcinogenesis, the utility of 254nm UV as a paradigm for broad spectrum solar mutagenesis is questionable. To address this issue, the spectrum of mutations induced by simulated sunlight (SSL) at the adrenine phosphoribosyltransferase locus of Chinese hamster ovary cells has been characterized, and aligned with that previously established for 254nm UV in the same gene. Virtually all SSL-induced events were recovered at potential dinucleotide target sites, most of which could also be implicated in UVC mutagenesis, confirming a preeminent role for cyclobutane dimers and/or (6-4) photoproducts in sunlight-exposed rodent cells. However, striking differences were also noted in the frequency and distribution of mutational classes generated by SSL vs. UVc. Whereas C->T transitions were clearly the most frequent UVC-induced event (58%), three types of base substitution contributed substantially to the SSL spectrum; C->T transitions (35%), T->G transversions (25%), and tandem double CC->TT events (25%). In addition, a significantly greater fraction of SSL-induced mutations (94%) could be attributed to dipyrimidine photoproducts on the non-transcribed strand of the aprt gene than was observed following treatment with 254nm UV (63%). Taken together, the data indicate remarkable differences between UVC- and sunlight-exposed rodent cells in the distribution, strand-specific repair, and/or metabolic processing of similar premutagenic (dipyrimidine) photoproducts.

  20. ##### 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

  1. The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

    SciTech Connect (OSTI)

    Mak, Amanda Nga-Sze; Bradley, Philip; Cernadas, Raul A.; Bogdanove, Adam J.; Stoddard, Barry L. (FHCRC); (Iowa State)

    2012-02-10T23:59:59.000Z

    DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.

  2. 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.

  3. 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.

  4. Double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2006-02-22T23:59:59.000Z

    The present status of double beta decay experiments are reviewed. The results of the most sensitive experiments, NEMO-3 and CUORICINO, are discussed. Proposals for future double beta decay experiments are considered. In these experiments sensitivity for the effective neutrino mass will be on the level of (0.1-0.01) eV.

  5. Double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2011-07-28T23:59:59.000Z

    The present status of double beta decay experiments is reviewed. The results of the most sensitive experiments are discussed. Proposals for future double beta decay experiments with a sensitivity to the $$ at the level of (0.01--0.1) eV are considered.

  6. 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

  7. 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

  8. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

    E-Print Network [OSTI]

    Martin, Jeffrey

    2011-01-01T23:59:59.000Z

    transcriptome assembly pipeline from stranded RNA-Seq readsRnnotator assembly pipeline. Figure 2. Read dereplicationan automated software pipeline that generates transcript

  9. 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

  10. Double field theory

    E-Print Network [OSTI]

    Hull, Chris

    The zero modes of closed strings on a torus — the torus coordinates plus dual coordinates conjugate to winding number — parameterize a doubled torus. In closed string field theory, the string field depends on all zero-modes ...

  11. Neutrinoless double beta decay

    E-Print Network [OSTI]

    K. Zuber

    2012-01-23T23:59:59.000Z

    The physics potential of neutrinoless double beta decay is discussed. Furthermore, experimental considerations are presented as well as the current status of experiments. Finally an outlook towards the future, work on nuclear matrix elements and alternative processes is given.

  12. Double Beta Decay

    E-Print Network [OSTI]

    Steven R. Elliott; Petr Vogel

    2002-02-27T23:59:59.000Z

    The motivation, present status, and future plans of the search for the neutrinoless double beta decay are reviewed. It is argued that, motivated by the recent observations of neutrino oscillations, there is a reasonable hope that neutrinoless double beta decay corresponding to the neutrino mass scale suggested by oscillations, of about 50 meV, actually exists. The challenges to achieve the sensitivity corresponding to this mass scale, and plans to overcome them, are described.

  13. 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.

  14. Specificity, flexibility and valence of DNA bonds guide emulsion architecture

    E-Print Network [OSTI]

    Lang Feng; Lea-Laetitia Pontani; Remi Dreyfus; Paul Chaikin; Jasna Brujic

    2013-03-25T23:59:59.000Z

    The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new architectural possibilities due to the mobility of the DNA ligands and the patches they form between bound droplets. Here we show that the size and number of these adhesion patches (valency) can be controlled. Valence 2 leads to flexible polymers of emulsion droplets, while valence above 4 leads to rigid droplet networks. A simple thermodynamic model quantitatively describes the increase in the patch size with droplet radii, DNA concentration and the stiffness of the tether to the sticky-end. The patches are formed between droplets with complementary DNA strands or alternatively with complementary colloidal nanoparticles to mediate DNA binding between droplets. This emulsion system opens the route to directed self-assembly of more complex structures through distinct DNA bonds with varying strengths and controlled valence and flexibility.

  15. 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...

  16. Algorithms and statistics for advanced DNA analysis For the first time in history, humankind has the ability to easily read and write DNA sequence, a code

    E-Print Network [OSTI]

    University of Technology, Sydney

    , humankind has the ability to easily read and write DNA sequence, a code which describes the very essence of life itself. Global DNA sequencing operations currently generate 30TB data every day and the rate of this data generation more than doubles every year, outpacing Moore's Law. Sequence analysis has entered

  17. 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.

  18. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

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

    Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; Riera, Alberto; Tognetti, Sivia; Yuan, Zuanning; Stillman, Bruce; Speck, Christian

    2014-10-15T23:59:59.000Z

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex andmore »an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.« less

  19. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

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

    Sun, Jingchuan [Brookhaven National Laboratory (BNL), Upton, NY (United States); Li, Huilin [Brookhaven National Laboratory (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States); Fernandez-Cid, Alejandra [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group; Riera, Alberto [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Tognetti, Sivia [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Yuan, Zuanning [Stony Brook Univ., Stony Brook, NY (United States); Stillman, Bruce [Cold Spring Harbor Lab., NY (United States); Speck, Christian [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group

    2014-10-15T23:59:59.000Z

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

  20. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Heinrich Päs; Werner Rodejohann

    2015-07-01T23:59:59.000Z

    We review the potential to probe new physics with neutrinoless double beta decay $(A,Z) \\to (A,Z+2) + 2 e^-$. Both the standard long-range light neutrino mechanism as well as short-range mechanisms mediated by heavy particles are discussed. We also stress aspects of the connection to lepton number violation at colliders and the implications for baryogenesis.

  1. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Päs, Heinrich

    2015-01-01T23:59:59.000Z

    We review the potential to probe new physics with neutrinoless double beta decay $(A,Z) \\to (A,Z+2) + 2 e^-$. Both the standard long-range light neutrino mechanism as well as short-range mechanisms mediated by heavy particles are discussed. We also stress aspects of the connection to lepton number violation at colliders and the implications for baryogenesis.

  2. DOUBLE MAJORS Imaging Science + ...

    E-Print Network [OSTI]

    Zanibbi, Richard

    DOUBLE MAJORS Imaging Science + ... Applied Mathematics Biomedical Sciences Computer Science Undergraduate Research Internships and Cooperative Education (Co-op) (optional) Study Abroad WHY IMAGING SCIENCE Science: BS, MS, PhD Color Science: MS, PhD BS + MS/PhD Combos HUMAN VISION BIO- MEDICAL ASTRO- PHYSICS

  3. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, D.R.

    1982-09-23T23:59:59.000Z

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  4. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, Dale R. (Albuquerque, NM)

    1984-01-01T23:59:59.000Z

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  5. Neutrinoless double beta decay

    E-Print Network [OSTI]

    Petr Vogel

    2006-11-17T23:59:59.000Z

    The status of the search for neutrinoless double beta decay is reviewed. The effort to reach the sensitivity needed to cover the effective Majorana neutrino mass corresponding to the degenerate and inverted mass hierarchy is described. Various issues concerning the theory (and phenomenology) of the relation between the $0\

  6. Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: a joint theory-experiment study

    E-Print Network [OSTI]

    Brunet, Annaël; Salomé, Laurence; Rousseau, Philippe; Destainville, Nicolas; Manghi, Manoel

    2015-01-01T23:59:59.000Z

    Using high-throughput Tethered Particle Motion single molecule experiments, the double-stranded DNA persistence length, $L_p$, is measured in solutions with Na$^+$ and Mg$^{2+}$ ions of various ionic strengths, $I$. Several theoretical equations for $L_p(I)$ are fitted to the experimental data, but no decisive theory is found which fits all the $L_p$ values for the two ion valencies. Properly extracted from the particle trajectory using simulations, $L_p$ varies from 30~nm to 55~nm, and is compared to previous experimental results. For the Na$^+$ only case, $L_p$ is an increasing concave function of $I^{-1}$, well fitted by Manning's electrostatic stretching approach, but not by classical Odjik-Skolnick-Fixman theories with or without counter-ion condensation. With added Mg$^{2+}$ ions, $L_p$ shows a marked decrease at low $I$, interpreted as an ion-ion correlation effect, with an almost linear law in $I^{-1}$, fitted by a proposed variational approach.

  7. Journal of the Mechanics and Physics of Solids 51 (2003) 18151847

    E-Print Network [OSTI]

    Ortiz, Michael

    2003-01-01T23:59:59.000Z

    of the DNA is de˙ned as a functional of the director ˙eld which accounts for bending, torsion years, the structure of the portal motor which translocates double-stranded DNA into the capsid

  8. Elucidation of the Mechanisms of Nucleosome Binding and Repositioning by a Chromatin Remodeler: Monomeric ISWI Remodels Nucleosomes Through a Random Walk

    E-Print Network [OSTI]

    Al-Ani, Gada K.

    2014-05-31T23:59:59.000Z

    remodeler ISWI with fluorophore-labeled nucleosomes and DNA through associated changes in fluorescence anisotropy of the fluorophore upon ISWI binding to these substrates. We determined that one ISWI molecule binds to a 20 bp double stranded DNA substrate...

  9. WHY SEARCH FOR DOUBLE BETA DECAY?

    E-Print Network [OSTI]

    Kayser, B.

    2010-01-01T23:59:59.000Z

    the search for neutrinoless double beta decay may prove verySearching for neutrinoless double beta decay is the onlysensitivity of neutrinoless double beta decay. The potential

  10. Double field theory at order ??

    E-Print Network [OSTI]

    Hohm, Olaf

    We investigate ?? corrections of bosonic strings in the framework of double field theory. The previously introduced “doubled ??-geometry” gives ??-deformed gauge transformations arising in the Green-Schwarz anomaly ...

  11. 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.

  12. Behavior of Supercoiled DNA T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette

    E-Print Network [OSTI]

    Croquette, Vincent

    . The over- wound or underwound double helix can assume exotic forms known as plectonemes (like the braided contain 3 m of DNA, divided into 46 chromosomes. If these chromosomes were in the form of a random coil it to be over- wound and underwound from its natural state. Today we know that DNA is topologically polymorphic

  13. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-07-27T23:59:59.000Z

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  14. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, J.J.; Quesada, M.A.; Randesi, M.

    1999-07-27T23:59:59.000Z

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

  15. 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.

  16. 5-Hydroxymethylcytosine is a predominantly stable DNA modification

    E-Print Network [OSTI]

    Bachman, Martin; Uribe-Lewis, Santiago; Yang, Xiaoping; Williams, Michael; Murrell, Adele; Balasubramanian, Shankar

    2014-09-21T23:59:59.000Z

    in the CRUK Cambridge Institute from a C57BL/6 mouse and cultured on a gelatin-coated plate in a DMEM-KO medium (Invitrogen) supplemented with 10% FCS, MEM non-essential amino acids, glutamine, sodium pyruvate, penicillin, streptomycin, mouse leukemia... global hmC levels in cells treated with either thymidine (Supplementary Fig. S3 and Otani et al.24) or a high dose of ascorbic acid (Supplementary Fig S17, Minor et al.35 and Blaschke et al.36), the high hmC level found in ‘immortal’ DNA strands37...

  17. Seasonal occurrence and distribution of stranded sea turtles along the Texas and southwest Louisiana coasts

    E-Print Network [OSTI]

    Heinly, Robert Wayne

    1990-01-01T23:59:59.000Z

    SEASONAL OCCURRENCE AND DISTRIBUTION OF STRANDED SEA TURTLES ALONG THE TEXAS AND SOUTHWEST LOUISIANA COASTS A Thesis by ROBERT WAYNE HEINLY Submitted to the Office of Graduate Studies Texas A&M University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE December 1990 Major Subject: Wildlife and Fisheries Sciences SEASONAL OCCURRENCE AND DISTRIBUTION OF STRANDED SEA TURTLES ALONG THE TEXAS AND SOUTHWEST LOUISIANA COASTS A Thesis by ROBERT WAYNE HEINLY...

  18. for doubling solar panel

    E-Print Network [OSTI]

    An outline for doubling solar panel efficiency C o l o ra do S c ho o l of M i ne s Ma g a z i ne Take a look at a solar panel on a sunny Colorado day and, if you're like most people, you won't see physics professor and solar energy researcher, who admits to checking out his panels and their energy

  19. Double Beta Decay Experiments

    SciTech Connect (OSTI)

    Nanal, Vandana [Dept. of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Mumbai 400 005 (India)

    2011-11-23T23:59:59.000Z

    At present, neutrinoless double beta decay is perhaps the only experiment that can tell us whether the neutrino is a Dirac or a Majorana particle. Given the significance of the 0{nu}{beta}{beta}, there is a widespread interest for these rare event studies employing a variety of novel techniques. This paper describes the current status of DBD experiments. The Indian effort for an underground NDBD experiment at the upcoming INO laboratory is also presented.

  20. Magnetization anomaly of Nb3Al strands and instability of Nb3Al Rutherford cables

    SciTech Connect (OSTI)

    Yamada, Ryuji; /Fermilab; Kikuchi, Akihiro; /Tsukuba Magnet Lab; Wake, Masayoshi; /KEK, Tsukuba

    2006-08-01T23:59:59.000Z

    Using a Cu stabilized Nb{sub 3}Al strand with Nb matrix, a 30 meter long Nb{sub 3}Al Rutherford cable was made by a collaboration of Fermilab and NIMS. Recently the strand and cable were tested. In both cases instability was observed at around 1.5 Tesla. The magnetization of this Nb{sub 3}Al strand was measured first using a balanced coil magnetometer at 4.2 K. Strands showed an anomalously large magnetization behavior around at 1.6 T, which is much higher than the usual B{sub c2} {approx} 0.5 Tesla (4.2 K) of Nb matrix. This result is compared with the magnetization data of short strand samples using a SQUID magnetometer, in which a flux-jump signal was observed at 0.5 Tesla, but not at higher field. As a possible explanation for this magnetization anomaly, the interfilament coupling through the thin Nb films in the strands is suggested. The instability problem observed in low field tests of the Nb{sub 3}Al Rutherford cables is attributed to this effect.

  1. Increase Jc by Improving the Array of Nb3Sn strands for Fusion Application

    SciTech Connect (OSTI)

    Dr. Xuan Peng

    2012-12-17T23:59:59.000Z

    During Phase I, our efforts were focusing on improving the array of subelement in the tube type strands by hardening the Sn core and the subelement matrix to effectively increase the Jc of the strands. Below is a summary of the results. 1) We were unsuccessful in improving the array using a Cu-Sn matrix approach. 2) We slightly improved the array using Sn with 1.5at%Ti doped core, and a 217-subelement restacked strand was made and drawn down without any breakage. 3) We greatly improved the array using the Glidcop Al-15 to replace the pure Cu sheath in the subelement, and a 217-subelement restacked strand was made and drawn down. Both strands have very good drawability and the array showed good improvement. 4) We also improved the array using improved wire drawing techniques using Hyper Tech�¢����s new caterpillar wire drawing machines to enable straight wire drawing for the entire wire drawing process. 5) The 919-subelement restack strand shows its non-Cu Jc over 2100 A/mm2 at 12 T/4.2 K and AC loss of 508 mJ/cm3.

  2. 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.

  3. 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

  4. Double Beta Decay

    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 ManagementDiscovering HowAna Moore Anne Jones DevensforDouble Beta

  5. Advance the DNA computing

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30T23:59:59.000Z

    of the huge possible memory by generating a ``lookup table'' during the implementation of the algorithms. If the initial condition changes, the answer changes accordingly. In addition, the new model has the advantage of decoding all the strands in the final...

  6. Engineering & Technology January 2012 www.EandTmagazine.com 68 InformatIon technology SYNTHETIC BIOLOGY

    E-Print Network [OSTI]

    Winfree, Erik

    that interact by strand- displacement (see box, right) in a kind of computational soup. The project to build `velcro' that binds the two strands of the DnA double helix together. Methods to exploit this phenomenon strand-displacement. The researchers made four fully-connected artificial neurons from these elements

  7. 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.

  8. Probing Protein-DNA Interactions by Unzipping a Single DNA Double Helix

    E-Print Network [OSTI]

    Wang, Michelle

    ., 2000; Bianco et al., 2001; Dohoney and Gelles, 2001; Strick et al., 2000), as well as the investigation

  9. 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

  10. 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

  11. Neutrinoless Double Phys 135c Spring 2007

    E-Print Network [OSTI]

    Golwala, Sunil

    Neutrinoless Double Beta Decay Phys 135c Spring 2007 Michael Mendenhall #12;Theory Overview #12 beta decays #12;neutrinoless double beta decays n e- p beta decay e #12;neutrinoless double beta decays n e- p beta decay e n e- p n e- p double beta decay e e #12;neutrinoless double beta decays n e- p

  12. 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.

  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. Double acting bit holder

    DOE Patents [OSTI]

    Morrell, Roger J. (Blommington, MN); Larson, David A. (Minneapolis, MN); Ruzzi, Peter L. (Eagan, MN)

    1994-01-01T23:59:59.000Z

    A double acting bit holder that permits bits held in it to be resharpened during cutting action to increase energy efficiency by reducing the amount of small chips produced. The holder consist of: a stationary base portion capable of being fixed to a cutter head of an excavation machine and having an integral extension therefrom with a bore hole therethrough to accommodate a pin shaft; a movable portion coextensive with the base having a pin shaft integrally extending therefrom that is insertable in the bore hole of the base member to permit the moveable portion to rotate about the axis of the pin shaft; a recess in the movable portion of the holder to accommodate a shank of a bit; and a biased spring disposed in adjoining openings in the base and moveable portions of the holder to permit the moveable portion to pivot around the pin shaft during cutting action of a bit fixed in a turret to allow front, mid and back positions of the bit during cutting to lessen creation of small chip amounts and resharpen the bit during excavation use.

  16. Double Chooz: Latest results

    E-Print Network [OSTI]

    J. I. Crespo-Anadón; for the Double Chooz collaboration

    2014-12-11T23:59:59.000Z

    The latest results from the Double Chooz experiment on the neutrino mixing angle $\\theta_{13}$ are presented. A detector located at an average distance of 1050 m from the two reactor cores of the Chooz nuclear power plant has accumulated a live time of 467.90 days, corresponding to an exposure of 66.5 GW-ton-year (reactor power $\\times$ detector mass $\\times$ live time). A revised analysis has boosted the signal efficiency and reduced the backgrounds and systematic uncertainties compared to previous publications, paving the way for the two detector phase. The measured $\\sin^2 2\\theta_{13} = 0.090^{+0.032}_{-0.029}$ is extracted from a fit to the energy spectrum. A deviation from the prediction above a visible energy of 4 MeV is found, being consistent with an unaccounted reactor flux effect, which does not affect the $\\theta_{13}$ result. A consistent value of $\\theta_{13}$ is measured in a rate-only fit to the number of observed candidates as a function of the reactor power, confirming the robustness of the result.

  17. Chemical contaminants in gray whales (eschichtius robustus) stranded in Alaska, Washington, and California, USA. Technical memo

    SciTech Connect (OSTI)

    Varanasi, U.; Stein, J.E.; Tilbury, K.L.; Meador, J.P.; Sloan, C.A.

    1993-08-01T23:59:59.000Z

    The concentrations of chlorinated hydrocarbons (CHs) such as polychlorinated biphenyls (PCBs), 1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethanes (DDTs), 1,1-dichloro-2,2-bis(p- chlorophenyl) ethenes (DDEs), and chlordanes, and essential (e.g., zinc, selenium, copper) and toxic (e.g., mercury, lead) elements were measured in tissues and stomach contents from 22 gray whales (Eschrichtius robustus) stranded between 1988 and 1991. The stranding sites ranged from the relatively pristine areas of Kodiak Island, Alaska, to more urbanized areas in Puget Sound, Washington, and San Francisco Bay, California, with the majority of the sites on the Washington outer coast and in Puget Sound. Similar to concentrations in tissues, no significant differences were observed in concentrations of elements in stomach contents between whales stranded in Puget Sound and whales stranded at the more pristine sites. The lack of data from apparently healthy gray whales limits the assessment of whether the levels of anthropogenic contaminants found in tissues may have deleterious effects on the health of gray whales.

  18. Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault

    E-Print Network [OSTI]

    Savage, Heather M.

    Collateral damage: Evolution with displacement of fracture distribution and secondary fault strands in fault damage zones Heather M. Savage1,2 and Emily E. Brodsky1 Received 22 April 2010; revised 10 of fracture distributions as a function of displacement to determine whether damage around small and large

  19. EFFECTS OF RESIN AND WAX ON THE WATER UPTAKE BEHAVIOR OF WOOD STRANDS

    E-Print Network [OSTI]

    Wang, Siqun

    EFFECTS OF RESIN AND WAX ON THE WATER UPTAKE BEHAVIOR OF WOOD STRANDS Yang2hang1 Post and wax are essential additives in the manufactureof composite panels such as OSB. Resin binds wood elements together while wax acts as a water repellent. The objective of this study was to investigate

  20. Critical Current Test Facilities for LHC Superconducting NbTi Cable Strands

    E-Print Network [OSTI]

    Boutboul, T; Denarié, C H; Oberli, L R; Richter, D

    2001-01-01T23:59:59.000Z

    The Rutherford-type superconducting Cu/NbTi cables of the LHC accelerator are currently mass-produced by a few industrial firms. As a part of the acceptance tests, the critical current of superconducting multifilamentary wires is systematically measured on virgin strands to qualify the wires and on extracted strands to qualify the cables. For this purpose, four test stations are in operation at CERN to measure the critical current of strands at both 4.2 K and 1.9 K in magnetic fields in the 6-11 T range. The measurement setup and procedures of these facilities are reported in this article. The quality of the critical current test is guaranteed by supervising the SPC (Statistical Process Control) charts of a reference sample. The measurement repeatability and reproducibility of the stations are found to be excellent. Moreover, the measured critical current of a strand is found to be almost independent of the test station in which the measurement is performed.

  1. 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.

  2. 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.

  3. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1999-08-31T23:59:59.000Z

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.

  4. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S. (Oak Ridge, TN)

    1997-01-01T23:59:59.000Z

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  5. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S. (Oak Ridge, TN)

    1999-01-01T23:59:59.000Z

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  6. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1997-08-26T23:59:59.000Z

    A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.

  7. Neutrinoless Double Beta-Decay

    E-Print Network [OSTI]

    S. M. Bilenky

    2010-01-12T23:59:59.000Z

    The neutrinoless double $\\beta$-decay of nuclei is reviewed. We discuss neutrino mixing and 3x3 PMNS neutrino mixing matrix. Basic theory of neutrinoless double $\\beta$-decay is presented in some details. Results of different calculations of nuclear matrix element are discussed. Experimental situation is considered. The Appendix is dedicated to E. Majorana (brief biography and his paper in which the theory of Majorana particles is given)

  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. Low energy electron stimulated desorption from DNA films dosed with oxygen

    SciTech Connect (OSTI)

    Mirsaleh-Kohan, Nasrin; Bass, Andrew D.; Cloutier, Pierre; Massey, Sylvain; Sanche, Leon [Groupe en sciences des radiations, Faculte de medecine et des sciences de la sante, Universite de Sherbrooke, Sherbrooke, Quebec J1H 5N4 (Canada)

    2012-06-21T23:59:59.000Z

    Desorption of anions stimulated by 1-18 eV electron impact on self-assembled monolayer (SAM) films of single DNA strands is measured as a function of film temperature (50-250 K). The SAMs, composed of 10 nucleotides, are dosed with O{sub 2}. The OH{sup -} desorption yields increase markedly with exposure to O{sub 2} at 50 K and are further enhanced upon heating. In contrast, the desorption yields of O{sup -}, attributable to dissociative electron attachment to trapped O{sub 2} molecules decrease with heating. Irradiation of the DNA films prior to the deposition of O{sub 2} shows that this surprising increase in OH{sup -} desorption, at elevated temperatures, arises from the reaction of O{sub 2} with damaged DNA sites. These results thus appear to be a manifestation of the so-called 'oxygen fixation' effect, well known in radiobiology.

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

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

  11. Effective charge and free energy of DNA inside an ion channel

    E-Print Network [OSTI]

    Jingshan Zhang; B. I. Shklovskii

    2008-03-03T23:59:59.000Z

    Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is approximately 12 (in units of electron charge) measurements of different effective charges resulted in values between one and two. We explain these challenging observations by a large self-energy of a charge in the narrow water filled gap between ssDNA and channel walls, related to large difference between dielectric constants of water and lipid, and calculate effective charges of ssDNA. We start from the most fundamental stall charge $q_s$, which determines the force $F_s= q_s V/L$ stalling DNA against the voltage V (L is the length of the channel). We show that the stall charge $q_s$ is proportional to the ion current blocked by DNA, which is small due to the self-energy barrier. Large voltage V reduces the capture barrier which DNA molecule should overcome in order to enter the channel by $|q_c|V$, where $q_c$ is the effective capture charge. We expressed it through the stall charge $q_s$. We also relate the stall charge $q_s$ to two other effective charges measured for ssDNA with a hairpin in the back end: the charge $q_u$ responsible for reduction of the barrier for unzipping of the hairpin and the charge $q_e$ responsible for DNA escape in the direction of hairpin against the voltage. At small V we explain reduction of the capture barrier with the salt concentration.

  12. 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.

  13. 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

  14. Fabrication and Test Results for Rutherford-Type Cables Made from BSCCO Strands

    SciTech Connect (OSTI)

    Scanlan, R.M.; Dietderich, D.R.; Higley, H.C.; Marken, K.R.; Motowidlo, L.R.; Solokowski, R.; Hasegawa, T.

    1998-09-01T23:59:59.000Z

    Wires based on the Bi-2212 HTS superconductor are becoming available commercially, with current densities that are attractive for some applications. We report here on our success in using these Bi-2212 wires to fabricate multistrand, kiloamp conductors that can be used to construct dipole and quadrupole magnets for particle accelerator applications. Multistrand cables have been made from several types of Bi-2212 wire supplied by two manufacturers. These cables were made with cores of various compositions and dimensions in order to optimize the fabrication process. In addition, cables have been made from aspected strands as well as round strands. Cable critical currents will be reported and compared for the various cable parameters investigated in this study.

  15. 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.

  16. Evaluation of Juvenile Fall Chinook Stranding on the Hanford Reach, 1997-1999 Interim Report.

    SciTech Connect (OSTI)

    Wagner, Paul; Nugent, John; Price, William (Washington Department of Fish and Wildlife, Olympia, WA)

    1999-02-15T23:59:59.000Z

    Pilot work conducted in 1997 to aid the development of the study for the 1998 Evaluation of Juvenile Fall Chinook Stranding on The Hanford Reach. The objectives of the 1997 work were to: (1) identify juvenile chinook production and rearing areas..., (2) identify sampling sites and develop the statistical parameters necessary to complete the study, (3) develop a study plan..., (4) conduct field sampling activities...

  17. New Double Soft Emission Theorems

    E-Print Network [OSTI]

    Freddy Cachazo; Song He; Ellis Ye Yuan

    2015-03-16T23:59:59.000Z

    We study the behavior of the tree-level S-matrix of a variety of theories as two particles become soft. By analogy with the recently found subleading soft theorems for gravitons and gluons, we explore subleading terms in double soft emissions. We first consider double soft scalar emissions and find subleading terms that are controlled by the angular momentum operator acting on hard particles. The order of the subleading theorems depends on the presence or not of color structures. Next we obtain a compact formula for the leading term in a double soft photon emission. The theories studied are a special Galileon, DBI, Einstein-Maxwell-Scalar, NLSM and Yang-Mills-Scalar. We use the recently found CHY representation of these theories in order to give a simple proof of the leading order part of all these theorems

  18. Predicting Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    M. Hirsch; Ernest Ma; J. W. F. Valle; A. Villanova del Moral

    2005-07-12T23:59:59.000Z

    We give predictions for the neutrinoless double beta decay rate in a simple variant of the A_4 family symmetry model. We show that there is a lower bound for the neutrinoless double beta decay amplitude even in the case of normal hierarchical neutrino masses, corresponding to an effective mass parameter |m_{ee}| >= 0.17 \\sqrt{\\Delta m^2_{ATM}}. This result holds both for the CP conserving and CP violating cases. In the latter case we show explicitly that the lower bound on |m_{ee}| is sensitive to the value of the Majorana phase. We conclude therefore that in our scheme, neutrinoless double beta decay may be accessible to the next generation of high sensitivity experiments.

  19. Increasing the Jc of Tube-Type Nb3Sn Strands

    SciTech Connect (OSTI)

    Dr. Xuan Peng

    2012-12-17T23:59:59.000Z

    In this Phase I, we successfully made strands with better Cu/Sn ratio to reduce the coarse Nb3Sn grain region, thereby providing the potential of increasing the non-Cu Jc in the Phase II and scaling up to 2�¢��� billets with 331 subelements. In order to improve the strand�¢����s high field properties, we successfully doped low amount of Ti in the subelements and made a 217-subelement wire which has been drawn down to 0.7 mm without any breakage. This strand gave subelement size of 35 ���µm. We will scale up the Ti-doped billet to 271-subelement in 1.5�¢��� billet in this proposed Phase II. The hexagonal shaped subelements with round Nb-Sn have been developed for a 61-subelement restack. Thus the results indicated that for 217-subelement restack in a 2�¢��� billet we have the potential to draw down this type of construction without problems while maintaining a good array to react more Nb to get higher non-Cu Jc in the Phase II.

  20. Attosecond Double-Slit Experiment

    SciTech Connect (OSTI)

    Lindner, F.; Schaetzel, M.G.; Baltuska, A.; Goulielmakis, E. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Walther, H. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Krausz, F. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Institut fuer Photonik, Technische Universitaet Wien, Gusshausstr. 27, A-1040 Vienna (Austria); Milosevic, D.B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, 71000 Sarajevo (Bosnia and Herzegowina); Bauer, D. [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Becker, W. [Max-Born-Institut, Max-Born-Str. 2a, 12489 Berlin (Germany); Paulus, G.G. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Department of Physics, Texas A and M University, College Station, Texas 77843-4242 (United States)

    2005-07-22T23:59:59.000Z

    A new scheme for a double-slit experiment in the time domain is presented. Phase-stabilized few-cycle laser pulses open one to two windows (slits) of attosecond duration for photoionization. Fringes in the angle-resolved energy spectrum of varying visibility depending on the degree of which-way information are measured. A situation in which one and the same electron encounters a single and a double slit at the same time is observed. The investigation of the fringes makes possible interferometry on the attosecond time scale. From the number of visible fringes, for example, one derives that the slits are extended over about 500 as.

  1. Double beta decay: present status

    E-Print Network [OSTI]

    A. S. Barabash

    2008-07-18T23:59:59.000Z

    The present status of double beta decay experiments (including the search for $2\\beta^{+}$, EC$\\beta^{+}$ and ECEC processes) are reviewed. The results of the most sensitive experiments are discussed. Average and recommended half-life values for two-neutrino double beta decay are presented. Conservative upper limits on effective Majorana neutrino mass and the coupling constant of the Majoron to the neutrino are established as $ beta decay experiments with a sensitivity for the $$ at the level of (0.01-0.1) eV are considered.

  2. Neutrinoless double beta decay experiments

    E-Print Network [OSTI]

    K. Zuber

    2006-10-04T23:59:59.000Z

    The study of neutrinoless double beta decay is of outmost importance for neutrino physics. It is considered to be the gold plated channel to probe the fundamental character of neutrinos and to determine the neutrino mass. From the experimental point about nine different isotopes are explored for the search. After a general introduction follows a short discussion on nuclear matrix element calculations and supportive measurements. The current experimental status of double beta searches is presented followed by a short discussion of the ideas and proposals for large scale experiments.

  3. Neutrinoless Double Beta Decay Constraints

    E-Print Network [OSTI]

    Hiroaki Sugiyama

    2003-07-25T23:59:59.000Z

    A brief overview is given of theoretical analyses with neutrinoless double beta decay experiments. Theoretical bounds on the ``observable'', _betabeta, are presented. By using experimental bounds on _betabeta, allowed regions are obtained on the m_l-cos{2theta_12} plane, where m_l stands for the lightest neutrino mass. It is shown that Majorana neutrinos can be excluded by combining possible results of future neutrinoless double beta decay and {}^3H beta decay experiments. A possibility to constrain one of two Majorana phases is discussed also.

  4. -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

  5. Amino Triazole : A New Abscission Chemical and Growth Inhibitor. 

    E-Print Network [OSTI]

    Leinweber, C. L. (Charles Lee); Johnson, S. P. (Samuel Park); Hall, Wayne C. (Wayne Clark)

    1954-01-01T23:59:59.000Z

    Most bacteriophages release progeny virions at the end of the infection cycle by lysis of the host. Large phages with double-stranded DNA genomes use a multigene strategy based on holins, small membrane proteins, and ...

  6. Analysis of cell cycle surveillance mechanisms in meiosis

    E-Print Network [OSTI]

    Hochwagen, Andreas

    2006-01-01T23:59:59.000Z

    Numerous DNA double-strand breaks (DSBs) are introduced into the genome in the course of meiotic recombination. This poses a significant hazard to the genomic integrity of the cell. Studies in a number of organisms have ...

  7. The impact of age, exposure and genetics on homologous recombination at the engineered repeat sequence in mice

    E-Print Network [OSTI]

    Wiktor-Brown, Dominika M

    2007-01-01T23:59:59.000Z

    Mitotic homologous recombination is a critical pathway for the repair of DNA double-strand breaks and broken replication forks. Although homologous recombination is generally error-free, recombination between misaligned ...

  8. Genes and structural proteins of the phage SYN5 of the marine cyanobacteria, Synechococcus

    E-Print Network [OSTI]

    Pope, Welkin Hazel

    2005-01-01T23:59:59.000Z

    Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10łą particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed ...

  9. Sound strand design : designing mechanical joints to facilitate user interaction within a physical representation of digital music

    E-Print Network [OSTI]

    Shen, Yan, S.B. Massachusetts Institute of Technology

    2011-01-01T23:59:59.000Z

    This project involved the mechanical design of a modular musical instrument, named the "Sound Strand." Intended to be attached end-to-end one onto another in order to produce a string of music, each module was constructed ...

  10. Single Molecule DNA Detection with an Atomic Vapor Notch Filter

    E-Print Network [OSTI]

    Uhland, Denis; Widmann, Matthias; Lee, Sang-Yun; Wrachtrup, Jörg; Gerhardt, Ilja

    2015-01-01T23:59:59.000Z

    The detection of single molecules has facilitated many advances in life- and material-sciences. Commonly, it founds on the fluorescence detection of single molecules, which are for example attached to the structures under study. For fluorescence microscopy and sensing the crucial parameters are the collection and detection efficiency, such that photons can be discriminated with low background from a labeled sample. Here we show a scheme for filtering the excitation light in the optical detection of single stranded labeled DNA molecules. We use the narrow-band filtering properties of a hot atomic vapor to filter the excitation light from the emitted fluorescence of a single emitter. The choice of atomic sodium allows for the use of fluorescent dyes, which are common in life-science. This scheme enables efficient photon detection, and a statistical analysis proves an enhancement of the optical signal of more than 15% in a confocal and in a wide-field configuration.

  11. Quadratic $?'$-Corrections to Heterotic Double Field Theory

    E-Print Network [OSTI]

    Kanghoon Lee

    2015-04-01T23:59:59.000Z

    We investigate $\\alpha'$-corrections of heterotic double field theory up to quadratic order in the language of supersymmetric O(D,D+dim G) gauged double field theory. After introducing double-vielbein formalism with a parametrization which reproduces heterotic supergravity, we show that supersymmetry for heterotic double field theory up to leading order $\\alpha'$-correction is obtained from supersymmetric gauged double field theory. We discuss the necessary modifications of the symmetries defined in supersymmetric gauged double field theory. Further, we construct supersymmetric completion at quadratic order in $\\alpha'$.

  12. Studies on the integration pattern of FBDV genome in host cell DNA

    E-Print Network [OSTI]

    Baig, Mirza Amanatulla

    1992-01-01T23:59:59.000Z

    at characterization of the virus was made based on its morphology as visualized by electron microscopy, nucleic acid type, and protein composition (Ritchie et al. , 1989a). In these studies it has been shown that the virus is icosahedral in structure, 14-16 nm...- enveloped DNA: size (kb) type 2. 2-2. 3 1. 76 1. 7-2. 0 1. 5-2. 0 ----- circular, single stranded -- ?? POLYPEPTIDES: Number MW (kD) 50 36 26. 3, 23 ' 7/ 15. 9 Not done a: Todd et al. (1990). b: Tischer et al. (1982) c: Graham (1985b), & Ritchie...

  13. Constraining neutrinoless double beta decay

    E-Print Network [OSTI]

    L. Dorame; D. Meloni; S. Morisi; E. Peinado; J. W. F. Valle

    2011-11-23T23:59:59.000Z

    A class of discrete flavor-symmetry-based models predicts constrained neutrino mass matrix schemes that lead to specific neutrino mass sum-rules (MSR). We show how these theories may constrain the absolute scale of neutrino mass, leading in most of the cases to a lower bound on the neutrinoless double beta decay effective amplitude.

  14. What can we learn from neutrinoless double beta decay experiments?

    E-Print Network [OSTI]

    Bahcall, John N.

    2009-01-01T23:59:59.000Z

    Limits From Neutrinoless Double-Beta Decay (Rev. ),” ina next generation neutrinoless double beta decay search andPARTICLES? NO NEUTRINOLESS DOUBLE BETA DECAY AND INVERTED

  15. 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

  16. 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.

  17. 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...

  18. Final Report-MATERIALS, STRANDS, AND CABLES FOR SUPERCONDUCTING ACCELERATOR MAGNETS

    SciTech Connect (OSTI)

    Sumption, Mike D [OSU; Collings, E W

    2014-09-19T23:59:59.000Z

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the “intermediate-temperature superconductor”, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of “Strands” in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, “Cables”, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  19. 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.

  20. 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.

  1. Electrochemical DNA biosensor for detection of porcine oligonucleotides using ruthenium(II) complex as intercalator label redox

    SciTech Connect (OSTI)

    Halid, Nurul Izni Abdullah; Hasbullah, Siti Aishah; Heng, Lee Yook; Karim, Nurul Huda Abd [School of Chemical Sciences and Food Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan (Malaysia); Ahmad, Haslina; Harun, Siti Norain [Chemistry Department, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor (Malaysia)

    2014-09-03T23:59:59.000Z

    A DNA biosensor detection of oligonucleotides via the interactions of porcine DNA with redox active complex based on the electrochemical transduction is described. A ruthenium(II) complex, [Ru(bpy){sub 2}(PIP)]{sup 2+}, (bpy = 2,2?bipyridine, PIP = 2-phenylimidazo[4,5-f[[1,10-phenanthroline]) as DNA label has been synthesized and characterized by 1H NMR and mass spectra. The study was carried out by covalent bonding immobilization of porcine aminated DNA probes sequences on screen printed electrode (SPE) modified with succinimide-acrylic microspheres and [Ru(bpy){sub 2}(PIP)]{sup 2+} was used as electrochemical redox intercalator label to detect DNA hybridization event. Electrochemical detection was performed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) over the potential range where the ruthenium (II) complex was active. The results indicate that the interaction of [Ru(bpy){sub 2}(PIP)]{sup 2+} with hybridization complementary DNA has higher response compared to single-stranded and mismatch complementary DNA.

  2. Neutrinoless Double Beta Decay Experiments

    E-Print Network [OSTI]

    Garfagnini, Alberto

    2014-01-01T23:59:59.000Z

    Neutrinoless double beta decay is the only process known so far able to test the neutrino intrinsic nature: its experimental observation would imply that the lepton number is violated by two units and prove that neutrinos have a Majorana mass components, being their own anti-particle. While several experiments searching for such a rare decay have been performed in the past, a new generation of experiments using different isotopes and techniques have recently released their results or are taking data and will provide new limits, should no signal be observed, in the next few years to come. The present contribution reviews the latest public results on double beta decay searches and gives an overview on the expected sensitivities of the experiments in construction which will be able to set stronger limits in the near future.

  3. Neutrinoless Double Beta Decay Experiments

    E-Print Network [OSTI]

    Alberto Garfagnini

    2014-08-11T23:59:59.000Z

    Neutrinoless double beta decay is the only process known so far able to test the neutrino intrinsic nature: its experimental observation would imply that the lepton number is violated by two units and prove that neutrinos have a Majorana mass components, being their own anti-particle. While several experiments searching for such a rare decay have been performed in the past, a new generation of experiments using different isotopes and techniques have recently released their results or are taking data and will provide new limits, should no signal be observed, in the next few years to come. The present contribution reviews the latest public results on double beta decay searches and gives an overview on the expected sensitivities of the experiments in construction which will be able to set stronger limits in the near future.

  4. 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, ...

  5. Pair extended coupled cluster doubles

    E-Print Network [OSTI]

    Henderson, Thomas M; Scuseria, Gustavo E

    2015-01-01T23:59:59.000Z

    The accurate and efficient description of strongly correlated systems remains an important challenge for computational methods. Doubly occupied configuration interaction (DOCI), in which all electrons are paired and no correlations which break these pairs are permitted, can in many cases provide an accurate account of strong correlations, albeit at combinatorial computational cost. Recently, there has been significant interest in a method we refer to as pair coupled cluster doubles (pCCD), a variant of coupled cluster doubles in which the electrons are paired. This is simply because pCCD provides energies nearly identical to those of DOCI, but at mean-field computational cost (disregarding the cost of the two-electron integral transformation). Here, we introduce the more complete pair extended coupled cluster doubles (pECCD) approach which, like pCCD, has mean-field cost and reproduces DOCI energetically. We show that unlike pCCD, pECCD also reproduces the DOCI wave function with high accuracy. Moreoever, pEC...

  6. Final Report: MATERIALS, STRANDS, AND CABLES FOR SUPERCONDUCTING ACCELERATOR MAGNETS [Grant Number DE-SC0010312

    SciTech Connect (OSTI)

    Sumption, Mike; Collings, E.

    2014-10-29T23:59:59.000Z

    Our program consisted of the two components: Strand Research and Cable Research, with a focus on Nb3Sn, Bi2212, and YBCO for accelerator magnet applications. We demonstrated a method to refine the grains in Nb3Sn by a factor of two, reaching 45 nm grain sizes, and layer Jcs of 6 kA/mm2 at 12 T. W also measured conductor magnetization for field quality. This has been done both with Nb3Sn conductor, as well as Bi:2212 strand. Work in support of quench studies of YBCO coils was also performed. Cable loss studies in Nb3Sn focused on connecting and comparing persistent magnetization and coupling magnetization for considering their relative impact on HEP machines. In the area of HTS cables, we have investigated both the quench in multistrand YBCO CORC cables, as well as the magnetization of these cables for use in high field magnets. In addition, we examined the magnetic and thermal properties of large (50 T) solenoids.

  7. 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

  8. 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.

  9. Base sequence effects on interactions of aromatic mutagens with DNA

    SciTech Connect (OSTI)

    Geacintov, N.E.

    1991-09-19T23:59:59.000Z

    Within this period, we have completed our investigations on the thermodynamic characteristics and base sequence dependence of duplex formation of benzo(a)pyrene diol epoxide (BPDE) DNA adducts. Different 11-mer oligonucleotides containing covalently bound BPDE moieties at the exocyclic amino group of a single guanine base were utilized in these studies. Last year, in the three-year progress report, some preliminary data were discussed. A final account is provided here. New techniques were developed for assessing the preferred orientations of the enantiomers of (+)-BPDE and ({minus})-BPDE relative to the 5in {r arrow} 3in polarity of DNA strands; these investigations were prompted by predictions derived from our computer modeling studies. Significant progress was made towards synthesizing BPDE-adenine adducts in base sequence-specific oligonucleotides. We failed, on the other hand, to synthesize nitrosopyrene-oligonucleotide adducts because of intrinsic low reactivities of the nitrenium derivative ions with oligonucleotides. Nature was against us in this effort. Therefore, this particular goal to be abandoned. 14 refs., 8 figs., 4 tabs.

  10. Monosporascus root rot/vine decline: a study of double-stranded (DS) RNA and its role in the pathogenesis of Monosporascus cannonballus on muskmelon

    E-Print Network [OSTI]

    Batten, Jeffrey Samuel

    1997-01-01T23:59:59.000Z

    dodecyl sulfate (SDS), and 10 mg of carborundum (Sigma Chemical Co. , St. Louis, MO) for 1 min and incubated for 30 min at 37'C to allow for degradation of host RNAs. Nucleic acids were extracted with an equal volume of TE saturated phenol...

  11. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families

    SciTech Connect (OSTI)

    Carbonell, Alberto; Martinez de Alba, Angel-Emilio [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain); Flores, Ricardo [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain)], E-mail: rflores@ibmcp.upv.es; Gago, Selma [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain)

    2008-02-05T23:59:59.000Z

    Infection by viroids, non-protein-coding circular RNAs, occurs with the accumulation of 21-24 nt viroid-derived small RNAs (vd-sRNAs) with characteristic properties of small interfering RNAs (siRNAs) associated to RNA silencing. The vd-sRNAs most likely derive from dicer-like (DCL) enzymes acting on viroid-specific dsRNA, the key elicitor of RNA silencing, or on the highly structured genomic RNA. Previously, viral dsRNAs delivered mechanically or agroinoculated have been shown to interfere with virus infection in a sequence-specific manner. Here, we report similar results with members of the two families of nuclear- and chloroplast-replicating viroids. Moreover, homologous vd-sRNAs co-delivered mechanically also interfered with one of the viroids examined. The interference was sequence-specific, temperature-dependent and, in some cases, also dependent on the dose of the co-inoculated dsRNA or vd-sRNAs. The sequence-specific nature of these effects suggests the involvement of the RNA induced silencing complex (RISC), which provides sequence specificity to RNA silencing machinery. Therefore, viroid titer in natural infections might be regulated by the concerted action of DCL and RISC. Viroids could have evolved their secondary structure as a compromise between resistance to DCL and RISC, which act preferentially against RNAs with compact and relaxed secondary structures, respectively. In addition, compartmentation, association with proteins or active replication might also help viroids to elude their host RNA silencing machinery.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Double perovskite catalysts for oxidative coupling

    DOE Patents [OSTI]

    Campbell, K.D.

    1991-01-01T23:59:59.000Z

    Alkali metal doped double perovskites containing manganese and at least one of cobalt, iron and nickel are useful in the oxidative coupling of alkane to higher hydrocarbons.

  17. Review of double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2014-03-12T23:59:59.000Z

    The brief review of current experiments on search and studying of double beta decay processes is done. Best present limits on $\\langle m_{\

  18. Operator Analysis of Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Kiwoon Choi; Kwang Sik Jeong; Wan Young Song

    2002-07-19T23:59:59.000Z

    We study the effective operators of the standard model fields which would yield an observable rate of neutrinoless double beta decay. We particularly focus on the possibility that neutrinoless double beta decay is dominantly induced by lepton-number-violating higher dimensional operators other than the Majorana neutrino mass. Our analysis can be applied to models in which neutrinoless double beta decay is induced either by a strong dynamics or by quantum gravity effects at a fundamental scale near the TeV scale as well as the conventional models in which neutrinoless double beta decay is induced by perturbative renormalizable interactions.

  19. Neutrinoless Double Beta Decay: Present and Future

    E-Print Network [OSTI]

    Oliviero Cremonesi

    2002-10-04T23:59:59.000Z

    Present status, and future plans for Double Beta Decay searches are reviewed. Given the recent observations of neutrino oscillations, a possibility to observe $\\beta\\beta(0\

  20. Losses in 23 strands NbTi and Nb/sub 3/Sn flat cables

    SciTech Connect (OSTI)

    Polak, M.; Krempasky, L.; Hlasnik, I.; Perot, J.

    1981-09-01T23:59:59.000Z

    Losses in different samples made of 23 strands multifilamentary NbTi and Nb/sub 3/Sn Rutherford type superconducting cables in pulsed magnetic fields were measured using the magnetization technique. Two technologies were used for sample preparation. One reason for this was to simulate the different winding structure of the pulsed magnets. Another reason was to obtain the samples with different average transverse resistivity across the unsoldered cable. For comparison, one sample, having a low average transverse resistivity, was made of the soldered cable. The influence of the cable pieces length, used for samples, on the rate dependent losses is demonstrated. Problems concerning the measurement of the time constant of the rate dependent magnetization are discussed. 4 refs.

  1. Accepted SNAME Annual Meeting T&R 2003 and SNAME Transactions 2003 Modeling Motion and Loads on Stranded Ships in Waves

    E-Print Network [OSTI]

    Brown, Alan

    and motions on a stranded ship in waves. In this paper, a model for predict- ing ship motion and ground jk - ground reaction dynamic stiffness matrix - wave frequency kx - complex ship motion magnitude-grounding structural loads. This paper describes the dynamic effect of waves on stranded ship motion and loads

  2. Improved Beta-Protein Structure Prediction by Multilevel Optimization of NonLocal Strand Pairings and Local

    E-Print Network [OSTI]

    Baker, David

    using backbone torsion-space moves. An iterative, energy-biased resampling strategy is used to exploreImproved Beta-Protein Structure Prediction by Multilevel Optimization of NonLocal Strand Pairings and Local Backbone Conformation Philip Bradley and David Baker* University of Washington, Seattle

  3. www.iaei.org July.August 2005 IAEI NEWS 83 GROUNDING PV AND SYSTEMS FINE STRANDED CONDUCTORS

    E-Print Network [OSTI]

    Johnson, Eric E.

    with single inverters sized below about 10 kW. Figure 1 shows the dc grounding for a PV system as spelled outwww.iaei.org July.August 2005 IAEI NEWS 83 GROUNDING PV AND SYSTEMS FINE STRANDED CONDUCTORS Grounding In the "Perspectives on PV" article in the September- October 2004 issue of the IAEI News

  4. The tropical double description method

    E-Print Network [OSTI]

    Allamigeon, Xavier; Goubault, Eric

    2010-01-01T23:59:59.000Z

    We develop a tropical analogue of the classical double description method allowing one to compute an internal representation (in terms of vertices) of a polyhedron defined externally (by inequalities). The heart of the tropical algorithm is a characterization of the extreme points of a polyhedron in terms of a system of constraints which define it. We show that checking the extremality of a point reduces to checking whether there is only one minimal strongly connected component in an hypergraph. The latter problem can be solved in almost linear time, which allows us to eliminate quickly redundant generators. We report extensive tests (including benchmarks from an application to static analysis) showing that the method outperforms experimentally the previous ones by orders of magnitude. The present tools also lead to worst case bounds which improve the ones provided by previous methods.

  5. Predicting neutrinoless double beta decay

    SciTech Connect (OSTI)

    Hirsch, M.; Villanova del Moral, A.; Valle, J.W.F. [AHEP Group, Instituto de Fisica Corpuscular - C.S.I.C./Universitat de Valencia, Edificio Institutos de Paterna, Apt 22085, E-46071 Valencia (Spain); Ma, Ernest [Physics Department, University of California, Riverside, California 92521 (United States); Institute for Particle Physics Phenomenology, University of Durham, Durham, DH1 3LE (United Kingdom)

    2005-11-01T23:59:59.000Z

    We give predictions for the neutrinoless double beta decay rate in a simple variant of the A{sub 4} family symmetry model. We show that there is a lower bound for the {beta}{beta}{sub 0{nu}} amplitude even in the case of normal hierarchical neutrino masses, corresponding to an effective mass parameter vertical bar m{sub ee} vertical bar {>=}0.17{radical}({delta}m{sub ATM}{sup 2}). This result holds both for the CP conserving and CP violating cases. In the latter case we show explicitly that the lower bound on vertical bar m{sub ee} vertical bar is sensitive to the value of the Majorana phase. We conclude therefore that in our scheme, {beta}{beta}{sub 0{nu}} may be accessible to the next generation of high sensitivity experiments.

  6. 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

  7. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1988-10-11T23:59:59.000Z

    A double or multiple bevel culet geometry is used on a diamond anvil in a high pressure cell apparatus to provide increased sample pressure and stability for a given force applied to the diamond tables. Double or multiple bevel culet geometries can also be used for sapphire or other hard crystal anvils. Pressures up to and above 5 Megabars can be reached. 8 figs.

  8. Double beta decay: experiments and theory review

    E-Print Network [OSTI]

    A. Nucciotti

    2007-07-28T23:59:59.000Z

    Neutrinoless double beta decay is one of the most powerful tools to set the neutrino mass absolute scale and establish whether the neutrino is a Majorana particle. After a summary of the neutrinoless double beta decay phenomenology, the present status of the experimental search for this rare decay is reported and the prospects for next generation experiments are reviewed.

  9. Neutrinoless double beta decay and neutrino physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2012-08-20T23:59:59.000Z

    The connection of neutrino physics with neutrinoless double beta decay is reviewed. After presenting the current status of the PMNS matrix and the theoretical background of neutrino mass and lepton mixing, we will summarize the various implications of neutrino physics for double beta decay. The influence of light sterile neutrinos and other exotic modifications of the three neutrino picture is also discussed.

  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. Instability limits for spontaneous double layer formation

    SciTech Connect (OSTI)

    Carr, J. Jr. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Department of Physics, Texas Lutheran University, Seguin, Texas 78155 (United States); Galante, M. E.; McCarren, D.; Scime, E. E.; Sears, S.; VanDervort, R. W. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States)] [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Magee, R. M. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); TriAlpha Energy, Inc., Foothill Ranch, California 92610 (United States); Reynolds, E. [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)] [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)

    2013-11-15T23:59:59.000Z

    We present time-resolved measurements that demonstrate that large amplitude electrostatic instabilities appear in pulsed, expanding helicon plasmas at the same time as particularly strong double layers appear in the expansion region. A significant cross-correlation between the electrostatic fluctuations and fluctuations in the number of ions accelerated by the double layer electric field is observed. No correlation is observed between the electrostatic fluctuations and ions that have not passed through the double layer. These measurements confirm that the simultaneous appearance of the electrostatic fluctuations and the double layer is not simple coincidence. In fact, the accelerated ion population is responsible for the growth of the instability. The double layer strength, and therefore, the velocity of the accelerated ions, is limited by the appearance of the electrostatic instability.

  14. Reliability Estimation for Double Containment Piping

    SciTech Connect (OSTI)

    L. Cadwallader; T. Pinna

    2012-08-01T23:59:59.000Z

    Double walled or double containment piping is considered for use in the ITER international project and other next-generation fusion device designs to provide an extra barrier for tritium gas and other radioactive materials. The extra barrier improves confinement of these materials and enhances safety of the facility. This paper describes some of the design challenges in designing double containment piping systems. There is also a brief review of a few operating experiences of double walled piping used with hazardous chemicals in different industries. This paper recommends approaches for the reliability analyst to use to quantify leakage from a double containment piping system in conceptual and more advanced designs. The paper also cites quantitative data that can be used to support such reliability analyses.

  15. 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.

  16. A Study of Stranding of Juvenile Salmon by Ship Wakes Along the Lower Columbia River Using a Before-and-After Design: Before-Phase Results

    SciTech Connect (OSTI)

    Pearson, Walter H.; Skalski, J R.; Sobocinski, Kathryn L.; Miller, Martin C.; Johnson, Gary E.; Williams, Greg D.; Southard, John A.; Buchanan, Rebecca A.

    2006-02-01T23:59:59.000Z

    Ship wakes produced by deep-draft vessels transiting the lower Columbia River have been observed to cause stranding of juvenile salmon. Proposed deepening of the Columbia River navigation channel has raised concerns about the potential impact of the deepening project on juvenile salmon stranding. The Portland District of the U.S. Army Corps of Engineers requested that the Pacific Northwest National Laboratory design and conduct a study to assess stranding impacts that may be associated with channel deepening. The basic study design was a multivariate analysis of covariance of field observations and measurements under a statistical design for a before and after impact comparison. We have summarized field activities and statistical analyses for the ?before? component of the study here. Stranding occurred at all three sampling sites and during all three sampling seasons (Summer 2004, Winter 2005, and Spring 2005), for a total of 46 stranding events during 126 observed vessel passages. The highest occurrence of stranding occurred at Barlow Point, WA, where 53% of the observed events resulted in stranding. Other sites included Sauvie Island, OR (37%) and County Line Park, WA (15%). To develop an appropriate impact assessment model that accounted for relevant covariates, regression analyses were conducted to determine the relationships between stranding probability and other factors. Nineteen independent variables were considered as potential factors affecting the incidence of juvenile salmon stranding, including tidal stage, tidal height, river flow, current velocity, ship type, ship direction, ship condition (loaded/unloaded), ship speed, ship size, and a proxy variable for ship kinetic energy. In addition to the ambient and ship characteristics listed above, site, season, and fish density were also considered. Although no single factor appears as the primary factor for stranding, statistical analyses of the covariates resulted in the following equations: (1) Stranding Probability {approx} Location + Kinetic Energy Proxy + Tidal Height + Salmonid Density + Kinetic energy proxy ? Tidal Height + Tidal Height x Salmonid Density. (2) Stranding Probability {approx} Location + Total Wave Distance + Salmonid Density Index. (3) Log(Total Wave Height) {approx} Ship Block + Tidal Height + Location + Ship Speed. (4) Log(Total Wave Excursion Across the Beach) {approx} Location + Kinetic Energy Proxy + Tidal Height The above equations form the basis for a conceptual model of the factors leading to salmon stranding. The equations also form the basis for an approach for assessing impacts of dredging under the before/after study design.

  17. 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

  18. Neutrinoless Double Beta Decay in Light of SNO Salt Data

    E-Print Network [OSTI]

    Murayama, Hitoshi

    2009-01-01T23:59:59.000Z

    Limits From Neutrinoless Double-Beta Decay (Rev. ),” incan also cause neutrinoless double-beta decay (see e.g. , [LBNL-53996 Neutrinoless Double Beta Decay in Light of SNO

  19. A Search for Neutrinoless Double Beta Decay of Te-130

    E-Print Network [OSTI]

    Bryant, Adam Douglas

    2010-01-01T23:59:59.000Z

    A Search for Neutrinoless Double Beta Decay of Te by AdamA Search for Neutrinoless Double Beta Decay of CopyrightA Search for Neutrinoless Double Beta Decay of Te by Adam

  20. Dynamic Phase Shifts in Nanoscale Distance Measurements by Double...

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

    by Double Electron Electron Resonance (DEER)† . Abstract: The off-resonant pump pulse used in double electron electron resonance (DEER) measurements produces dynamic...

  1. antigen doubling time: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  2. acute double blockade: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  3. albicans double infection: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  4. air double contrast: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  5. ammonium lanthanide double: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  6. Search for: "neutrinoless double beta decay" | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    neutrinoless double beta decay" Find + Advanced Search Advanced Search All Fields: "neutrinoless double beta decay" Title: Full Text: Bibliographic Data: Creator Author: Name...

  7. Neutrinoless Double Beta Decay and Neutrino Masses

    E-Print Network [OSTI]

    Michael Duerr

    2012-06-04T23:59:59.000Z

    Neutrinoless double beta decay is a promising test for lepton number violating physics beyond the standard model of particle physics. There is a deep connection between this decay and the phenomenon of neutrino masses. In particular, we will discuss the relation between neutrinoless double beta decay and Majorana neutrino masses provided by the so-called Schechter--Valle theorem in a quantitative way. Furthermore, we will present an experimental cross check to discriminate neutrinoless double beta decay from unknown nuclear background using only one isotope, i.e., within one experiment.

  8. 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.

  9. The Double-Dark Portal

    E-Print Network [OSTI]

    David Curtin; Yuhsin Tsai

    2014-12-04T23:59:59.000Z

    In most models of the dark sector, dark matter is charged under some new symmetry to make it stable. We explore the possibility that not just dark matter, but also the force carrier connecting it to the visible sector is charged under this symmetry. This dark mediator then acts as a Double-Dark Portal. We realize this setup in the \\emph{dark mediator Dark matter} model (dmDM), featuring a fermionic DM candidate $\\chi$ with Yukawa couplings to light scalars $\\phi_i$. The scalars couple to SM quarks via the operator $\\bar q q \\phi_i^* \\phi_j/\\Lambda_{ij}$. This can lead to large direct detection signals via the $2\\rightarrow3$ process $\\chi N \\rightarrow \\chi N \\phi$ if one of the scalars has mass $ \\lesssim 10$ keV. For dark matter Yukawa couplings $y_\\chi \\sim 10^{-3} - 10^{-2}$, dmDM features a thermal relic dark matter candidate while also implementing the SIDM scenario for ameliorating inconsistencies between dwarf galaxy simulations and observations. We undertake the first systematic survey of constraints on light scalars coupled to the SM via the above operator. The strongest constraints are derived from a detailed examination of the light mediator's effects on stellar astrophysics. LHC experiments and cosmological considerations also yield important bounds. Observations of neutron star cooling exclude the minimal model with one dark mediator, but a scenario with two dark mediators remains viable and can give strong direct detection signals. We explore the direct detection consequences of this scenario and find that a heavy $\\mathcal{O}(100)$ GeV dmDM candidate fakes different $\\mathcal{O}(10)$ GeV WIMPs at different experiments. Large regions of dmDM parameter space are accessible above the irreducible neutrino background.

  10. Formation of double-$?$ hypernuclei at PANDA

    E-Print Network [OSTI]

    T. Gaitanos; A. B. Larionov; H. Lenske; U. Mosel

    2012-01-17T23:59:59.000Z

    We study the formation of single- and double-$\\Lambda$ hypernuclei in antiproton-induced reactions relevant for the forthcoming PANDA experiment at FAIR. We use the Giessen Boltzmann-Uehling-Uhlenbeck (GiBUU) transport model with relativistic mean-fields for the description of non-equilibrium dynamics and the statistical multifragmentation model (SMM) for fragment formation. This combined approach describes the dynamical properties of strangeness and fragments in low energy $\\bar{p}$-induced reactions fairly well. We then focus on the formation of double-$\\Lambda$ hypernuclei in high energy $\\bar{p}$-nucleus collisions on a primary target including the complementary $\\Xi$-induced reactions to a secondary one, as proposed by the PANDA collaboration. Our results show that a copious production of double-$\\Lambda$ hyperfragments is possible at PANDA. In particular, we provide first theoretical estimations on the double-$\\Lambda$ production cross section, which strongly rises with decreasing energy of the secondary $\\Xi$-beam.

  11. Double field theory of type II strings

    E-Print Network [OSTI]

    Hohm, Olaf

    We use double field theory to give a unified description of the low energy limits of type IIA and type IIB superstrings. The Ramond-Ramond potentials fit into spinor representations of the duality group O(D, D) and ...

  12. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    J. J. Gómez-Cadenas; Justo Martín-Albo

    2015-02-25T23:59:59.000Z

    This paper reviews the current status and future outlook of neutrinoless double beta decay searches, which try to provide an answer to the fundamental question of whether neutrinos are Dirac or Majorana particles.

  13. Probing neutrinoless double beta decay with SNO+

    E-Print Network [OSTI]

    Evelina Arushanova; Ashley R. Back

    2015-05-01T23:59:59.000Z

    Probing neutrinoless double beta decay is one of the primary goals for SNO+, SNOLAB's multi-purpose neutrino detector. In order to achieve this goal the SNO detector has been adapted so that it can be filled with Te-loaded liquid scintillator. During the initial double beta phase the target loading is 0.3% natural Te, which equates to $\\sim790$ kg of double beta isotope. Estimating the sensitivity to neutrinoless double beta decay requires a well understood background model. For SNO+ this is provided by a comprehensive study considering all possible background contributions, whether they originate from within the liquid scintillator cocktail, the surrounding parts of the detector or other irreducible backgrounds. Given these considerations, for five years running in the initial phase, the expected sensitivity is $T_{1/2}^{0\

  14. Probing neutrinoless double beta decay with SNO+

    E-Print Network [OSTI]

    Arushanova, Evelina

    2015-01-01T23:59:59.000Z

    Probing neutrinoless double beta decay is one of the primary goals for SNO+, SNOLAB's multi-purpose neutrino detector. In order to achieve this goal the SNO detector has been adapted so that it can be filled with Te-loaded liquid scintillator. During the initial double beta phase the target loading is 0.3% natural Te, which equates to $\\sim790$ kg of double beta isotope. Estimating the sensitivity to neutrinoless double beta decay requires a well understood background model. For SNO+ this is provided by a comprehensive study considering all possible background contributions, whether they originate from within the liquid scintillator cocktail, the surrounding parts of the detector or other irreducible backgrounds. Given these considerations, for five years running in the initial phase, the expected sensitivity is $T_{1/2}^{0\

  15. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    Gómez-Cadenas, J J

    2015-01-01T23:59:59.000Z

    This paper reviews the current status and future outlook of neutrinoless double beta decay searches, which try to provide an answer to the fundamental question of whether neutrinos are Dirac or Majorana particles.

  16. Double layer capacitors : automotive applications and modeling

    E-Print Network [OSTI]

    New, David Allen, 1976-

    2004-01-01T23:59:59.000Z

    This thesis documents the work on the modeling of double layer capacitors (DLCs) and the validation of the modeling procedure. Several experiments were conducted to subject the device under test to a variety of ...

  17. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1987-02-06T23:59:59.000Z

    Use of double or multiple bevel culet geometry on a diamond anvil to provide increased sample pressure and stability for a given force applied to the diamond tables. 7 figs.

  18. Double Importance Sampling Val'erie Ventura

    E-Print Network [OSTI]

    Double Importance Sampling Val'erie Ventura Department of Statistics Carnegie Mellon University (Newton and Geyer, 1994, Ventura, 1998), where estimation must be made with respect to many first

  19. CP Violation in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    T. Fukuyama; K. Matsuda; H. Nishiura

    1997-08-19T23:59:59.000Z

    We argue three-flavour neutrino mixing. We consider the neutrinos as Majorana particles and see how the neutrinoless double beta decay constrains the neutrino mixing angles. Our formulation is widely valid and is applied to the neutrino oscillation experiment.

  20. Development and test of Nb3sn cos-theta coils made of high-jc rrp strands

    SciTech Connect (OSTI)

    Bossert, R.; Ambrosio, G.; Andreev, N.; Barzi, E.; Carcagno, R.; Feher, S.; Kashikhin, V.S.; Kashikhin, V.V.; Lamm, M.J.; Novitski, I.; Pischalnikov, Yu.; Sylvester, C.; Tartaglia, M.; Turrioni, D.; Yamada, R.; Zlobin, A.V.; /Fermilab

    2005-10-01T23:59:59.000Z

    A series of 1-m long Nb3Sn dipole magnets have been built at Fermilab in an attempt to refine the wind-and-react technology for Nb{sub 3}Sn conductor. Models have been made with MJR and PIT strand with varying degrees of success. Subsequently two new dipole ''mirror'' magnets based on RRP Nb{sub 3}Sn coils were constructed and tested. This paper describes the design, fabrication and test results of those magnets.

  1. Wavelength-doubling optical parametric oscillator

    DOE Patents [OSTI]

    Armstrong, Darrell J. (Albuquerque, NM); Smith, Arlee V. (Albuquerque, NM)

    2007-07-24T23:59:59.000Z

    A wavelength-doubling optical parametric oscillator (OPO) comprising a type II nonlinear optical medium for generating a pair of degenerate waves at twice a pump wavelength and a plurality of mirrors for rotating the polarization of one wave by 90 degrees to produce a wavelength-doubled beam with an increased output energy by coupling both of the degenerate waves out of the OPO cavity through the same output coupler following polarization rotation of one of the degenerate waves.

  2. Double shell tank waste analysis plan

    SciTech Connect (OSTI)

    Mulkey, C.H.; Jones, J.M.

    1994-12-15T23:59:59.000Z

    Waste analysis plan for the double shell tanks. SD-WM-EV-053 is Superseding SD-WM-EV-057.This document provides the plan for obtaining information needed for the safe waste handling and storage of waste in the Double Shell Tank Systems. In Particular it addresses analysis necessary to manage waste according to Washington Administrative Code 173-303 and Title 40, parts 264 and 265 of the Code of Federal Regulations.

  3. Neutrinoless double beta decay with scalar bilinears

    E-Print Network [OSTI]

    H. V. Klapdor-Kleingrothaus; U. Sarkar

    2002-11-18T23:59:59.000Z

    One possible probe to physics beyond the standard model is to look for scalar bilinears, which couple to two fermions of the standard model. We point out that the scalar bilinears allow new diagrams contributing to the neutrinoless double beta decay. The upper bound on the neutrinoless double beta decay lifetime would then give new constraints on the ratio of the masses of these scalars to their couplings to the fermions.

  4. Searches for neutrinoless double beta decay

    E-Print Network [OSTI]

    B. Schwingenheuer

    2012-01-24T23:59:59.000Z

    Neutrinoless double beta decay is a lepton number violating process whose observation would also establish that neutrinos are their own anti-particles. There are many experimental efforts with a variety of techniques. Some (EXO, Kamland-Zen, GERDA phase I and CANDLES) started take data in 2011 and EXO has reported the first measurement of the half life for the double beta decay with two neutrinos of $^{136}$Xe. The sensitivities of the different proposals are reviewed.

  5. Neutrinoless Double Beta Decay and CP Violation

    E-Print Network [OSTI]

    Patrick J. O'Donnell; Utpal Sarkar

    1993-05-27T23:59:59.000Z

    We study the relation between the Majorana neutrino mass matrices and the neutrinoless double beta decay when CP is not conserved. We give an explicit form of the decay rate in terms of a rephasing invariant quantity and demonstrate that in the presence of CP violation it is impossible to have vanishing neutrinoless double beta decay in the case of two neutrino generations (or when the third generation leptons do not mix with other leptons and hence decouple).

  6. Fabrication and test of 4m long Nb3Sn quadrupole coil made of RRP-114-127 strand

    SciTech Connect (OSTI)

    Bossert, R.; Ambrosio, G.; Andreev, N.; Barzi, E.; Chlachidze, G.; Kashikhin, V.V.; Lamm, M.; Nobrega, A.; Novitski, I.; Orris, D.; Tartaglia, M.; /Fermilab

    2011-06-01T23:59:59.000Z

    Fermilab is collaborating with LBNL and BNL (US-LARP collaboration) to develop a large-aperture Nb{sub 3}Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade. Several two-layer quadrupole models of the 1-meter and 3.4-meter length with 90mm apertures have been fabricated and tested by the US-LARP collaboration. High-Jc RRP-54/61 strand was used for nearly all models. Large flux jumps typical for this strand due to the large sub-element diameter limited magnet quench performance at temperatures below 2.5-3K. This paper summarizes the fabrication and test by Fermilab of LQM01, a long quadrupole coil test structure (quadrupole mirror) with the first 3.4m quadrupole coil made of more stable RRP-114/127 strand. The coil and structure are fully instrumented with voltage taps, full bridge strain gauges and strip heaters to monitor preload, thermal properties and quench behavior. Measurements during fabrication are reported, including preload during the yoke welding process. Testing is done at 4.5K, 1.9K and a range of intermediate temperatures. The test results include magnet strain and quench performance during training, as well as quench studies of current ramp rate and temperature dependence from 1.9K to 4.5K.

  7. Solid-state NMR analysis of the {beta}-strand orientation of the protofibrils of amyloid {beta}-protein

    SciTech Connect (OSTI)

    Doi, Takashi [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan)] [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Masuda, Yuichi, E-mail: masuda@mail.pharm.tohoku.ac.jp [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan) [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578 (Japan); Irie, Kazuhiro [Graduate School of Agriculture, Kyoto University, Kyoto 606-8502 (Japan)] [Graduate School of Agriculture, Kyoto University, Kyoto 606-8502 (Japan); Akagi, Ken-ichi; Monobe, Youko; Imazawa, Takayoshi [Section of Laboratory Equipment, Division of Biomedical Research, National Institute of Biomedical Innovation, Osaka 567-0085 (Japan)] [Section of Laboratory Equipment, Division of Biomedical Research, National Institute of Biomedical Innovation, Osaka 567-0085 (Japan); Takegoshi, K. [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan)] [Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan)

    2012-11-30T23:59:59.000Z

    Highlights: Black-Right-Pointing-Pointer The supramolecular structure of A{beta}42 protofibrils was analyzed by solid-state NMR. Black-Right-Pointing-Pointer The Ala-21 residue in the A{beta}42 protofibrils is included in a slightly disordered {beta}-strand. Black-Right-Pointing-Pointer The A{beta}42 protofibrils do not form intermolecular in-register parallel {beta}-sheets. -- Abstract: Alzheimer's disease (AD) is caused by abnormal deposition (fibrillation) of a 42-residue amyloid {beta}-protein (A{beta}42) in the brain. During the process of fibrillation, the A{beta}42 takes the form of protofibrils with strong neurotoxicity, and is thus believed to play a crucial role in the pathogenesis of AD. To elucidate the supramolecular structure of the A{beta}42 protofibrils, the intermolecular proximity of the Ala-21 residues in the A{beta}42 protofibrils was analyzed by {sup 13}C-{sup 13}C rotational resonance experiments in the solid state. Unlike the A{beta}42 fibrils, an intermolecular {sup 13}C-{sup 13}C correlation was not found in the A{beta}42 protofibrils. This result suggests that the {beta}-strands of the A{beta}42 protofibrils are not in an in-register parallel orientation. A{beta}42 monomers would assemble to form protofibrils with the {beta}-strand conformation, then transform into fibrils by forming intermolecular parallel {beta}-sheets.

  8. 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.

  9. 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.

  10. Titanium subhydride potassium perchlorate (TiH1.65/KClO4) burn rates from hybrid closed bomb-strand burner experiments.

    SciTech Connect (OSTI)

    Cooper, Marcia A.; Oliver, Michael S.

    2012-08-01T23:59:59.000Z

    A hybrid closed bomb-strand burner is used to measure the burning behavior of the titanium subhydride potassium perchlorate pyrotechnic with an equivalent hydrogen concentration of 1.65. This experimental facility allows for simultaneous measurement of the closed bomb pressure rise and pyrotechnic burn rate as detected by electrical break wires over a range of pressures. Strands were formed by pressing the pyrotechnic powders to bulk densities between 60% and 90% theoretical maximum density. The burn rate dependance on initial density and vessel pressure are measured. At all initial strand densities, the burn is observed to transition from conductive to convective burning within the strand. The measured vessel pressure history is further analyzed following the closed bomb analysis methods developed for solid propellants.

  11. 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.

  12. 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.

  13. Ortho-positronium observation in the Double Chooz Experiment

    E-Print Network [OSTI]

    Y. Abe; J. C. dos Anjos; J. C. Barriere; E. Baussan; I. Bekman; M. Bergevin; T. J. C. Bezerra; L. Bezrukov; E. Blucher; C. Buck; J. Busenitz; A. Cabrera; E. Caden; L. Camilleri; R. Carr; M. Cerrada; P. -J. Chang; E. Chauveau; P. Chimenti; A. P. Collin; E. Conover; J. M. Conrad; J. I. Crespo-Anadon; K. Crum; A. S. Cucoanes; E. Damon; J. V. Dawson; J. Dhooghe; D. Dietrich; Z. Djurcic; M. Dracos; M. Elnimr; A. Etenko; M. Fallot; F. von Feilitzsch; J. Felde; S. M. Fernandes; V. Fischer; D. Franco; M. Franke; H. Furuta; I. Gil-Botella; L. Giot; M. Goger-Neff; L. F. G. Gonzalez; L. Goodenough; M. C. Goodman; C. Grant; N. Haag; T. Hara; J. Haser; M. Hofmann; G. A. Horton-Smith; A. Hourlier; M. Ishitsuka; J. Jochum; C. Jollet; F. Kaether; L. N. Kalousis; Y. Kamyshkov; D. M. Kaplan; T. Kawasaki; E. Kemp; H. de Kerret; D. Kryn; M. Kuze; T. Lachenmaier; C. E. Lane; T. Lasserre; A. Letourneau; D. Lhuillier; H. P. Lima Jr; M. Lindner; J. M. Lopez-Castano; J. M. LoSecco; B. Lubsandorzhiev; S. Lucht; J. Maeda; C. Mariani; J. Maricic; J. Martino; T. Matsubara; G. Mention; A. Meregaglia; T. Miletic; R. Milincic; A. Minotti; Y. Nagasaka; Y. Nikitenko; P. Novella; L. Oberauer; M. Obolensky; A. Onillon; A. Osborn; C. Palomares; I. M. Pepe; S. Perasso; P. Pfahler; A. Porta; G. Pronost; J. Reichenbacher; B. Reinhold; M. Rohling; R. Roncin; S. Roth; B. Rybolt; Y. Sakamoto; R. Santorelli; A. C. Schilithz; S. Schonert; S. Schoppmann; M. H. Shaevitz; R. Sharankova; S. Shimojima; D. Shrestha; V. Sibille; V. Sinev; M. Skorokhvatov; E. Smith; J. Spitz; A. Stahl; I. Stancu; L. F. F. Stokes; M. Strait; A. Stuken; F. Suekane; S. Sukhotin; T. Sumiyoshi; Y. Sun; R. Svoboda; K. Terao; A. Tonazzo; H. H. Trinh Thi; G. Valdiviesso; N. Vassilopoulos; C. Veyssiere; M. Vivier; S. Wagner; N. Walsh; H. Watanabe; C. Wiebusch; L. Winslow; M. Wurm; G. Yang; F. Yermia; V. Zimmer

    2014-10-07T23:59:59.000Z

    The Double Chooz experiment measures the neutrino mixing angle $\\theta_{13}$ by detecting reactor $\\bar{\

  14. Computer code for double beta decay QRPA based calculations

    E-Print Network [OSTI]

    Bertulani, Carlos A. - Department of Physics and Astronomy, Texas A&M University

    . The Enriched Xenon Observatory for neutrinoless double beta decay (EXO) will search for the rare decays

  15. 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...

  16. 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.

  17. Excited states and energy transfer among DNA bases in double helices

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    spectroscopy. The present article points out contentious questions regarding the nature of the excited states at the University of Stockholm (Sweden) in 1988. He joined CNRS in 1991 where he is presently research director. He a PhD in Chemistry from the University of Bern (Switzerland). He worked in the field of gas phase

  18. 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

  19. 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

  20. 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

  1. The Polymerase Chain Reaction and Branching Processes Fengzhu Sun

    E-Print Network [OSTI]

    Sun, Fengzhu - Sun, Fengzhu

    The Polymerase Chain Reaction and Branching Processes Fengzhu Sun Department of Mathematics, DRB is studied. We also study the distribution of the Hamming distance between two randomly chosen sequences long. The double-stranded DNA molecules are heated to near boiling temperature so that the double

  2. 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.

  3. The search for neutrinoless double beta decay

    E-Print Network [OSTI]

    J. J. Gomez-Cadenas; J. Martin-Albo; M. Mezzetto; F. Monrabal; M. Sorel

    2012-01-16T23:59:59.000Z

    In the last two decades the search for neutrinoless double beta decay has evolved into one of the highest priorities for understanding neutrinos and the origin of mass. The main reason for this paradigm shift has been the discovery of neutrino oscillations, which clearly established the existence of massive neutrinos. An additional motivation for conducting such searches comes from the existence of an unconfirmed, but not refuted, claim of evidence for neutrinoless double decay in $^{76}\\text{Ge}$. As a consequence, a new generation of experiments, employing different detection techniques and $\\beta\\beta$ isotopes, is being actively promoted by experimental groups across the world. In addition, nuclear theorists are making remarkable progress in the calculation of the neutrinoless double beta decay nuclear matrix elements, thus eliminating a substantial part of the theoretical uncertainties affecting the particle physics interpretation of this process. In this report, we review the main aspects of the double beta decay process and some of the most relevant experiments. The picture that emerges is one where searching for neutrinoless double beta decay is recognized to have both far-reaching theoretical implications and promising prospects for experimental observation in the near future.

  4. The unknotted strands of life: knots are very rare in RNA structures

    E-Print Network [OSTI]

    Cristian Micheletti; Marco Di Stefano; Henri Orland

    2014-10-06T23:59:59.000Z

    The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the other hand, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the ~6,000 RNA structures present in the protein data bank. The search identified no more than three deeply-knotted RNA molecules. These are ribosomal RNAs solved by cryo-em and consist of about 3,000 nucleotides. Compared to the case of proteins and viral DNA, the observed incidence of RNA knots is therefore practically negligible. This suggests that either evolutionary selection, or thermodynamic and kinetic folding mechanisms act towards minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. The properties of the three observed RNA knotting patterns provide valuable clues for designing RNA sequences capable of self-tying in a twist-knot fold.

  5. 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 ...

  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. Precision Muon Reconstruction in Double Chooz

    E-Print Network [OSTI]

    Double Chooz collaboration; Y. Abe; J. C. dos Anjos; J. C. Barriere; E. Baussan; I. Bekman; M. Bergevin; T. J. C. Bezerra; L. Bezrukov; E. Blucher; C. Buck; J. Busenitz; A. Cabrera; E. Caden; L. Camilleri; R. Carr; M. Cerrada; P. -J. Chang; E. Chauveau; P. Chimenti; A. P. Collin; E. Conover; J. M. Conrad; J. I. Crespo-Anadón; K. Crum; A. Cucoanes; E. Damon; J. V. Dawson; D. Dietrich; Z. Djurcic; M. Dracos; M. Elnimr; A. Etenko; M. Fallot; F. von Feilitzsch; J. Felde; S. M. Fernandes; V. Fischer; D. Franco; M. Franke; H. Furuta; I. Gil-Botella; L. Giot; M. Göger-Neff; L. F. G. Gonzalez; L. Goodenough; M. C. Goodman; C. Grant; N. Haag; T. Hara; J. Haser; M. Hofmann; G. A. Horton-Smith; A. Hourlier; M. Ishitsuka; J. Jochum; C. Jollet; F. Kaether; L. N. Kalousis; Y. Kamyshkov; D. M. Kaplan; T. Kawasaki; E. Kemp; H. de Kerret; D. Kryn; M. Kuze; T. Lachenmaier; C. E. Lane; T. Lasserre; A. Letourneau; D. Lhuillier; H. P. Lima Jr; M. Lindner; J. M. López-Casta no; J. M. LoSecco; B. Lubsandorzhiev; S. Lucht; J. Maeda; C. Mariani; J. Maricic; J. Martino; T. Matsubara; G. Mention; A. Meregaglia; T. Miletic; R. Milincic; A. Minotti; Y. Nagasaka; Y. Nikitenko; P. Novella; M. Obolensky; L. Oberauer; A. Onillon; A. Osborn; C. Palomares; I. M. Pepe; S. Perasso; P. Pfahler; A. Porta; G. Pronost; J. Reichenbacher; B. Reinhold; M. Röhling; R. Roncin; S. Roth; B. Rybolt; Y. Sakamoto; R. Santorelli; A. C. Schilithz; S. Schönert; S. Schoppmann; M. H. Shaevitz; R. Sharankova; S. Shimojima; V. Sibille; V. Sinev; M. Skorokhvatov; E. Smith; J. Spitz; A. Stahl; I. Stancu; L. F. F. Stokes; M. Strait; A. Stüken; F. Suekane; S. Sukhotin; T. Sumiyoshi; Y. Sun; R. Svoboda; K. Terao; A. Tonazzo; H. H. Trinh Thi; G. Valdiviesso; N. Vassilopoulos; C. Veyssiere; M. Vivier; S. Wagner; H. Watanabe; C. Wiebusch; L. Winslow; M. Wurm; G. Yang; F. Yermia; V. Zimmer

    2014-08-15T23:59:59.000Z

    We describe a muon track reconstruction algorithm for the reactor anti-neutrino experiment Double Chooz. The Double Chooz detector consists of two optically isolated volumes of liquid scintillator viewed by PMTs, and an Outer Veto above these made of crossed scintillator strips. Muons are reconstructed by their Outer Veto hit positions along with timing information from the other two detector volumes. All muons are fit under the hypothesis that they are through-going and ultrarelativistic. If the energy depositions suggest that the muon may have stopped, the reconstruction fits also for this hypothesis and chooses between the two via the relative goodness-of-fit. In the ideal case of a through-going muon intersecting the center of the detector, the resolution is ~40 mm in each transverse dimension. High quality muon reconstruction is an important tool for reducing the impact of the cosmogenic isotope background in Double Chooz.

  8. Double hadron leptoproduction in the nuclear medium

    E-Print Network [OSTI]

    Airapetian, A; Akopov, Z; Amarian, M; Andrus, A; Aschenauer, E C; Augustyniak, W; Avakian, R; Avetisian, A; Avetissian, E; Bailey, P; Belostotskii, S; Bianchi, N; Blok, H P; Böttcher, Helmut B; Borisov, A; Borysenko, A; Brüll, A; Bryzgalov, V; Capiluppi, M; Capitani, G P; Ciullo, G; Contalbrigo, M; Dalpiaz, P F; Deconinck, W; De Leo, R; Demey, M; De Nardo, L; De Sanctis, E; Devitsin, E G; Diefenthaler, M; Di Nezza, P; Dreschler, J; Düren, M; Ehrenfried, M; Elalaoui-Moulay, A; Elbakian, G; Ellinghaus, F; Elschenbroich, U; Fabbri, R; Fantoni, A; Felawka, L; Frullani, S; Funel, A; Gapienko, G; Gapienko, V; Garibaldi, F; Garrow, K; Gavrilov, G; Karibian, V; Giordano, F; Grebenyuk, O; Gregor, I M; Griffioen, K; Guler, H; Hadjidakis, C; Hartig, M; Hasch, D; Hasegawa, T; Hesselink, W H A; Hillenbrand, A; Hoek, M; Holler, Y; Hommez, B; Hristova, I; Iarygin, G; Ivanilov, A; Izotov, A; Jackson, H E; Jgoun, A; Kaiser, R; Keri, T; Kinney, E; Kiselev, A; Kobayashi, T; Kopytin, M; Korotkov, V; Kozlov, V; Krauss, B; Kravchenko, P; Krivokhizhin, V G; Lagamba, L; Lapikas, L; Lenisa, P; Liebing, P; Linden-Levy, L A; Lorenzon, W; Lü, J; Lu, S; Ma, B Q; Maiheu, B; Makins, N C R; Mao, Y; Marianski, B; Marukyan, H; Masoli, F; Mexner, V; Meyners, N; Michler, T; Miklukho, O; Miller, C A; Miyachi, Y; Muccifora, V; Murray, M; Nagaitsev, A; Nappi, E; Naryshkin, Yu; Negodaev, M; Nowak, Wolf-Dieter; Ohsuga, H; Osborne, A; Perez-Benito, R; Pickert, N; Raithel, M; Reggiani, D; Reimer, P E; Reischl, A; Reolon, A R; Riedl, C; Rith, K; Rosner, G; Rostomyan, A; Rubacek, L; Rubin, J; Ryckbosch, D; Salomatin, Y; Sanjiev, I; Savin, I; Schäfer, A; Schnell, G; Schüler, K P; Seele, J; Seidl, R; Seitz, B; Shearer, C; Shibata, T A; Shutov, V; Sinram, K; Stancari, M; Statera, M; Steffens, E; Steijger, J J M; Stenzel, H; Stewart, J; Stinzing, F; Streit, J; Tait, P; Tanaka, H; Taroian, S P; Tchuiko, B; Terkulov, A R; Trzcinski, A; Tytgat, M; Vandenbroucke, A; Van der Nat, P B; van der Steenhoven, G; Van Haarlem, Y; Veretennikov, D; Vikhrov, V; Vogel, C; Wang, S; Ye, Y; Ye, Z; Yen, S; Zihlmann, B; Zupranski, P

    2006-01-01T23:59:59.000Z

    First measurement of double-hadron production in deep-inelastic scattering has been measured with the HERMES spectrometer at HERA using a 27.6 GeV positron beam with deuterium, nitrogen, krypton and xenon targets. The influence of the nuclear medium on the ratio of double-hadron to single-hadron yields has been investigated. Nuclear effects are clearly observed but with substantially smaller magnitude and reduced $A$-dependence compared to previously measured single-hadron multiplicity ratios. The data are in fair agreement with models based on partonic or pre-hadronic energy loss, while they seem to rule out a pure absorptive treatment of the final state interactions. Thus, the double-hadron ratio provides an additional tool for studying modifications of hadronization in nuclear matter.

  9. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    M. Hirsch

    2006-09-15T23:59:59.000Z

    Neutrinoless double beta decay violates lepton number by two units, a positive observation therefore necessarily implies physics beyond the standard model. Here, three possible contributions to neutrinoless double beta decay are briefly reviewed: (a) The mass mechanism and its connection to neutrino oscillations; (b) Left-right symmetric models and the lower limit on the right-handed W boson mass; and (c) R-parity violating supersymmetry. In addition, the recently published ``extended black box'' theorem is briefly discussed. Combined with data from oscillation experiments this theorem provides proof that the neutrinoless double beta decay amplitude must receive a non-zero contribution from the mass mechanism, if neutrinos are indeed Majorana particles.

  10. Recent Results in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Lisa J. Kaufman

    2013-05-14T23:59:59.000Z

    The search for neutrinoless double beta decay is a rich source for new physics. The observation of this decay will lead to understanding of the absolute mass scale of neutrinos, the Majorana nature of the neutrino (whether the neutrino is its own anti-particle), and lepton number violation. Double beta decay is being investigated around the world by several experiments using different candidate isotopes. There has been much progress made in experimental techniques recently such that achieving sensitivity to neutrino masses at 50 meV and below will be possible in the near future. A summary of recent results in neutrinoless double beta decay is discussed with a look toward the experimental goals for the future.

  11. The double-beta decay: Theoretical challenges

    SciTech Connect (OSTI)

    Horoi, Mihai [Department of Physics, Central Michigan University, Mount Pleasant, Michigan, 48859 (United States)

    2012-11-20T23:59:59.000Z

    Neutrinoless double beta decay is a unique process that could reveal physics beyond the Standard Model of particle physics namely, if observed, it would prove that neutrinos are Majorana particles. In addition, it could provide information regarding the neutrino masses and their hierarchy, provided that reliable nuclear matrix elements can be obtained. The two neutrino double beta decay is an associate process that is allowed by the Standard Model, and it was observed for about ten nuclei. The present contribution gives a brief review of the theoretical challenges associated with these two process, emphasizing the reliable calculation of the associated nuclear matrix elements.

  12. Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

    SciTech Connect (OSTI)

    Benjamin Bolduc; Daniel P. Shaughnessy; Yuri I. Wolf; Eugene V. Koonin; Francisco F. Roberto; Mark Young

    2012-05-01T23:59:59.000Z

    There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.

  13. 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

  14. 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

  15. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 1999 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John

    2002-01-24T23:59:59.000Z

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the third year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 1999 field season.

  16. On the feasibility of using the intrinsic fluorescence of nucleotides for DNA sequencing.

    SciTech Connect (OSTI)

    Chowdhury, M. H.; Ray, K.; Johnson, R. L.; Gray, S. K.; Pond, J.; Lakowicz, J. R.; Univ. of Maryland; Univ. of Virginia; Lumerical Solutions, Inc.

    2010-04-29T23:59:59.000Z

    There is presently a worldwide effort to increase the speed and decrease the cost of DNA sequencing as exemplified by the goal of the National Human Genome Research Institute (NHGRI) to sequence a human genome for under $1000. Several high throughput technologies are under development. Among these, single strand sequencing using exonuclease appear very promising. However, this approach requires complete labeling of at least two bases at a time, with extrinsic high quantum yield probes. This is necessary because nucleotides absorb in the deep ultraviolet (UV) and emit with extremely low quantum yields. Hence intrinsic emission from DNA and nucleotides is not being exploited for DNA sequencing. In the present paper we consider the possibility of identifying single nucleotides using their intrinsic emission. We used the finite-difference time-domain (FDTD) method to calculate the effects of aluminum nanoparticles on nearby fluorophores that emit in the UV. We find that the radiated power of UV fluorophores is significantly increased when they are in close proximity to aluminum nanostructures. We show that there will be increased localized excitation near aluminum particles at wavelengths used to excite intrinsic nucleotide emission. Using FDTD simulation we show that a typical DNA base when coupled to appropriate aluminum nanostructures leads to highly directional emission. Additionally we present experimental results showing that a thin film of nucleotides show enhanced emission when in close proximity to aluminum nanostructures. Finally we provide Monte Carlo simulations that predict high levels of base calling accuracy for an assumed number of photons that is derived from the emission spectra of the intrinsic fluorescence of the bases. Our results suggest that single nucleotides can be detected and identified using aluminum nanostructures that enhance their intrinsic emission. This capability would be valuable for the ongoing efforts toward the $1000 genome.

  17. Neutrino oscillations and neutrinoless double beta decay

    E-Print Network [OSTI]

    D. Falcone; F. Tramontano

    2001-03-16T23:59:59.000Z

    The relation between neutrino oscillation parameters and neutrinoless double beta decay is studied, assuming normal and inverse hierarchies for Majorana neutrino masses. For normal hierarchy the crucial dependence on U_{e3} is explored. The link with tritium beta decay is also briefly discussed.

  18. Scale evolution of double parton correlations

    E-Print Network [OSTI]

    Tomas Kasemets

    2014-11-17T23:59:59.000Z

    We review the effect of scale evolution on a number of different correlations in double parton scattering (DPS). The strength of the correlations generally decreases with the scale but at a rate which greatly varies between different types. Through studies of the evolution, an understanding of which correlations can be of experimental relevance in different processes and kinematical regions is obtained.

  19. Double layer capacitor prospects look good

    SciTech Connect (OSTI)

    NONE

    1995-07-01T23:59:59.000Z

    The Fourth International Seminar in Double Layer Capacitors and similar energy devices has been sponsored again by Dr. S.P. Wolsky and Dr. Nikola Marincic. The seminar was held in December 1994, at Deerfield Beach, FL. This report provides a brief description of information on supercapacitors.

  20. Double tracks test site characterization report

    SciTech Connect (OSTI)

    NONE

    1996-05-01T23:59:59.000Z

    This report presents the results of site characterization activities performed at the Double Tracks Test Site, located on Range 71 North, of the Nellis Air Force Range (NAFR) in southern Nevada. Site characterization activities included reviewing historical data from the Double Tracks experiment, previous site investigation efforts, and recent site characterization data. The most recent site characterization activities were conducted in support of an interim corrective action to remediate the Double Tracks Test Site to an acceptable risk to human health and the environment. Site characterization was performed using a phased approach. First, previously collected data and historical records sere compiled and reviewed. Generalized scopes of work were then prepared to fill known data gaps. Field activities were conducted and the collected data were then reviewed to determine whether data gaps were filled and whether other areas needed to be investigated. Additional field efforts were then conducted, as required, to adequately characterize the site. Characterization of the Double Tracks Test Site was conducted in accordance with the US Department of Energy`s (DOE) Streamlined Approach for Environmental Restoration (SAFER).

  1. Cretan Hieroglyphic Wool Units (LANA, double mina)

    E-Print Network [OSTI]

    Younger, John G.

    2005-01-01T23:59:59.000Z

    Minoan Hieroglyphic document CHIC *089, on analogy with Linear A and B wool documents, records the wool of a certain type of cloth as the equivalent in weight of 3 double minas, that is 1 wool unit (or the wool from 4 sheep).

  2. Neutrinoless double beta decay in seesaw models

    E-Print Network [OSTI]

    Mattias Blennow; Enrique Fernandez-Martinez; Jacobo Lopez-Pavon; Javier Menendez

    2014-05-12T23:59:59.000Z

    We study the general phenomenology of neutrinoless double beta decay in seesaw models. In particular, we focus on the dependence of the neutrinoless double beta decay rate on the mass of the extra states introduced to account for the Majorana masses of light neutrinos. For this purpose, we compute the nuclear matrix elements as functions of the mass of the mediating fermions and estimate the associated uncertainties. We then discuss what can be inferred on the seesaw model parameters in the different mass regimes and clarify how the contribution of the light neutrinos should always be taken into account when deriving bounds on the extra parameters. Conversely, the extra states can also have a significant impact, cancelling the Standard Model neutrino contribution for masses lighter than the nuclear scale and leading to vanishing neutrinoless double beta decay amplitudes even if neutrinos are Majorana particles. We also discuss how seesaw models could reconcile large rates of neutrinoless double beta decay with more stringent cosmological bounds on neutrino masses.

  3. The COBRA Double Beta Decay Experiment

    SciTech Connect (OSTI)

    Dawson, J. V. [Department of Physics and Astronomy, University of Sussex, Brighton. BN1 9QH (United Kingdom)

    2007-03-28T23:59:59.000Z

    The progress of the COBRA neutrinoless double beta decay experiment is discussed. Potential backgrounds are described. Estimates on the contamination levels of 214Bi in the detectors have been made using previously acquired low background data. New crystals with a different passivation material show an improved background count rate of approximately one order of magnitude.

  4. Double Tracks revegetation and monitoring plan

    SciTech Connect (OSTI)

    NONE

    1997-07-01T23:59:59.000Z

    This document is a reclamation plan for short-term and long-term stabilization of land disturbed by activities associated with interim clean-up of radionuclide-contaminated surface soil at the Double Tracks site. This document has been prepared to provide general reclamation practices and procedures that will be followed during restoration of the cleanup site. Reclamation demonstration plots were established near the site in the fall of 1994 to evaluate the performance of several native species and to evaluate different irrigation strategies. Results of the study at Double Tracks, as well as the results from numerous studies conducted at other sites (Area 11 and Area 19 of the Nevada Test Site), have been summarized and incorporated into this final reclamation plan for the interim cleanup of the Double Tracks site, located northwest of the Nevada Test Site on the Nellis Air Force Range. Surface soils at Double Tracks were contaminated as a result of the detonation of a device containing plutonium and depleted uranium using chemical explosives. The total amount of Pu deposited on the site was between 980 and 1,600 grams and was scattered downwind south of the detonation site. Short-term stabilization consists of the application of a chemical soil stabilizer that is applied immediately following excavation of the contaminated soils to minimize Pu resuspension. Long-term stabilization is accomplished by the establishment of a permanent vegetation.

  5. Characterization of telomerase RNP in Arabidopsis thaliana

    E-Print Network [OSTI]

    Kannan, Kalpana

    2010-01-14T23:59:59.000Z

    ? single-stranded tails that are coated by a non- specific single-stranded DNA-binding complex RPA (reviewed in (266)). RPA bound to single-stranded DNA then recruits and activates ATR/Mec1. The activation of the checkpoint kinases leads to a cascade... in humans and yeast causes telomere shortening (114, 247, 266). Yeast mec1? strains do not show a significant telomere length defect, but mec1? tel1? and mec1? mrx? double mutants are unable to maintain telomeres and display an increased loss of viability...

  6. Directed nucleation assembly of DNA tile complexes for barcodepatterned lattices

    E-Print Network [OSTI]

    Reif, John H.

    readable by advanced microscopic techniques. A functioning visual output method would not only increase. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands has been advanced as a useful material for constructing periodically patterned structures (3--9), nano

  7. 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 ...

  8. 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...

  9. National CHP Roadmap: Doubling Combined Heat and Power Capacity...

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

    CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States by 2010, March 2001 National CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States...

  10. The effects of double-diffusion on a baroclinic vortex

    E-Print Network [OSTI]

    Smith, Wendy Marie

    1987-01-01T23:59:59.000Z

    Laboratory experiments were performed to study the combined effects of double-diffusion and rotation on an oceanic intrusion. Intrusions are driven across density-compensated fronts by the divergence of the double-diffusive ...

  11. Diapycnal advection by double diffusion and turbulence in the ocean

    E-Print Network [OSTI]

    St. Laurent, Louis C

    1999-01-01T23:59:59.000Z

    Observations of diapycnal mixing rates are examined and related to diapycnal advection for both double-diffusive and turbulent regimes. The role of double-diffusive mixing at the site of the North Atlantic Tracer Release ...

  12. The spacetime of double field theory: Review, remarks, and outlook

    E-Print Network [OSTI]

    Hohm, Olaf

    We review double field theory (DFT) with emphasis on the doubled spacetime and its generalized coordinate transformations, which unify diffeomorphisms and b-field gauge transformations. We illustrate how the composition ...

  13. Progress Towards Doubling the Beam Power at Fermilab's Accelerator Complex

    SciTech Connect (OSTI)

    Kourbanis, ioanis

    2014-06-01T23:59:59.000Z

    After a 14 month shutdown accelerator modifications and upgrades are in place to allow us doubling of the Main Injector beam power. We will discuss the past MI high power operation and the current progress towards doubling the power.

  14. 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.

  15. 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

  16. 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).

  17. 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

  18. The Neutrinoless Double Beta Decay: The Case for Germanium Detectors

    E-Print Network [OSTI]

    A. Morales; J. Morales

    2002-11-21T23:59:59.000Z

    An overview of the current status of Neutrinoless Double Beta Decay is presented, emphasizing on the case of Germanium Detectors.

  19. Neutrinoless Double Beta Decay and Physics Beyond the Standard Model

    E-Print Network [OSTI]

    Frank F. Deppisch; Martin Hirsch; Heinrich Päs

    2012-08-03T23:59:59.000Z

    Neutrinoless double beta decay is the most powerful tool to probe not only for Majorana neutrino masses but for lepton number violating physics in general. We discuss relations between lepton number violation, double beta decay and neutrino mass, review a general Lorentz invariant parametrization of the double beta decay rate, highlight a number of different new physics models showing how different mechanisms can trigger double beta decay, and finally discuss possibilities to discriminate and test these models and mechanisms in complementary experiments.

  20. 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

  1. 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.

  2. Homotopy BV-algebra structure on the double cobar construction

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Homotopy BV-algebra structure on the double cobar construction Alexandre Quesney Abstract We show that the double cobar construction, 2C(X), of a simplicial set X is a homotopy BV-algebra if X is a double.2 The bar and cobar constructions . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Hopf algebras

  3. Double Beta Decay Experiments Department of Physics and Astronomy

    E-Print Network [OSTI]

    Piepke, Andreas G.

    1 Double Beta Decay Experiments A. Piepkea a Department of Physics and Astronomy University. The experimen- tal investigation of the nuclear double beta decay is one of the key techniques for solving, such as the evaluation of the beta spec- tra near their endpoint, or neutrinoless double beta decay. The latter technique

  4. The Majorana Neutrinoless Double-Beta Decay Experiment

    E-Print Network [OSTI]

    Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

    The Majorana Neutrinoless Double-Beta Decay Experiment Pre-conceptual Design Proposal November 22 Motivation for Neutrinoless Double-Beta Decay Experiments . . . . . . . . . 4 2.1.1 Community Guidance Neutrinoless Double-Beta Decay Results . . . . . . . . . . . . . . . . . . . . 12 2.5 Next

  5. Sensitivity of CUORE to Neutrinoless Double-Beta Decay

    E-Print Network [OSTI]

    Alessandria, F.

    2013-01-01T23:59:59.000Z

    of CUORE to Neutrinoless Double-Beta Decay b c,:L d e f F .s t results on neutrinoless double beta decay of T e w i t hthe study of neutrinoless double beta decay, J . C r y s t .

  6. 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

  7. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Ge, Shao-Feng

    2015-01-01T23:59:59.000Z

    We study the impact of the precision determination of oscillation parameters in the JUNO experiment on half-life predictions for neutrinoless double beta decay. We show that the solar neutrino mixing angle can be measured by JUNO with below 1% uncertainty. This implies in particular that the minimal value of the effective mass in the inverted mass ordering will be known essentially without uncertainty. We demonstrate that this reduces the range of half-life predictions in order to test this value by a factor of two. The remaining uncertainty is caused by nuclear matrix elements. This has important consequences for future double beta decay experiments that aim at ruling out the inverted mass ordering or the Majorana nature of neutrinos.

  8. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Shao-Feng Ge; Werner Rodejohann

    2015-07-20T23:59:59.000Z

    We study the impact of the precision determination of oscillation parameters in the JUNO experiment on half-life predictions for neutrinoless double beta decay. We show that the solar neutrino mixing angle can be measured by JUNO with below 1% uncertainty. This implies in particular that the minimal value of the effective mass in the inverted mass ordering will be known essentially without uncertainty. We demonstrate that this reduces the range of half-life predictions in order to test this value by a factor of two. The remaining uncertainty is caused by nuclear matrix elements. This has important consequences for future double beta decay experiments that aim at ruling out the inverted mass ordering or the Majorana nature of neutrinos.

  9. Importance of neutrinoless double beta decay

    E-Print Network [OSTI]

    Utpal Sarkar

    2007-12-17T23:59:59.000Z

    A natural explanation for the smallness of the neutrino mass requires them to be Majorana particles violating lepton number by two units. Since lepton number violation can have several interesting consequences in particle physics and cosmology, it is of utmost importance to find out if there is lepton number violation in nature and what is its magnitude. The neutrinoless double beta decay experiment can answer these questions: if there is lepton number violation and if neutrinos are Majorana particles. In addition, the magnitude of neutrinoless double beta decay will constrain any other lepton number violating processes. This lepton number violation may also be relatd to the matter-antimatter asymmetry of the universe, dark matter and cosmological constant.

  10. Simulation of Double-Pulse Laser Ablation

    SciTech Connect (OSTI)

    Povarnitsyn, Mikhail E.; Khishchenko, Konstantin V.; Levashov, Pavel R. [Joint Institute for High Temperatures of RAS, Izhorskaya 13 Bldg 2, Moscow, 125412 (Russian Federation); Itina, Tatian E. [Laboratoire Hubert Curien, UMR CNRS 5516, 18 rue Benoit Lauras, Bat. F, 42000, St-Etienne (France)

    2010-10-08T23:59:59.000Z

    We investigate the physical reasons of a strange decrease in the ablation depth observed in femtosecond double-pulse experiments with increasing delay between the pulses. Two ultrashort pulses of the same energy produce the crater which is less than that created by a single pulse. Hydrodynamic simulation shows that the ablation mechanism is suppressed when the delay between the pulses exceeds the electron-ion relaxation time. In this case, the interaction of the second laser pulse with the expanding target material leads to the formation of the second shock wave suppressing the rarefaction wave created by the first pulse. The modeling of the double-pulse ablation for different delays between pulses confirms this explanation.

  11. Double-clad nuclear fuel safety rod

    DOE Patents [OSTI]

    McCarthy, William H. (Los Altos, CA); Atcheson, Donald B. (Cupertino, CA); Vaidyanathan, Swaminathan (San Jose, CA)

    1984-01-01T23:59:59.000Z

    A device for shutting down a nuclear reactor during an undercooling or overpower event, whether or not the reactor's scram system operates properly. This is accomplished by double-clad fuel safety rods positioned at various locations throughout the reactor core, wherein melting of a secondary internal cladding of the rod allows the fuel column therein to shift from the reactor core to place the reactor in a subcritical condition.

  12. Neutrinoless Double Beta Decay in Particle Physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2010-11-22T23:59:59.000Z

    Neutrinoless double beta decay is a process of fundamental importance for particle physics. It can be mediated by light massive Majorana neutrinos (standard interpretation) or by something else (non-standard interpretations). We review its dependence on the neutrino parameters, its complementarity to other observables sensitive to neutrino mass, and emphasize its ability to distinguish different neutrino mass models. Then we discuss mechanisms different from light Majorana neutrino exchange, and show what can be learned from those and how they could be tested.

  13. Neutrinoless Double Beta Decay and its "Inverse"

    E-Print Network [OSTI]

    Clemens A. Heusch; Peter Minkowski

    1996-11-18T23:59:59.000Z

    Recent considerations by these authors pointed out the attractive features which a search for the exchange of heavy Majorana neutrinos could have for solving the mass and the lepton number puzzles for all neutrinos, in TeV-level electron-electron scattering. In the present note, we show that, contrary to subsequently published arguments, non-observation of neutrinoless double beta decay has, to date, no bearing on the promise of this important task for future linear electron colliders.

  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. Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors

    E-Print Network [OSTI]

    Artusa, D. R.

    2014-01-01T23:59:59.000Z

    Exploring the Neutrinoless Double Beta Decay in the InvertedC. Giunti, Neutrinoless double-beta decay. A brief review,el- ements for neutrinoless double-beta decay and double-

  16. Double-Difference Tomography for Sequestration MVA

    SciTech Connect (OSTI)

    Westman, Erik

    2008-12-31T23:59:59.000Z

    Analysis of synthetic data was performed to determine the most cost-effective tomographic monitoring system for a geologic carbon sequestration injection site. Double-difference tomographic inversion was performed on 125 synthetic data sets: five stages of CO2 plume growth, five seismic event regions, and five geophone arrays. Each resulting velocity model was compared quantitatively to its respective synthetic velocity model to determine an accuracy value. The results were examined to determine a relationship between cost and accuracy in monitoring, verification, and accounting applications using double-difference tomography. The geophone arrays with widely-varying geophone locations, both laterally and vertically, performed best. Additionally, double difference seismic tomography was performed using travel time data from a carbon sequestration site at the Aneth oil field in southeast Utah as part of a Department of Energy initiative on monitoring, verification, and accounting (MVA) of sequestered CO2. A total of 1,211 seismic events were recorded from a borehole array consisting of 22 geophones. Artificial velocity models were created to determine the ease with which different CO2 plume locations and sizes can be detected. Most likely because of the poor geophone arrangement, a low velocity zone in the Desert Creek reservoir can only be detected when regions of test site containing the highest ray path coverage are considered. MVA accuracy and precision may be improved through the use of a receiver array that provides more comprehensive ray path coverage.

  17. Double beta decays of {sup 106}Cd

    SciTech Connect (OSTI)

    Suhonen, Jouni [Department of Physics, P.O. Box 35 (YFL), FI-40014 University of Jyvaeskylae (Finland)

    2011-12-16T23:59:59.000Z

    The two-neutrino (2{nu}2{beta}) and neutrinoless (0{nu}2{beta}) double beta decays of {sup 106}Cd are studied for the transitions to the ground state 0{sub gs}{sup +} and 0{sup +} and 2{sup +} excited states in {sup 106}Pd by using realistic many-body wave functions calculated in the framework of the quasiparticle random-phase approximation. Effective, G-matrix-derived nuclear forces are used in realistic single-particle model spaces. All the possible channels, {beta}{sup +}{beta}{sup +}, {beta}{sup +}EC, and ECEC, are discussed for both the 2{nu}2{beta} and 0{nu}2{beta} decays. The associated half-lives are computed and particular attention is devoted to the study of the detectability of the resonant neutrinoless double electron capture (R0{nu}ECEC) process in {sup 106}Cd. The calculations of the present article constitute the thus far most complete and up-to-date investigation of the double-beta-decay properties of {sup 106}Cd.

  18. Benzene-derived N2-(4-hydroxyphenyl)-deoxyguanosine adduct: UvrABC incision and its conformation in DNA

    SciTech Connect (OSTI)

    Hang, Bo; Rodriguez, Ben; Yang, Yanu; Guliaev, Anton B.; Chenna, Ahmed

    2010-06-14T23:59:59.000Z

    Benzene, a ubiquitous human carcinogen, forms DNA adducts through its metabolites such as p-benzoquinone (p-BQ) and hydroquinone (HQ). N(2)-(4-Hydroxyphenyl)-2'-deoxyguanosine (N(2)-4-HOPh-dG) is the principal adduct identified in vivo by (32)P-postlabeling in cells or animals treated with p-BQ or HQ. To study its effect on repair specificity and replication fidelity, we recently synthesized defined oligonucleotides containing a site-specific adduct using phosphoramidite chemistry. We here report the repair of this adduct by Escherichia coli UvrABC complex, which performs the initial damage recognition and incision steps in the nucleotide excision repair (NER) pathway. We first showed that the p-BQ-treated plasmid was efficiently cleaved by the complex, indicating the formation of DNA lesions that are substrates for NER. Using a 40-mer substrate, we found that UvrABC incises the DNA strand containing N(2)-4-HOPh-dG in a dose- and time-dependent manner. The specificity of such repair was also compared with that of DNA glycosylases and damage-specific endonucleases of E. coli, both of which were found to have no detectable activity toward N(2)-4-HOPh-dG. To understand why this adduct is specifically recognized and processed by UvrABC, molecular modeling studies were performed. Analysis of molecular dynamics trajectories showed that stable G:C-like hydrogen bonding patterns of all three Watson-Crick hydrogen bonds are present within the N(2)-4-HOPh-G:C base pair, with the hydroxyphenyl ring at an almost planar position. In addition, N(2)-4-HOPh-dG has a tendency to form more stable stacking interactions than a normal G in B-type DNA. These conformational properties may be critical in differential recognition of this adduct by specific repair enzymes.

  19. 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.

  20. 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.

  1. 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.

  2. Solid-State Nuclear Magnetic Resonance Measurements of HIV Fusion Peptide to Lipid Distances Reveal the Intimate Contact of Strand Peptide with Membranes

    E-Print Network [OSTI]

    Weliky, David

    Veland Clinic Foundation, CleVeland, Ohio 44195 ReceiVed December 1, 2006; ReVised Manuscript ReceiVed February 23, 2007 ABSTRACT: Human immunodeficiency virus (HIV) infection begins with fusion between viral of oligomeric strand HFP which are consistent with the experimental data are presented. Observation of intimate

  3. Solid-State Nuclear Magnetic Resonance Evidence for Parallel and Antiparallel Strand Arrangements in the Membrane-Associated HIV-1 Fusion Peptide

    E-Print Network [OSTI]

    Weliky, David

    Solid-State Nuclear Magnetic Resonance Evidence for Parallel and Antiparallel Strand Arrangements in the Membrane-Associated HIV-1 Fusion Peptide Jun Yang and David P. Weliky* Department of Chemistry, Michigan 7, 2003 ABSTRACT: The HIV-1 fusion peptide serves as a useful model system for understanding viral

  4. Solid-State Nuclear Magnetic Resonance Evidence for an Extended Strand Conformation of the Membrane-Bound HIV-1 Fusion Peptide

    E-Print Network [OSTI]

    Weliky, David

    Solid-State Nuclear Magnetic Resonance Evidence for an Extended Strand Conformation of the Membrane-Bound HIV-1 Fusion Peptide Jun Yang, Charles M. Gabrys, and David P. Weliky* Department of ChemistryVed May 4, 2001 ABSTRACT: Solid-state nuclear magnetic resonance (NMR) spectroscopy was applied

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

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01T23:59:59.000Z

    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 ...

  6. Complete characterization of double photoionization processes

    SciTech Connect (OSTI)

    Ivanov, I. A.; Kheifets, A. S. [Research School of Physical Sciences, Australian National University, Canberra ACT 0200 (Australia)

    2011-06-15T23:59:59.000Z

    We analyze correlated photoelectron spectra of single-photon two-electron ionization [double photoionization (DPI)] of helium to reconstruct the phase of the spectral amplitude of this process. The phase can be reconstructed reliably in a wide range of photoelectron momenta, thus allowing one to retrieve information about the wave function of the DPI process and its temporal evolution. Our simulation indicates that the proposed phase reconstruction technique can be applied in experiment to trace dynamics of the DPI process with attosecond precision.

  7. Simulated progress in double-beta decay

    SciTech Connect (OSTI)

    Miley, H.S.; Arthur, R.J. [Pacific Northwest Lab., Richland, WA (United States); Avignone, F.T. [South Carolina Univ., Columbia, SC (United States)] [and others

    1993-09-01T23:59:59.000Z

    A Monte Carlo code has been developed to accurately simulate double-beta decay measurements. Coincident gamma rays, beta spectra, and angular correlations have been added to adequately simulate a complete {sup 100}Mo nuclear decay and provide corrections to experimentally determined detector efficiencies. This code has been used to strip certain low-background spectra obtained in the Homestake gold mine in Lead, SD, for the purpose of extremely sensitive materials assay for the construction of new, large, enriched germanium detectors. Assays as low as 9 {mu}Bq/g of {sup 210}Pb in lead shielding were obtained.

  8. Neutrinoless double beta decay and neutrino masses

    SciTech Connect (OSTI)

    Duerr, Michael [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany)

    2012-07-27T23:59:59.000Z

    Neutrinoless double beta decay (0{nu}{beta}{beta}) is a promising test for lepton number violating physics beyond the standard model (SM) of particle physics. There is a deep connection between this decay and the phenomenon of neutrino masses. In particular, we will discuss the relation between 0{nu}{beta}{beta} and Majorana neutrino masses provided by the so-called Schechter-Valle theorem in a quantitative way. Furthermore, we will present an experimental cross check to discriminate 0{nu}{beta}{beta} from unknown nuclear background using only one isotope, i.e., within one experiment.

  9. Neutrinoless double beta decay and QCD corrections

    E-Print Network [OSTI]

    Namit Mahajan

    2014-01-30T23:59:59.000Z

    We consider one loop QCD corrections and renormalization group running of the neutrinoless double beta decay amplitude focusing on the short-range part of the amplitude (without the light neutrino exchange) and find that these corrections can be sizeable. Depending on the operator under consideration, there can be moderate to large cancellations or significant enhancements. We discuss several specific examples in this context. Such large corrections will lead to significant shifts in the half-life estimates which currently are known to be plagued with the uncertainties due to nuclear physics inputs to the physical matrix elements.

  10. Double acting stirling engine phase control

    DOE Patents [OSTI]

    Berchowitz, David M. (Scotia, NY)

    1983-01-01T23:59:59.000Z

    A mechanical device for effecting a phase change between the expansion and compression volumes of a double-acting Stirling engine uses helical elements which produce opposite rotation of a pair of crankpins when a control rod is moved, so the phase between two pairs of pistons is changed by +.psi. and the phase between the other two pairs of pistons is changed by -.psi.. The phase can change beyond .psi.=90.degree. at which regenerative braking and then reversal of engine rotation occurs.

  11. Double Coil Condenser Apparatus - Energy Innovation Portal

    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 AdministrationField Campaign:INEA : Papers69 FederalAdministration Donald6,Double Coil

  12. Dietary fish oil and butyrate increase apoptosis and decrease aberrant crypt foci in colon cancer by enhancing histone acetylation and p21waf1/cip1 expression

    E-Print Network [OSTI]

    Covert, Kristy Lynn

    2006-08-16T23:59:59.000Z

    shrinkage, mitochondrial membrane blebbing, nuclear degradation, and DNA fragmentation (Shanmugathasan and Jothy, 2000). As the DNA fragments, the remaining double-strand breaks can be identified by gel electrophoresis, producing a specific pattern..., the nuclear chromatin condenses and DNA is degraded. Cellular remnants are packaged into apoptotic bodies, which are then phagocytized or sloughed into the passing lumenal contents (Vaux and Strasser, 1996). p21Waf1/Cip1 One of the earliest events...

  13. 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.

  14. 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 ...

  15. 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 ...

  16. 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

  17. 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,

  18. Enzymatic Ligation Creates Discrete Multi-Nanoparticle Building Blocks for Self-Assembly

    SciTech Connect (OSTI)

    Claridge, Shelley A.; Mastroianni, Alexander J.; Au, Yeung B.; Liang, Huiyang W.; Micheel, Christine M.; Frechet, Jean M.J.; Alivisatos, A. Paul

    2008-05-27T23:59:59.000Z

    Enzymatic ligation of discrete nanoparticle?DNA conjugates creates nanoparticle dimer and trimer structures in which the nanoparticles are linked by single-stranded DNA, rather than double-stranded DNA as in previous experiments. Ligation is verified by agarose gel and small-angle X-ray scattering. This capability is utilized in two ways: first to create a new class of multiparticle building blocks for nanoscale self-assembly; second to develop a system which can amplify a population of discrete nanoparticle assemblies.

  19. Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus-Strand Transfer Mediated by the

    E-Print Network [OSTI]

    Levin, Judith G.

    Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus destabilizes the highly structured complementary trans-activation response ele- ment (TAR) stem-loop (TAR DNA) at the 3 -end of ( ) SSDNA and inhibits TAR-induced self-priming, a dead- end reaction that competes

  20. 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.