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1

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

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

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

2

ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND BREAK REPAIR CAPACITY IN HUMAN DIPLOID FIBROBLASTS  

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

ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND ASSESSMENT OF INDIVIDUAL VARIATION IN DNA DOUBLE-STRAND BREAK REPAIR CAPACITY IN HUMAN DIPLOID FIBROBLASTS Paul F. Wilson, John M. Hinz, Peter B. Nham, Salustra S. Urbin, Cynthia B. Thomas, Irene M. Jones, and Larry H. Thompson Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA The induction of bi-stranded clustered DNA damage (BCD), which includes direct DNA double-strand breaks (DSBs), is a hallmark of ionizing radiation (IR) exposure. Incorrectly repaired DSBs can cause chromosomal rearrangements and an increased risk of genomic instability and cancer. Because there is polymorphic variation in DNA repair genes and much of this variation is predicted to have a functional impact, healthy people likely vary in their capacity to repair DSBs and other BCD. This project

3

The Role of DNA double-strand break repair in cellular response to low  

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

DNA double-strand break repair in cellular response to low DNA double-strand break repair in cellular response to low dose radiation exposure. David J. Chen Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas TX 75390 It has been assumed that molecular pathways that involved in the biological response for low dose of radiation should be similar to those for high dose radiation in general. The low dose-rate effect and DNA double-strand break repair are inextricably linked in mammalian cells. It has been reported that mammalian mutant cells deficient in nonhomologous end join (NHEJ) pathway have little or no cellular recovery when expose to low-dose-rate radiation. Recently, it has also been reported that cells deficient in

4

Spin transport and spin polarization properties in double-stranded DNA  

SciTech Connect (OSTI)

We study the spin-dependent electron transport through a double-stranded DNA (dsDNA) using the Bogoliubov-de Gennes equations and non-equilibrium Green's function method. We calculate the spin-dependent electron conductance and spin-polarization for different lengths, helix angles, twist angles of dsDNA, the environment-induced dephasing factors, and hopping integral. It is shown that the conductance decreases by increasing the length and dephasing factor. Also, we show that the spin-polarization depends on the helical symmetry and the length of DNA. It is shown that the double-stranded DNA can act as a perfect spin filter. Finally, we show that the sign of spin polarization can be inverted from +1 (?1) to ?1 (+1) for some values of hopping integral.

Simchi, Hamidreza, E-mail: simchi@iust.ac.ir [Department of Physics, Iran University of Science and Technology, Narrmak, Tehran 16844 (Iran, Islamic Republic of); Semiconductor Technology Center, Tehran (Iran, Islamic Republic of); Esmaeilzadeh, Mahdi, E-mail: mahdi@iust.ac.ir; Mazidabadi, Hossein [Department of Physics, Iran University of Science and Technology, Narrmak, Tehran 16844 (Iran, Islamic Republic of)

2013-11-21T23:59:59.000Z

5

Recognition of double helical DNA by alternate strand triple helix formation  

SciTech Connect (OSTI)

The triplet specificities and required strand orientations of two classes of DNA triple helices can be combined to target double helical sequences containing all four base pairs by alternate strand triple helix formation. This allows for the use of oligonucleotides containing only natural 3{prime}-5{prime} phosphodiester linkages to simultaneously bind both strands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depend on whether the binding site sequences is 5{prime}-(purine){sub m}(pyrimidine){sub n}-3{prime} or 5{prime}-(pyrimidine){sub m}(purine){sub n}-3{prime}. The sequence type 5{prime}-(purine){sub m}- (pyrimidine){sub n}-3{prime} was targeted with an oligonucleotide consisting of a pyrimidine domain and a purine domain linked by a 3{prime}-5{prime} phosphodiester. To bind the duplex sequence type 5{prime}-(pyrimidine){sub m}(purine){sub n}-3{prime}, the third strand requires at least two nucleotides linking binding domains at the site of crossover in the major groove. A new class of oligonucleotides capable of binding mixed duplex sequences by crossovers in the major groove may be possible. 15 refs., 13 figs.

Beal, P.A.; Dervan, P.B. [California Institute of Technology, Pasadena, CA (United States)

1992-06-17T23:59:59.000Z

6

Gene Expression Pathways Activated and Repair of DNA of Double Strand  

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

Pathways Activated and Repair of DNA of Double Strand Pathways Activated and Repair of DNA of Double Strand Breaks (DSBs) Following Low Dose Ionizing Radiation in Human Bronchial Epithelial Cells (HBECs) With and Without Defined Premalignant Oncogenic Changes John Minna University of Texas Southwestern Medical Center at Dallas Abstract We want to determine the effect of low dose ionizing radiation on the molecular progression of lung epithelial cells towards lung cancer. Our endpoints are focused on specific molecular and cellular changes known to be associated with lung cancer development and quantitating those changes as a function of low dose ionizing radiation. We use immortalized human bronchial epithelial cells (HBECs) developed from >40 individuals (including those from current, former, and never smokers, males, females,

7

A Key Step in Repairing DNA Double-Strand Breaks | Advanced Photon Source  

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

X-ray Rainbow X-ray Rainbow An Insulating Breakthrough Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed A Key Step in Repairing DNA Double-Strand Breaks JANUARY 10, 2007 Bookmark and Share The atomic structure of the protein 53BP1 identified by Mayo researchers. (Courtesy: Mayo Clinic) A team of Mayo Clinic researchers has uncovered a key step in the molecular pathway of repairing DNA double-strand breaks. The studies were carried out using the 19-ID beamline (SBC-CAT) at the Advanced Photon Source (APS, Argonne) and the X12-C beamline at the National Synchrotron Light Source (NSLS, Brookhaven National Laboratory). Both the APS and the NSLS are funded by the U.S. Department of Energy's Office of Basic Energy

8

Proximity-induced superconductivity effect in a double-stranded DNA  

SciTech Connect (OSTI)

We study the proximity-induced superconductivity effect in a double-stranded DNA by solving the Bogoliubov-de Gennes equations and taking into account the effect of thermal fluctuations of the twist angle between neighboring base pairs. We show that the electron conductance is spin-dependent and the conductance of spin up (down) increases (decreases) due to the spin-orbit coupling (SOC). It is found that, for T?

Simchi, Hamidreza, E-mail: simchi@iust.ac.ir [Department of Physics, Iran University of Science and Technology, Narrmak, Tehran 16844 (Iran, Islamic Republic of); Semiconductor Technology Center, Tehran (Iran, Islamic Republic of); Esmaeilzadeh, Mahdi, E-mail: mahdi@iust.ac.ir; Mazidabadi, Hossein [Department of Physics, Iran University of Science and Technology, Narrmak, Tehran 16844 (Iran, Islamic Republic of)

2014-02-07T23:59:59.000Z

9

Telomeres and DNA double-strand breaks: ever the twain shall S. M. Baileya,* and M. N. Cornforthb  

E-Print Network [OSTI]

between the naturally occurring DNA double-strand breaks (DSBs) found at chromosome ends (i.e., telomeres Collins, CO 80523-1618 (USA), Fax: +19704917742, e-mail: sbailey@colostate.edu b Department of Radiation on their inability to rejoin with broken chromosome ends produced by radiation. Today, we recognize two essential

10

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

Science Journals Connector (OSTI)

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

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

2014-05-29T23:59:59.000Z

11

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

SciTech Connect (OSTI)

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.

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

12

Unzipping Kinetics of Double-Stranded DNA in a Nanopore Alexis F. Sauer-Budge,1,2  

E-Print Network [OSTI]

- technological applications [11,12]. To explore strand separation in a nanopore we designed two synthetic DNA

13

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

E-Print Network [OSTI]

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

Ballew, Bari Jane

2011-01-01T23:59:59.000Z

14

Human Polynucleotide Kinase Participates in Repair of DNA Double-Strand Breaks by Nonhomologous End Joining but not Homologous Recombination  

Science Journals Connector (OSTI)

...for the repair of topoisomerase I-mediated DNA lesions. DNA Repair (Amst) 2003;2:1087-100. 42 El-Khamisy SF, Saifi GM, Weinfeld M, et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1...

Feridoun Karimi-Busheri; Aghdass Rasouli-Nia; Joan Allalunis-Turner; Michael Weinfeld

2007-07-15T23:59:59.000Z

15

Epigenetic Modifications in Double-Strand Break DNA Damage Signaling and Repair  

Science Journals Connector (OSTI)

...Focus 10 14 31 DNA Damage and Repair in Translational Oncology...investigators, DNA damage and repair has been a major focus of anticancer...Plummer R . Perspective on the pipeline of drugs being developed with...break DNA damage signaling and repair. Clin Cancer Res 2010;16...

Dorine Rossetto; Andrew W. Truman; Stephen J. Kron; and Jacques Côté

2010-09-15T23:59:59.000Z

16

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

SciTech Connect (OSTI)

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.

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

17

Dyes designed for high sensitivity detection of double-stranded DNA  

DOE Patents [OSTI]

Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Oakland, CA)

2000-01-01T23:59:59.000Z

18

Specific and Efficient Binding of Xeroderma Pigmentosum Complementation Group A to Double-Strand/Single-Strand DNA Junctions with 3‘- and/or 5‘-ssDNA Branches  

Science Journals Connector (OSTI)

11.?Rademakers, S., Volker, M., Hoogstraten, D., Nigg, A. L., Mone, M. J., Van Zeeland, A. A., Hoeijmakers, J. H., Houtsmuller, A. B., and Vermeulen, W. (2003) Xeroderma pigmentosum group A protein loads as a separate factor onto DNA lesions, Mol. ... Rademakers, Suzanne; Volker, Marcel; Hoogstraten, Deborah; Nigg, Alex L.; Mone, Martijn J.; van Zeeland, Albert A.; Hoeijmakers, Jan H. J.; Houtsmuller, Adriaan B.; Vermeulen, Wim ...

Zhengguan Yang; Marina Roginskaya; Laureen C. Colis; Ashis K. Basu; Steven M. Shell; Yiyong Liu; Phillip R. Musich; Constance M. Harris; Thomas M. Harris; Yue Zou

2006-12-19T23:59:59.000Z

19

Induction of DNA Double-Strand Breaks and Cellular Migration Through Bystander Effects in Cells Irradiated With the Slit-Type Microplanar Beam of the Spring-8 Synchrotron  

SciTech Connect (OSTI)

Purpose: To determine whether glioma cells irradiated with a microplanar X-ray beam exert bystander effects. Methods and Materials: Microplanar beam irradiation of glioma cells in vitro was done using the SPring-8 synchrotron radiation facility. The amount of DNA double-strand breaks (dsbs) was measured by the fluorescence intensity of phosphorylated H2AX or the number of 53BP1 foci. The dose distribution in a cell population exposed to a single microplanar beam was determined by the amount of phosphorylated H2AX-positive cells. Bystander effects were determined by counting the number of 53BP1 foci in nonirradiated cells treated with conditioned medium from cultures of irradiated cells. Results: More DNA dsbs were detected in cells adjacent to an area irradiated by the single beam than in cells in distant, nonirradiated areas as a result of bystander effects caused by scattered X-rays and DNA dsbs. In support of this, more 53BP1 foci were observed in nonirradiated, conditioned medium-treated cells than in control cells (i.e., cells not treated with irradiation or conditioned medium). These results suggest that DNA dsbs were induced in nonirradiated cells by soluble factors in the culture medium. In addition, we observed cellular migration into areas irradiated with peak doses, suggesting that irradiated cells send signals that cause nonirradiated cells to migrate toward damaged cells. Conclusions: Bystander effects are produced by factors secreted as a result of slit-type microplanar X-ray beam irradiation.

Kashino, Genro [Research Reactor Institute, Kyoto University, Osaka (Japan)], E-mail: kashino@rri.kyoto-u.ac.jp; Kondoh, Takeshi [Department of Neurosurgery, Graduate School of Medicine, Kobe University, Kobe (Japan); Nariyama, Nobuteru; Umetani, Keiji; Ohigashi, Takuji [Japan Synchrotron Radiation Research Institute, Hyogo (Japan); Shinohara, Kunio [Japan Synchrotron Radiation Research Institute, Hyogo (Japan); Advanced Research Institute for Science and Engineering, Waseda University, Tokyo (Japan); Kurihara, Ai; Fukumoto, Manabu [Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai (Japan); Tanaka, Hiroki; Maruhashi, Akira; Suzuki, Minoru; Kinashi, Yuko; Liu Yong; Masunaga, Shin-ichiro; Watanabe, Masami; Ono, Koji [Research Reactor Institute, Kyoto University, Osaka (Japan)

2009-05-01T23:59:59.000Z

20

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

Science Journals Connector (OSTI)

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

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

2009-01-01T23:59:59.000Z

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


21

Investigating Deinococcus radiodurans RecA Protein Filament Formation on Double-Stranded DNA by a Real-Time  

E-Print Network [OSTI]

to desiccation.2 Many hypotheses have been proposed to explain the high- efficiency repair, including a ringlike condensed chromosome structure that could restrict fragment DNA diffusion,3-5 a high Mn2+ concentration: With the aid of an efficient, precise, and almost error-free DNA repair system, Deinococcus radiodurans can

Cox, Michael M.

22

Unidirectional Scaffold-Strand Arrangement in DNA Origami  

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

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

23

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

E-Print Network [OSTI]

regions of PAXX1-204 and PAXXV199A/F201A were amplified from the vectors by PCR and cloned into the pcDNA3.1(-) vector (a gift from Dr. V. Bolanos-Garcia) together with GFP or FLAG tags using In-Fusion (Clontech). Vectors were sequenced by the DNA... -treated or treated for 1 hour with 300 µM phleomycin to induce large numbers of DSBs, before being harvested either at this point or after an additional 1-hour recovery period in phleomycin-free medium after three PBS washes. Cells were washed twice in ice-cold PBS...

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

24

Induction and Rejoining of DNA Double Strand Breaks Assessed by H2AX Phosphorylation in Melanoma Cells Irradiated with Proton and Lithium Beams  

SciTech Connect (OSTI)

Purpose: The aim of this study was to evaluate the induction and rejoining of DNA double strand breaks (DSBs) in melanoma cells exposed to low and high linear energy transfer (LET) radiation. Methods and Materials: DSBs and survival were determined as a function of dose in melanoma cells (B16-F0) irradiated with monoenergetic proton and lithium beams and with a gamma source. Survival curves were obtained by clonogenic assay and fitted to the linear-quadratic model. DSBs were evaluated by the detection of phosphorylated histone H2AX ({gamma}H2AX) foci at 30 min and 6 h post-irradiation. Results: Survival curves showed the increasing effectiveness of radiation as a function of LET. {gamma}H2AX labeling showed an increase in the number of foci vs. dose for all the radiations evaluated. A decrease in the number of foci was found at 6 h post-irradiation for low LET radiation, revealing the repair capacity of DSBs. An increase in the size of {gamma}H2AX foci in cells irradiated with lithium beams was found, as compared with gamma and proton irradiations, which could be attributed to the clusters of DSBs induced by high LET radiation. Foci size increased at 6 h post-irradiation for lithium and proton irradiations in relation with persistent DSBs, showing a correlation with surviving fraction. Conclusions: Our results showed the response of B16-F0 cells to charged particle beams evaluated by the detection of {gamma}H2AX foci. We conclude that {gamma}H2AX foci size is an accurate parameter to correlate the rejoining of DSBs induced by different LET radiations and radiosensitivity.

Ibanez, Irene L. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Bracalente, Candelaria [Comision Nacional de Energia Atomica, San Martin (Argentina); Molinari, Beatriz L. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Palmieri, Monica A. [Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (Argentina); Policastro, Lucia [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Kreiner, Andres J. [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Burlon, Alejandro A. [Comision Nacional de Energia Atomica, San Martin (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Valda, Alejandro [Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina); Navalesi, Daniela [Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (Argentina); Davidson, Jorge; Davidson, Miguel [Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Vazquez, Monica; Ozafran, Mabel [Comision Nacional de Energia Atomica, San Martin (Argentina); Duran, Hebe [Comision Nacional de Energia Atomica, San Martin (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires (Argentina); Escuela de Ciencia y Tecnologia, Universidad Nacional de San Martin (Argentina)], E-mail: hduran@cnea.gov.ar

2009-07-15T23:59:59.000Z

25

Lattice ribbons: A model of double-stranded polymers  

Science Journals Connector (OSTI)

We introduce a discrete ribbon model for double-stranded polymers (such as duplex DNA) where the ribbon is constrained to lie on the simple cubic lattice Z3. The ribbon is made up of a sequence of plaquettes and can either be open or closed. We investigate the growth of the number of ribbons as a function of the number of plaquettes and use Monte Carlo methods to estimate the dimensions of the ribbon, the writhe of the backbone and, in the case of orientable closed ribbons, the linking number of the two boundary curves.

E.J. Janse van Rensburg; E. Orlandini; D.W Sumners; M.C. Tesi; S.G. Whittington

1994-12-01T23:59:59.000Z

26

Replication protein A and g-H2AX foci assembly is triggered by cellular response to DNA double-strand breaks  

E-Print Network [OSTI]

pathway that removes the oxidized base lesions from the genomic DNA [6]. Evidence for the stimulation

27

Fanconi Anemia FANCG Protein in Mitigating Radiation- and Enzyme-Induced DNA Double-Strand Breaks by Homologous Recombination in Vertebrate Cells  

Science Journals Connector (OSTI)

...Protein in Mitigating Radiation- and Enzyme-Induced...Okayama 701-0192, Japan. Phone: 81-86-462-1111...exhibit increased MMC and radiation-induced chromosome...Okayama 701-0192, Japan. | Journal Article...pharmacology DNA drug effects radiation effects DNA Damage DNA...

Kazuhiko Yamamoto; Masamichi Ishiai; Nobuko Matsushita; Hiroshi Arakawa; Jane E. Lamerdin; Jean-Marie Buerstedde; Mitsune Tanimoto; Mine Harada; Larry H. Thompson; Minoru Takata

2003-08-01T23:59:59.000Z

28

1 Dda Helicase Tightly Couples Translocation on 2 Single-Stranded DNA to Unwinding of Duplex DNA  

E-Print Network [OSTI]

, Slot 516, Little Rock, AR 72205, USA 9 2 Department of Chemistry, Harding University, 915 East Market Avenue, Searcy, AR 72143, USA 10 3 Laboratorie de Physique Statistique, Ecole Normale Superieure, UPMC 25 Helicases utilize the energy of ATP hydrolysis to unwind double- 26 stranded DNA while

29

RAD-51-Dependent and -Independent Roles of a Caenorhabditis elegans BRCA2-Related Protein during DNA Double-Strand Break Repair  

Science Journals Connector (OSTI)

...previously described (5). To test pair-wise interactions in yeast cells, Gal4 DNA...four BRCs) (11, 21, 41, 49). Pair-wise alignment of the single BRC of T07E3...In addition, we thank Juliet Reid, Alison Schuldt, John Diffley, Jesper Svejstrup...

Julie S. Martin; Nicole Winkelmann; Mark I. R. Petalcorin; Michael J. McIlwraith; Simon J. Boulton

2005-04-01T23:59:59.000Z

30

Genetics of x-ray induced double strand break repair in saccharomyces cerevisiae  

SciTech Connect (OSTI)

The possible fates of x-ray-induced double-strand breaks in Saccharomyces cerevisiae were examined. One possible pathway which breaks can follow, the repair pathway, was studied by assaying strains with mutations in the RAD51, RAD54, and RAD57 loci for double-strand break repair. In order of increasing radiation sensitivity one finds: rad57-1(23/sup 0/)> rad51-1(30/sup 0/)> rad54-3(36/sup 0/). At 36/sup 0/, rad54-3 cells cannot repair double-strand breaks, while 23/sup 0/, they can. Strains with the rad57-1 mutation can rejoin broken chromosomes at both temperatures. However, the low survival at 36/sup 0/ shows that the assay is not distinguishing large DNA fragments which allow cell survival from those which cause cell death. A rad51-1 strain could also rejoin broken chromosomes, and was thus capable of incomplete repair. The data can be explained with the hypothesis that rad54-3 cells are blocked in an early step of repair, while rad51-1 and rad57-1 strains are blocked in a later step of repair. The fate of double-strand breaks when they are left unrepaired was investigated with the rad54-3 mutation. If breaks are prevented from entering the RAD54 repair pathway they become uncommitted lesions. These lesions are repaired slower than the original breaks. One possible fate for an uncommitted lesion is conversion into a fixed lesion, which is likely to be an unrepairable or misrepaired double-strand break. The presence of protein synthesis after irradiation increases the probability that a break will enter the repair pathway. Evidence shows that increased probability of repair results from enhanced synthesis of repair proteins shortly after radiation. (ERB)

Budd, M.E.

1982-07-01T23:59:59.000Z

31

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

E-Print Network [OSTI]

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

Zhang, David Yu

32

Synthesis of DNA  

DOE Patents [OSTI]

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

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

2008-11-18T23:59:59.000Z

33

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

34

Characterization of a parallel-stranded DNA hairpin  

SciTech Connect (OSTI)

Recently, the authors have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure. In the present study, they have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3{prime}-d(T){sub 8}C{sub 4}(A){sub 8}-3{prime} and the related antiparallel (APS) hair 5{prime}-d(T){sub 8}C{sub 4}(A){sub 8}-3{prime}. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5{prime}-5{prime} phosphodiester linkage in the hairpin loop. Ultraviolet spectroscopic and fluorescence data of drug binding are consistent with the formation of PS and APS structures, respectively, in these two hairpins. Vacuum circular dichroism measurements in combination with theoretical CD calculations indicate that the PS structure forms a right-handed helix. {sup 31}P NMR measurements indicate that the conformation of the phosphodiester backbone of the PS structure is not drastically different from that of the APS control. The presence of slowly exchanging imino protons at 14 ppm and the observation of nuclear Overhauser enhancement between imino protons and the AH-2 protons demonstrate that similar base pairing and base stacking between T and A residues occur in both hairpins. On the basis of NOESY measurements, they find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2{prime}-endo range. The results indicate a B-like conformation for each of the strands in the stem part of the PS hairpin and reverse Watson-Crick base pairing between the T and A residues. These data are consistent with a previously calculated structure for parallel-stranded DNA.

Germann, M.W.; Vogel, H.J.; Pon, R.T.; van de Sande, J.H. (Univ. of Calgary, Alberta (Canada))

1989-07-25T23:59:59.000Z

35

The Sensitivity of MCF10A Breast Epithelial Cells to Alkylating Drugs is Enhanced by the Inhibition of O6-Methylguanine-DNA Methyltransferase Transcription with a Synthetic Double Strand DNA Oligonucleotide  

Science Journals Connector (OSTI)

Cytoxicity of alkylating chemotherapeutic drugs is affected by the cellular content of the enzyme O6-methylguanine-DNA methyl transferase (MGMT). Since high levels ... of the enzyme confer the efficient repair of...

Laura Mariani; Antonella Piccirilli; Lorenzo Citti…

2002-06-01T23:59:59.000Z

36

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein.  

E-Print Network [OSTI]

Regulation of Single Stranded DNA Binding by the C-termini of E. coli SSB protein. Alexander G@biochem.wustl.edu The homotetrameric E. coli single stranded DNA binding (SSB) protein plays a central role in DNA replication, repair domain (5). The E. coli SSB protein is the prototypical example of the homotetrameric class of SSB

Lohman, Timothy M.

37

The effect of double-stranded (DS) RNA on Monosporascus cannonballus culture morphology and virulence  

E-Print Network [OSTI]

Attempts to eliminate double-stranded (ds) RNA elements in Monosporascus cannonballus by subculturing on PDA amended with various concentrations of cycloheximide (O to 15 pg/ml) and incubating at elevated temperatures were partially effective...

Park, Yunjung

2012-06-07T23:59:59.000Z

38

Energetically Biased DNA Motor Containing a Thermodynamically Stable Partial Strand Displacements State  

Science Journals Connector (OSTI)

Current work in tuning DNA kinetics has focused on changing toehold lengths and DNA concentrations. However, kinetics can also be improved by enhancing the completion probability of the strand displacement process. Here, we execute this strategy by ...

Preston Boone Landon; Joon Lee; Michael Taeyoung Hwang; Alexander H Mo; Chen Zhang; Anthony Neuberger; Brian Meckes; Jose Juan Gutierrez; Gennadi Glinsky; Ratnesh Lal

2014-10-27T23:59:59.000Z

39

Exotic quantum transport in double-stranded Kronig-Penney model  

E-Print Network [OSTI]

We introduce 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.

Taksu Cheon; Sergey S. Poghosyan

2014-10-31T23:59:59.000Z

40

Increased apoptosis and DNA double-strand breaks in the embryonic mouse brain in response to very low-dose X-rays but not 50 Hz magnetic fields  

Science Journals Connector (OSTI)

...micronucleus formation, mutation induction and single-strand break...generated using a function generator and power amplifier connected...Assuming the same level of DSB induction, we conclude that the difference...low-dose radiation To assess the induction of 53BP1 foci after low-dose...

2014-01-01T23:59:59.000Z

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


41

Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA  

E-Print Network [OSTI]

Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA J. A. Abels, FRNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce. The introduction of these single-molecule techniques for dsRNA analysis opens the way for real-time, quantitative

Dekker, Nynke

42

Effect of catechins and tannins on depleted uranium-induced DNA strand breaks  

Science Journals Connector (OSTI)

The effects of polyphenols on plasmid DNA strand breaks by depleted uranium were studied using four catechins: (+)...2 2+) with hydrogen peroxide (H2O2) were strongly enhanced by EGC, EGCG, MMT, a...

Emiko Matsuda; Akira Nakajima

2012-08-01T23:59:59.000Z

43

Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1  

SciTech Connect (OSTI)

The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.

Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon; Dulberger, Charles L.; Manlick, Angela J.; Keck, James L.; Cox, Michael M. (UW)

2012-03-16T23:59:59.000Z

44

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]

Monosporascus Root Rot/Vine Decline: A Study of Double-Stranded (ds) RNA and Its Role in the Pathogenesis of Monosporascus cannonballus on Muskmelon. (May 1997) Jeffrey Samuel Batten, B. A. , Trinity University Co-Chairs of Advisory Committee: Dr. Raymond D... hybridization between cDNA clones (pJB14 and pJB38) and dsRNA from M 96+ cannonballus isolate, Ca91-17 55 IV-2 Agarose gel and corresponding northern blot showing hybridization between cDNA clones (pJB27, pJB28, pJB39, and pJB40) and dsRNA from M...

Batten, Jeffrey Samuel

2012-06-07T23:59:59.000Z

45

Control of DNA Strand Displacement Kinetics Using Toehold Exchange  

E-Print Network [OSTI]

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

Zhang, David Yu

46

Chemically accurate coarse graining of double-stranded DNA  

Science Journals Connector (OSTI)

...Phys Chem B 112, 9135 ZZQQhy9145. 8. Chen, A. A & Pappu, R. V. (2007) Parameters of monovalent ions in the amber-99...Chem B 111, 11884 ZZQQhy11887. 14 9. Chen, A. A & Pappu, R. V. (2007) Quantitative characterization of ion pairing...

Alexey Savelyev; Garegin A. Papoian

2010-01-01T23:59:59.000Z

47

Method for producing labeled single-stranded nucleic acid probes  

DOE Patents [OSTI]

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.

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

1999-10-19T23:59:59.000Z

48

Nucleic Acid Library Construction Using Synthetic DNA Constructs  

Science Journals Connector (OSTI)

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

Hani S. Zaher; Peter J. Unrau

2005-01-01T23:59:59.000Z

49

Jefferson Lab Science Series - DNA: The Strand That Connects Us All  

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

The Mysterious Universe The Mysterious Universe Previous Video (The Mysterious Universe) Science Series Video Archive Next Video (The Science of Chocolate) The Science of Chocolate DNA: The Strand That Connects Us All Dr. Matt Kaplan - University of Arizona Genetics Core March 29, 2011 Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. We will start with a short general review of human genetics and the biology behind this form of DNA testing. We will look at how DNA testing is performed and how samples are processed in our laboratory. We will also examine examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, I will describe the newest project in our laboratory, the DNA

50

The DNA Damage Response Signaling Cascade Regulates Proliferation of the Phytopathogenic Fungus Ustilago maydis in Planta  

Science Journals Connector (OSTI)

...and Sanchez, 2004) in a broad range of eukaryotes, including U. maydis...double-strand breaks in DNA; and ionizing radiation (IR), which generates double-strand...were irradiated at the indicated dose after being spotted. The spots...

Carmen de Sena-Tomás; Alfonso Fernández-Álvarez; William K. Holloman; José Pérez-Martín

2011-04-08T23:59:59.000Z

51

The single-strand DNA binding activity of human PC4 preventsmutagenesis and killing by oxidative DNA damage  

SciTech Connect (OSTI)

Human positive cofactor 4 (PC4) is a transcriptional coactivator with a highly conserved single-strand DNA (ssDNA) binding domain of unknown function. We identified PC4 as a suppressor of the oxidative mutator phenotype of the Escherichia coli fpg mutY mutant and demonstrate that this suppression requires its ssDNA binding activity. Yeast mutants lacking their PC4 ortholog Sub1 are sensitive to hydrogen peroxide and exhibit spontaneous and peroxide induced hypermutability. PC4 expression suppresses the peroxide sensitivity of the yeast sub l{Delta} mutant, suggesting that the human protein has a similar function. A role for yeast and human proteins in DNA repair is suggested by the demonstration that Sub1 acts in a peroxide-resistance pathway involving Rad2 and by the physical interaction of PC4 with the human Rad2 homolog XPG. We show XPG recruits PC4 to a bubble-containing DNA substrate with resulting displacement of XPG and formation of a PC4-DNA complex. We discuss the possible requirement for PC4 in either global or transcription-coupled repair of oxidative DNA damage to mediate the release of XPG bound to its substrate.

Wang, Jen-Yeu; Sarker, Altaf Hossain; Cooper, Priscilla K.; Volkert, Michael R.

2004-02-01T23:59:59.000Z

52

DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems  

Science Journals Connector (OSTI)

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

Nathan J. Hillson

2011-01-01T23:59:59.000Z

53

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

E-Print Network [OSTI]

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

Bansal, Manju

54

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

E-Print Network [OSTI]

of Advisory Committee: Dr R. D. Neff A quantitative comparison of strand breakage production rates, induced by 250 kvP X-rays, was examined for PM2 DNA, Form I and Form I . Assay of the irrad. iated DNA samples was 0 accomplished by tube gel... AND METHODS DNA Preparation Radiation Protocol Azarose 1 Buffer ~garose Gels Tube Gel Electrophoresis Spectrofluorometry with Electronic Quantif'ication RESULTS DISCUSSION AND CONCLUSION REFERENCES APPENDIX 1 APPENDIX 2 VITA ~Pa e ~ 22 22 24...

Myers, Peter Hall

1981-01-01T23:59:59.000Z

55

4 Transformation of Yeast by the Lithium Acetate/Single-Stranded Carrier DNA/PEG Method  

Science Journals Connector (OSTI)

Publisher Summary This chapter discusses the transformation of yeast by the lithium acetate/single-stranded carrier DNA/PEG (LiAc/SSDNA/PEG) method. High efficiency transformation of yeast is used most frequently for applications such as the two-hybrid screen for protein-protein interactions, for one-hybrid screens that detect protein–DNA interactions, for inverted one-hybrid screens to identify DNA elements that bind a transcription factor, and for the screens that detect protein–protein interactions dependent on phosphorylation. The high efficiency LiAc/SSDNA/PEG transformation procedure used to induce the yeast, Sacchuromyces cerevisiae, to take up exogenous DNA has aided in the development and utilization of sophisticated technologies, such as the one, two, and inverted one-hybrid systems. Also, the procedure is important for the efficient construction of libraries of null mutants for the functional analysis of novel yeast genes. These and other molecular genetic techniques have increased the usefulness of this premier eukaryotic model organism so that it can now be considered as a laboratory work horse, which will find its way into many research programs.

R. Daniel Gietz; Robin A. Woods

1998-01-01T23:59:59.000Z

56

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

SciTech Connect (OSTI)

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.

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

57

Evidence for the Involvement of Double-Strand Breaks in Heat-Induced Cell Killing  

Science Journals Connector (OSTI)

...between thermal tolerance for heat killing and heat-induced loss of DNA polymerase b activity...cells with different cell cycle distributions. Error bars, SD. Fig. 5...between thermotolerance and heat-induced H2AX foci formation...

Akihisa Takahashi; Hideki Matsumoto; Kosuke Nagayama; Mutsuko Kitano; Sayako Hirose; Hidenori Tanaka; Eiichiro Mori; Nobuhiro Yamakawa; Jun-ichi Yasumoto; Kazue Yuki; Ken Ohnishi; and Takeo Ohnishi

2004-12-15T23:59:59.000Z

58

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

SciTech Connect (OSTI)

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.

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

59

Evidence for the Coupling of ATP Hydrolysis to the Final (Extension) Phase of RecA Protein-mediated DNA Strand Exchange*  

E-Print Network [OSTI]

Evidence for the Coupling of ATP Hydrolysis to the Final (Extension) Phase of RecA Protein-Madison, Madison, Wisconsin 53706 RecA protein promotes a limited DNA strand ex- change reaction, without ATP. This nascent hybrid DNA is extended in a reaction that can be coupled to ATP hydrolysis. When ATP is hydrolyzed

Cox, Michael M.

60

SELF-ASSEMBLED DNA NANOSTRUCTURES AND DNA-TEMPLATED SILVER NANOWIRES  

E-Print Network [OSTI]

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

Reif, John H.

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


61

Distance-dependent photoinduced electron transfer in synthetic single-strand and hairpin DNA  

Science Journals Connector (OSTI)

?The singlet state of stilbene-4,4?-dicarboxamide can serve as a fluorescent probe of both DNA conformation and electron transfer. Covalent incorporation of the stilbene-dicarboxamide into DNA structures with ...

F. D. Lewis; Robert L. Letsinger

1998-04-01T23:59:59.000Z

62

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

DOE Patents [OSTI]

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.

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

1998-01-01T23:59:59.000Z

63

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

E-Print Network [OSTI]

that probe electronic and vibrational states of nucleobasessX-ray photoelectron (XPS), Fourier transform is not observed in DNA monolayers. The main type of local ordering that may be present in a DNA film is nucleobase, T25-SH). IR reflection absorption spectra were measured under a dry nitrogen purge using a p

Himpsel, Franz J.

64

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

E-Print Network [OSTI]

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

Finkelstein, Gleb

65

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

Science Journals Connector (OSTI)

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

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

2005-12-01T23:59:59.000Z

66

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

SciTech Connect (OSTI)

Highlights: •We report a novel mechanism of radiation protection of DNA by chemical activity of ascorbic acid. •The “chemical repair” of DNA damage was revealed using biochemical assay and chemical kinetics analysis. •We found that ascorbic acid significantly repairs precursors of nucleobase lesions and abasic sites. •However, ascorbic acid seldom repairs precursors of DNA-strand breaks. -- Abstract: We quantified the damage yields produced in plasmid DNA by ?-irradiation in the presence of low concentrations (10–100 ?M) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield of DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins. By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 50–60% of base lesions and AP-sites were repaired by 10 ?M ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.

Hata, Kuniki [Department of Nuclear Engineering and Management, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan) [Department of Nuclear Engineering and Management, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Urushibara, Ayumi; Yamashita, Shinichi; Shikazono, Naoya; Yokoya, Akinari [Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan)] [Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Katsumura, Yosuke, E-mail: katsu@n.t.u-tokyo.ac.jp [Department of Nuclear Engineering and Management, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan) [Department of Nuclear Engineering and Management, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Nuclear Professional School, School of Engineering, The University of Tokyo, 2-22 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1188 (Japan)

2013-05-03T23:59:59.000Z

67

The BLM Helicase Is Necessary for Normal DNA Double-Strand Break Repair  

Science Journals Connector (OSTI)

...control, corrected BS, BS, and AT cells in a DSB...EcoRI-cut CIP pUC18 in nuclear extracts are shown. Part...DSB repair assays. The costs of publication of this...abbreviations used are: BS, Blooms syndrome; AT...of linearized supF20 by nuclear extracts from control...

Gregory Langland; James Elliott; Yuling Li; Jenette Creaney; Kathleen Dixon; and Joanna Groden

2002-05-15T23:59:59.000Z

68

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

E-Print Network [OSTI]

eukaryotic cells by exposing the cells to particles from a small Americium source (Box 1). Each particle) EQUIPMENT Americium (Am-241) source (SupplementaryMethods and SupplementaryFigs.1­3 online) Polyester film

Cai, Long

69

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

E-Print Network [OSTI]

-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of IR-induced genomic instability

70

Sequence Specific Recognition of Double Helical DNA. A Synthetic Approach  

Science Journals Connector (OSTI)

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

P. B. Dervan

1988-01-01T23:59:59.000Z

71

DNA Duplication Revealed in New Beginnings | Department of Energy  

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

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

72

Chemical mapping of DNA and counter-ion content inside phage by energy-filtered TEM  

Science Journals Connector (OSTI)

Double-stranded DNA in many bacterial viruses (phage) is strongly confined, which results in internal genome pressures of tens of atmospheres. This pressure is strongly dependent on local ion concentration and di...

Pernilla Nevsten; Alex Evilevitch; Reine Wallenberg

2012-03-01T23:59:59.000Z

73

Artificial and Solar UV Radiation Induces Strand Breaks and Cyclobutane Pyrimidine Dimers in Bacillus subtilis Spore DNA  

Science Journals Connector (OSTI)

...ECOLOGY Artificial and Solar UV Radiation Induces Strand Breaks and Cyclobutane...to solar UV-B and UV-A radiation (Y. Xue and W. L. Nicholson...monitoring studies at Tokyo, Japan. . N. Munakata Biologically...effective dose of solar ultraviolet radiation estimated by spore dosimetry...

Tony A. Slieman; Wayne L. Nicholson

2000-01-01T23:59:59.000Z

74

Monitoring a genetically engineered bacterium in a freshwater environment by rapid enzymatic amplification of a synthetic DNA “number-plate”  

Science Journals Connector (OSTI)

In order to set up a sensitive and reliable detection method to monitor environmentally released genetically engineered microorganisms (GEMs) a 72-bp, double-stranded DNA fragment has been built by annealing and ...

Augusto Amici; Marco Bazzicalupo; Enzo Gallori…

1991-11-01T23:59:59.000Z

75

DNA  

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

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

76

Visualization of the synergistic effect of lithium acetate and single-stranded carrier DNA on Saccharomyces cerevisiae transformation  

Science Journals Connector (OSTI)

Transformation is an indispensable method for the genetic manipulation of cells. Saccharomyces cerevisiae...can be transformed by incubating intact cells and plasmid DNA in the presence of polyethylene glycol alo...

Tuan Anh Pham; Shigeyuki Kawai; Kousaku Murata

2011-08-01T23:59:59.000Z

77

Natural and synthetic double-stranded DNA binding studies of macrocyclic tetraamine zinc(II) complexes appended with polyaromatic groups  

Science Journals Connector (OSTI)

...?The characteristic binding mode of zinc(II) complexes of macrocyclic tetraamines (1,4,7,10-tetraazacyclododecane, cyclen) appended with one or two arylmethyl group(s) [(4-quinolyl)methyl-, 1,7-bis(4-quinolyl)...

Emiko Kikuta; Naomi Katsube; E. Kimura

1999-08-01T23:59:59.000Z

78

DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin  

Science Journals Connector (OSTI)

...7456 ): 50 – 54 . 11 Price BD D’Andrea AD ( 2013...Y Gursoy-Yuzugullu O Price BD ( 2012 ) The...Apochromat/1.25-N.A. oil objective (Leica...Plan APO 63×/1.4 oil M27 lens (magnification...proteins were released by heating for 5 min with 2× sample...

Marina K. Ayrapetov; Ozge Gursoy-Yuzugullu; Chang Xu; Ye Xu; Brendan D. Price

2014-01-01T23:59:59.000Z

79

Functional role of MRE11 in the repair of particulate chromium(VI)-induced DNA double strand breaks  

Science Journals Connector (OSTI)

...mast cells can behave alternatively as dangerous promoters, innocent bystanders, or...Italo Monzino, the Italian Ministry of Health, and Associazione Italiana Ricerca sul...mast cells can behave alternatively as dangerous promoters, innocent bystanders, or...

Hong Xie; Sandra S. Wise; Seme Dako; Spiros Katsifis; and John P. Wise

2006-04-15T23:59:59.000Z

80

Determination of nucleotide sequences in DNA  

Science Journals Connector (OSTI)

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

F Sanger

1981-12-11T23:59:59.000Z

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


81

A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus.  

Science Journals Connector (OSTI)

...hybridization with a different nick translated [32P]DNA probe...labeled with [32P]dATP by nick translation. Identification...50). This approach has the merit of not requiring synchronized...double-stranded [32P]DNA prepared by nick translation from the cloned...

E S Tasheva; D J Roufa

1994-09-01T23:59:59.000Z

82

Redmond Red as a Redox Probe for the DNA-Mediated Detection of Abasic Sites  

Science Journals Connector (OSTI)

Redmond Red, a fluoropore containing a redox-active phenoxazine core, has been explored as a new electrochemical probe for the detection of abasic sites in double-stranded DNA. The electrochemical behavior of Redmond Red-modified DNA at gold surfaces ...

Marisa C. Buzzeo; Jacqueline K. Barton

2008-10-03T23:59:59.000Z

83

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein*  

E-Print Network [OSTI]

ATP Hydrolysis and DNA Binding by the Escherichia coli RecF Protein* (Received for publication ATP hydrolytic activity. ATP hydrolysis leads to RecF dissociation from double-stranded (ds to DNA. A mutant RecF protein that can bind but cannot hydrolyze ATP (RecF K36R) does not readily

Cox, Michael M.

84

Proteogenomic Analysis Reveals Unanticipated Adaptations of Colorectal Tumor Cells to Deficiencies in DNA Mismatch Repair  

Science Journals Connector (OSTI)

...related double-strand break repair protein NBN, which are constituents...decreased DNA synthesis and repair in MMR- cells (Fig. 4...application of our newly developed pipeline for the detection of variant...in DNA and RNA synthesis and repair. The driving proteins behind...

Patrick J. Halvey; Xiaojing Wang; Jing Wang; Ajaz A. Bhat; Punita Dhawan; Ming Li; Bing Zhang; Daniel C. Liebler; and Robbert J.C. Slebos

2014-01-01T23:59:59.000Z

85

Protective effects of pulmonary epithelial lining fluid on oxidative stress and DNA single-strand breaks caused by ultrafine carbon black, ferrous sulphate and organic extract of diesel exhaust particles  

SciTech Connect (OSTI)

Pulmonary epithelial lining fluid (ELF) is the first substance to make contact with inhaled particulate matter (PM) and interacts chemically with PM components. The objective of this study was to determine the role of ELF in oxidative stress, DNA damage and the production of proinflammatory cytokines following physicochemical exposure to PM. Ultrafine carbon black (ufCB, 15 nm; a model carbonaceous core), ferrous sulphate (FeSO{sub 4}; a model transition metal) and a diesel exhaust particle (DEP) extract (a model organic compound) were used to examine the acellular oxidative potential of synthetic ELF and non-ELF systems. We compared the effects of exposure to ufCB, FeSO{sub 4} and DEP extract on human alveolar epithelial Type II (A549) cells to determine the levels of oxidative stress, DNA single-strand breaks and interleukin-8 (IL-8) production in ELF and non-ELF systems. The effects of ufCB and FeSO{sub 4} on the acellular oxidative potential, cellular oxidative stress and DNA single-strand breakage were mitigated significantly by the addition of ELF, whereas there was no decrease following treatment with the DEP extract. There was no significant effect on IL-8 production following exposure to samples that were suspended in ELF/non-ELF systems. The results of the present study indicate that ELF plays an important role in the initial defence against PM in the pulmonary environment. Experimental components, such as ufCB and FeSO{sub 4}, induced the production of oxidative stress and led to DNA single-strand breaks, which were moderately prevented by the addition of ELF. These findings suggest that ELF plays a protective role against PM-driven oxidative stress and DNA damage. -- Highlights: ? To determine the role of ELF in ROS, DNA damage and IL-8 after exposure to PM. ? ufCB, FeSO{sub 4} and DEP extract were used to examine the protective effects of ELF. ? PM-driven oxidative stress and DNA single-strand breakage were mitigated by ELF. ? The findings suggest that ELF has a protective role against PM. ? The synthetic ELF system could reduce the use of animals in PM-driven ROS testing.

Chuang, Hsiao-Chi [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China) [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan (China); Cheng, Yi-Ling; Lei, Yu-Chen [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China)] [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Chang, Hui-Hsien [Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China)] [Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Cheng, Tsun-Jen, E-mail: tcheng@ntu.edu.tw [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China) [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China)

2013-02-01T23:59:59.000Z

86

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

Science Journals Connector (OSTI)

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

Stéphanie Solier and Yves Pommier

2011-02-01T23:59:59.000Z

87

Live Cell Imaging and in situ analysis of cellular responses to DNA doublestrand  

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

Live Cell Imaging and in situ analysis of cellular responses to DNA double- Live Cell Imaging and in situ analysis of cellular responses to DNA double- strand breaks in mammalian cells. David J. Chen Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas TX 75390 The integrity of the human genome is constantly threatened by internal as well as external factors with the propensity to cause DNA damage. Of the various types of DNA damage that can occur within the mammalian cell nucleus, the DNA double strand break (DSB) is perhaps the most dangerous. Estimates put the number of endogenous DSBs anywhere between 10-100 per nucleus per day. A direct link between DSBs and cancer has been surmised by researchers based upon the fact that many cancer-predisposition

88

Derivatized versions of ligase enzymes for constructing DNA sequences  

SciTech Connect (OSTI)

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.

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

89

AID Associates with Single-Stranded DNA with High Affinity and a Long Complex Half-Life in a Sequence-Independent Manner  

Science Journals Connector (OSTI)

...indicating that AID binds these bubble substrates with very high affinities...binding affinities of AID to bubble substrates suggests that AID...of relatively high complex stability. AID complex formation on...single-stranded region of the bubble, it remained plausible that...

Mani Larijani; Alexander P. Petrov; Oxana Kolenchenko; Maribel Berru; Sergey N. Krylov; Alberto Martin

2006-10-23T23:59:59.000Z

90

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

SciTech Connect (OSTI)

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

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

1996-07-15T23:59:59.000Z

91

Essential Residues in the C Terminus of the Bacteriophage T7 Gene 2.5 Single-stranded DNA-binding Protein*  

E-Print Network [OSTI]

/thioredoxin (T7 DNA pol/trx) complex (2). However, the host ssDNA-binding protein, E. coli SSB protein-binding core (OB-fold) (10). This OB-fold is essentially superimposable with the OB-fold found in the E. coli on structural homology and amino acid sequence conservation of amino acids known to contact ssDNA in the E. coli

Richardson, Charles C.

92

Structure of gramicidin D-RbCl complex at atomic resolution from low-temperature synchrotron data: interactions of double-stranded gramicidin channel contents and cations with channel wall  

SciTech Connect (OSTI)

Gramicidin D (gD) is a naturally occurring ionophoric antibiotic that forms membrane channels specific for monovalent cations. The crystal structure of the RbCl complex of gD has been determined at 1.14 {angstrom} resolution from low-temperature (100 K) synchrotron-radiation data with a final R of 16%. The structure was refined with anisotropic temperature factors for all non-H atoms and with partial occupancies for many of them. The asymmetric unit in the crystal contains four crystallographically independent molecules that form two right-handed antiparallel double-stranded dimers. There are seven distinct rubidium-binding sites in each dimeric channel. The occupancy factors of Rb cations are between 0.11 and 0.35 and the total ion contents of the two crystallographically independent channels are 1.59 and 1.22 ions, respectively. Although each channel is 'chemically symmetrical', the side-chain conformations, the distributions of rubidium cations and their binding sites in the two independent channels are not. Cations are 'coordinated' by delocalized {pi}-electrons of three to five carbonyl groups that together with peptide backbone chains form the gramicidin channel walls. The water:cation ratio in the channel interior is four or five:one, and five or six waters separate Rb cations during their passage through the channel.

Glówka, M.L.; Olczak, A.; Bojarska, J.; Szczesio, M.; Duax, W.L.; Burkhart, B.M.; Pangborn, W.A.; Langs, D.A.; Wawrzak, Z. (Poland); (NWU); (Hauptman)

2010-03-05T23:59:59.000Z

93

High-resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus Pribnow promoter sequence  

SciTech Connect (OSTI)

The nonsymmetrical double-helical hybrid dodecamer d(CGTTATAATGCG){center dot}r(CGCAUUAUAACG) was synthesized with solid-phase phosphoramidite methods and studied by high-resolution 2D-NMR. The imino protons were assigned by one-dimensional nuclear Overhauser methods. All the base protons and H1', H2', H2'', H3', and H4' sugar protons of the DNA strand and the base protons, H1', H2', and most of the H3'-H4' protons of the RNA strand were assigned by 2D NMR techniques. The well-resolved spectra allowed a qualitative analysis of relative proton-proton distances in both strands of the dodecamer. The chemical shifts of the hybrid duplex were compared to those of the pure DNA double helix with the same sequence. The intrastrand and cross-strand NOEs from adenine H2 to H1' resonances of neighboring base pairs exhibited characteristic patterns that were very useful for checking the spectral assignments, and their highly nonsymmetric nature reveals that the conformations of the two strands are quite different. Detailed analysis of the NOESY and COSY spectra, as well as the chemical shift data, indicate that the RNA strand assumes a normal A-type conformation (C3'-endo) whereas the DNA strand is in the general S domain but not exactly in the normal C2'-endo conformation.

Chou, S.H.; Flynn, P.; Reid, B. (Univ. of Washington, Seattle (USA))

1989-03-21T23:59:59.000Z

94

Divalent Ion and Thermally Induced DNA Conformational Polymorphism on Single-walled  

E-Print Network [OSTI]

coverage on nanotubes dispersed in aqueous solution decreases, the emission energy decreases (due Nanotubes Hong Jin1 , Esther S. Jeng1 , Daniel A. Heller2 , Prakrit V. Jena3 , Robert Kirmse4 , Jörg and double stranded DNA can wrap and colloidally stabilize single walled carbon nanotubes in solution

Langowski, Jörg

95

1 15/03/2006 Complexity of excited state dynamics in DNA  

E-Print Network [OSTI]

of model DNA helices using femtosecond transient absorption spectroscopy1 and by observing been assigned to excimer emission9, 10 . We observe that, in contrast to the transient absorption of these single and double strands at identical wavelengths. Neither in fluorescence nor in transient absorption

Boyer, Edmond

96

Chronic hepatitis in chimpanzee carriers of hepatitis B virus: morphologic, immunologic, and viral DNA studies  

Science Journals Connector (OSTI)

...core antigen (anti-HBc), and Dane particles in the serum. Therefore, it appeared...Acad. Sc. USA 77 (1980) 6149 _ 4 ' God. wl., CA _> ~ ~ ~~~~ - -4o...represents fully double-stranded Dane particle DNA. Characterization of the 4100-base-pair...

D Shouval; P R Chakraborty; N Ruiz-Opazo; S Baum; I Spigland; E Muchmore; M A Gerber; S N Thung; H Popper; D A Shafritz

1980-01-01T23:59:59.000Z

97

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

SciTech Connect (OSTI)

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

Hingerty, B.E.

1992-07-01T23:59:59.000Z

98

Mutations & DNA Repair I. What are Mutations?  

E-Print Network [OSTI]

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

Dever, Jennifer A.

99

Low Dose Radiation Research Program: Assessing Biological Function of DNA  

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

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

100

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]

Expression of functional breast cancer susceptibility gene 1 (BRCA1) in human cancers is associated with resistance to platinum-based chemotherapeutics and poly(ADP-ribose) polymerase (PARP) inhibitors. BRCA1 is a nuclear phosphoprotein with broad...

Stecklein, Shane Richard

2012-05-12T23:59:59.000Z

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


101

Synergistic Anticancer Activity of Arsenic Trioxide with Erlotinib Is Based on Inhibition of EGFR-Mediated DNA Double-Strand Break Repair  

Science Journals Connector (OSTI)

...erlotinib (B). C, the diagrams on the left show viability...molecular mechanisms. Materials and Methods Chemicals...camera. Subsequent image handling was carried out in Adobe...in vivo. A schematic diagram illustrating the molecular...Administrative, technical, or material support (i.e...

Kushtrim Kryeziu; Ute Jungwirth; Mir Alireza Hoda; Franziska Ferk; Siegfried Knasmüller; Claudia Karnthaler-Benbakka; Christian R. Kowol; Walter Berger; and Petra Heffeter

2013-06-01T23:59:59.000Z

102

DNA hydration studied by neutron fiber diffraction  

SciTech Connect (OSTI)

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

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

1994-12-31T23:59:59.000Z

103

Persistent DNA damage foci, cellular senescence and low dose radiation  

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

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

104

Synthetic DNA Replication Bubbles Bound and Unwound with Twofold Symmetry by a Simian Virus 40 T-Antigen Double Hexamer  

Science Journals Connector (OSTI)

ARTICLE ANIMAL VIRUSES Synthetic DNA Replication Bubbles Bound and...examined the binding of TAgDH to synthetic DNA replication bubbles. Tests of...characterized the binding and unwinding of synthetic DNA replication bubbles by the TAgDH...

Natalia V. Smelkova; James A. Borowiec

1998-11-01T23:59:59.000Z

105

Photophysical Characterization of a FRET System Using Tailor-Made DNA Oligonucleotide Sequences  

Science Journals Connector (OSTI)

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. ... Feasibility studies for the FRET system were first carried out in peptides (30, 31) and later also in synthetic DNA (32, 33). ... The unique combination of chemically robust dye-labeled building blocks and remarkable spectroscopic properties of the FRET system prompted us to perform a detailed study concerning synthetic DNA, in which the distance between donor and acceptor was systematically varied by the number of separating base pairs. ...

Roman Flehr; Andrea Kienzler; Willi Bannwarth; Michael U. Kumke

2010-11-29T23:59:59.000Z

106

Meta-DNA: synthetic biology via DNA nanostructures and  

E-Print Network [OSTI]

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

Reif, John H.

107

Normalized cDNA libraries  

DOE Patents [OSTI]

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

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

1997-01-01T23:59:59.000Z

108

Normalized cDNA libraries  

DOE Patents [OSTI]

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

Soares, M.B.; Efstratiadis, A.

1997-06-10T23:59:59.000Z

109

Thermodynamic relations for DNA phase transitions  

E-Print Network [OSTI]

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

Poulomi Sadhukhan; Somendra M. Bhattacharjee

2014-01-21T23:59:59.000Z

110

The Initiation of Bacterial DNA Replication  

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

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

111

Synthetic DNA Replication Bubbles Bound and Unwound with Twofold Symmetry by a Simian Virus 40 T-Antigen Double Hexamer  

Science Journals Connector (OSTI)

...yielded similar results. When the stabilities of TAgDH-DNA substrate complexes...antigen bound to the replication bubble substrates. Standard binding reactions...There was no effect of CaCl2 on the stability of the TAgDH-DNA substrate complexes...

Natalia V. Smelkova; James A. Borowiec

1998-11-01T23:59:59.000Z

112

Neutrino Physics AAPT Strand Day  

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

Physics AAPT Strand Day NSTA Regional, 2005 Jocelyn Monroe, Columbia University 1. What Is a Neutrino Anyway? 2. The Question Of Neutrino Mass 3. Searching For Neutrino...

113

Oligonucleotide Assembly in Yeast to Produce Synthetic DNA Fragments  

Science Journals Connector (OSTI)

The yeast Saccharomyces cerevisiae...can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can o...

Daniel G. Gibson

2012-01-01T23:59:59.000Z

114

DNA repair: Dynamic defenders against cancer and aging  

SciTech Connect (OSTI)

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

Fuss, Jill O.; Cooper, Priscilla K.

2006-04-01T23:59:59.000Z

115

The Initiation of Bacterial DNA Replication  

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

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

116

The Initiation of Bacterial DNA Replication  

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

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

117

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

E-Print Network [OSTI]

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

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

2015-01-27T23:59:59.000Z

118

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

119

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

Science Journals Connector (OSTI)

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

Jonathan M. Fogg; David M. J. Lilley

2000-12-01T23:59:59.000Z

120

THE ROLE OF SYNTHETIC DNA IN THE PREPARATION OF STRUCTURAL GENES CODING FOR PROTEINS  

Science Journals Connector (OSTI)

Publisher Summary This chapter discusses the role of synthetic DNA in the preparation of structural genes coding for proteins. One of the key steps in the production of proteins by recombinant DNA technology is the preparation of structural genes coding for the desired proteins. There may be two approaches to this goal: (1) artificial gene synthesis and (2) a combination of cloned cDNA sequences and synthetic DNAs. The method of artificial gene synthesis for the preparation of artificial genes was developed for the synthesis of genes for tRNAs in the late 1960s. The approach of combination of cloned cDNA sequences and synthetic DNA has been developed for the preparation of a gene coding for the human growth hormone. The chapter describes an alternative approach for the synthesis of polydeoxyribonucleotides with defined sequences longer than those accessible by conventional chemical methods. Recent advances in the chemical synthesis of oligonucleotides help to synthesize single-stranded oligonucleotides of up to 40 bases in length, rapidly. It is now possible to synthesize double-stranded DNA fragments using DNA polymerase I in the presence of four deoxynucleoside triphosphosphates.

John J. Rossi; Ryszard Kierzek; Ting Huang; Peter Walker; Keiichi Itakura

1982-01-01T23:59:59.000Z

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


121

Determining orientation and direction of DNA sequences  

DOE Patents [OSTI]

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

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

2000-01-01T23:59:59.000Z

122

Low Dose Radiation Induced DNA Damage Signaling and Repair Responses in  

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

Induced DNA Damage Signaling and Repair Responses in Induced DNA Damage Signaling and Repair Responses in Human 3-Dimensional Skin Model System Yanrong Su, Jarah Meador and Adayabalam S. Balajee Center for Radiological Research, College of Physicians and Surgeons, Columbia University, 630 West, 168th Street, New York, NY 10032. Exposure to ionizing radiation (IR) inflicts a wide variety of lesions in the genomic DNA. Among them, DNA double strand break (DSB) is considered to be the critical lesion for most of the deleterious radiation effects including carcinogenesis. Much of our knowledge on induction and repair kinetics of DSB has come from studies in two dimensional cell culture systems. However, the damage signaling and repair responses to DSB in tissue microenvironment are largely unknown. Knowledge of tissue responses to

123

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA  

Science Journals Connector (OSTI)

... correction is reported for encoding a record amount of information (including images, text and audio files) in DNA strands; a ‘DNA archive’ has been synthesized, shipped from ... robust error correction for encoding a record amount of information (including images, text and audio files) in DNA strands. After synthesizing a 'DNA archive' and shipping it from ...

Nick Goldman; Paul Bertone; Siyuan Chen; Christophe Dessimoz; Emily M. LeProust; Botond Sipos; Ewan Birney

2013-01-23T23:59:59.000Z

124

Nanoscale Molecular Transport by Synthetic DNA Machines  

E-Print Network [OSTI]

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

Pierce, Niles A.

125

DNA Sequencing apparatus  

DOE Patents [OSTI]

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

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

1992-01-01T23:59:59.000Z

126

Photoaffinity Labeling of Mouse Fibroblast Enzymes by a Base Excision Repair Intermediate: New Evidence on the Role of PARP-1 in DNA Repair  

SciTech Connect (OSTI)

To examine mammalian base excision repair (BER) enzymes interacting with DNA intermediates formed during BER, we used a novel photoaffinity labeling probe and mouse embryonic fibroblast (MEF) crude extract. The probe was formed in situ, using an end-labeled oligonucleotide containing a synthetic abasic site; this site was incised by AP endonuclease creating a nick with 3' hydroxyl and 5' reduced sugar phosphate groups at the margins, and then a dNMP carrying a photoreactive adduct was introduced at the 3' hydroxyl group. With near UV-light exposure (312nm) of the extract-probe mixture, only six proteins were strongly labeled, including poly (ADP-ribose) polymerase (PARP-1) and the well-known BER participants flap endonuclease (FEN-1), DNA polymerase b (b-pol), and AP endonuclease (APE). The amount of probe crosslinked to PARP-1 was greater than that crosslinked to the other proteins. The specificity of PARP-1 labeling was examined by competition experiments involving various oligonucleotide competitors; competition of labeling by the probe was much greater for the BER intermediates tested than for normal double-stranded DNA. The specificity of PARP-1 labeling also was examined using DNA probes with alternate structures; PARP-1 labeling was stronger with a DNA oligomer representing a BER intermediate than with a molecule representing a nick in double-stranded DNA. These results identifying interaction of PARP-1 with a BER intermediate are discussed in light of PARP-1's role in mammalian BER.

Lavrik, Olga I.(National Institute of Environmental Health Sciences) [National Institute of Environmental Health Sciences; Prasad, Rajendra (National Institute of Environmental Health Sciences) [National Institute of Environmental Health Sciences; Sobol, Robert W.(National Institute of Environmental Health Sciences) [National Institute of Environmental Health Sciences; Horton, Julie K.(National Institute of Environmental Health Sciences) [National Institute of Environmental Health Sciences; Ackerman, Eric J.(BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB); Wilson, Samuel H.(National Institute of Environmental Health Sciences) [National Institute of Environmental Health Sciences

2001-07-06T23:59:59.000Z

127

Procedure for normalization of cDNA libraries  

DOE Patents [OSTI]

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.

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

1997-01-01T23:59:59.000Z

128

End group characterization in DNA of thymocytes after low doses of ionizing radiation  

Science Journals Connector (OSTI)

Investigations into the configuration of the radiation induced strand breaks in the low dose range are presented. DNA sections containing the radiation induced strand breaks were separated from the undamaged s...

Th. Coquerelle; C. Sexauer

1977-01-01T23:59:59.000Z

129

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

E-Print Network [OSTI]

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

Kokkoli, Efie

130

Template Role of Double-Stranded RNA in Tombusvirus Replication  

Science Journals Connector (OSTI)

...repRNA). Briefly, the method for the CFE assay is as follows: in vitro TBSV replication assays were performed by using 2 mul of CFE, 0.25 mug DI-72 (+)repRNA T7-made...32P]UTP in a 20-mul total volume. The CFE assay was performed at 25C for 3 h and stopped...

Nikolay Kovalev; Judit Pogany; Peter D. Nagy

2014-03-05T23:59:59.000Z

131

Recognition of Double-Stranded RNA by Proteins  

E-Print Network [OSTI]

. Stephens Peter A. Beal University of Utah, Department of Chemistry, 315 South 1400 East, Room 2020, Salt level. In contrast, Correspondence to: Peter A. Beal; email: beal@chemistry. utah.edu). Contract grant

Beal, Peter A.

132

Mass determination of megadalton-DNA Electrospray Ions usingCharge Detection Mass Spectrometry  

SciTech Connect (OSTI)

Charge detection mass spectrometry (CD-MS) has been used to determine the mass of double-stranded, circular DNA and single-stranded, circular DNA in the range of 2500 to 8000 base pairs (1.5-5.0 MDa). Simultaneous measurement of the charge and velocity of an electrostatically accelerated ion allows a mass determination of the ion, with instrument calibration determined independently of samples. Positive ion mass spectra of electrosprayed commercial DNA samples supplied in tris(hydroxymethyl)ethylenediamine tetraacetic acid buffer, diluted in 50 vol. percent acetonitrile, were obtained without cleanup of the sample. ACD mass spectrum constructed from 3000 ion measurements takes 10 min to acquire and yields the DNA molecular mass directly (mass resolution = 6). The data collected represent progress toward a more automatable alternative to sizing of DNA by gel electrophoresis. In addition to the mass spectra, CD-MS generates charge versus mass plots, which provide another means to investigate the creation and fate of large electrospray ions.

Schultz, Jocelyn C.; Hack, Christopher; Benner, Henry W.

1997-10-01T23:59:59.000Z

133

Scaling down DNA circuits with competitive neural networks  

Science Journals Connector (OSTI)

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

2013-01-01T23:59:59.000Z

134

Method for construction of normalized cDNA libraries  

DOE Patents [OSTI]

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

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

1996-01-01T23:59:59.000Z

135

Backbone-induced effects in the charge transport efficiency of synthetic DNA  

Science Journals Connector (OSTI)

We report on a theoretical study pointing out the fundamental role of the backbone energetics in the charge transfer efficiency of polyG–polyC and polyA–polyT chains. The double-strand DNA (ds-DNA) molecules are modelled in terms of a single channel effective Hamiltonian. By introducing a two-step renormalization scheme analytical results for the energy spectrum and transmission coefficient are derived, and current–voltage characteristics are numerically investigated. Significant modulations of the main I–V features (voltage threshold, current amplitude) are reported and their physical origin is traced back to backbone-induced electronic effects. These results open new perspectives for experimental work aimed at controlling the charge transfer efficiency in nanodevices based on synthetic DNA.

Enrique Maciá; Stephan Roche

2006-01-01T23:59:59.000Z

136

HELICASE DEPENDENT AMPLICATION transfer the DNA  

E-Print Network [OSTI]

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

137

The effect of magnesium ions on dielectric relaxation in semidilute DNA aqueous solutions  

E-Print Network [OSTI]

The effect of magnesium ion Mg2+ on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy. Two dielectric relaxations in the 100 Hz - 100 MHz frequency range, originating in the motion of DNA counterions, were probed as a function of DNA and Mg2+ ion concentration in added MgCl2 salt. The high-frequency mode in the MHz range, stemming from the structural organization of the DNA network, reveals de Gennes-Pfeuty-Dobrynin correlation length as the pertinent fundamental length scale for sufficiently low concentration of added salt. No relaxation fingerprint of DNA denaturation bubbles, leading to exposed hydrophobic core scaling, was detected at low DNA concentrations, thus indicating an increased stability of the double-stranded conformation as compared to the case of DNA solutions with univalent counterions. The presence of Mg2+ does not change qualitatively the low frequency mode in the kHz range correlated with single DNA conformational properties....

Grgi?in, Danijel; Ivek, Tomislav; Tomi?, Silvia; Podgornik, Rudi

2013-01-01T23:59:59.000Z

138

Structure of the guide-strand-containing argonaute silencing complex  

SciTech Connect (OSTI)

The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

Wang, Yanli; Sheng, Gang; Juranek, Stefan; Tuschl, Thomas; Patel, Dinshaw J. (MSKCC); (HHMI)

2009-01-15T23:59:59.000Z

139

Damage of supercoiled DNA by an ultrafast laser-driven electron x-ray source  

Science Journals Connector (OSTI)

Using magnetic fields to differentiate the effects of electrons and x-rays, it was discovered that single strand breaks in supercoiled DNA were

Shan, Fang; Carter, Joshua D; Guo, Ting

2007-01-01T23:59:59.000Z

140

After Cajun, what next for stranded costs?  

SciTech Connect (OSTI)

Members of FERC have said that the Cajun decision does not pose a serious problem to its proposed rulemaking on stranded costs. But the D.C. Circuit`s Cajun decision, criticizing the concept of recovery for stranded investment in broad terms, promises to make that task difficult, if not impossible. The United States Court of Appeals for the District of Columbia Circuit, in its July 12, 1994 opinion in Cajun Electric Power Cooperative, Inc. v. Federal Energy Regulatory Commission, subjected the Entergy Corporations`s transmission tariff`s stranded investment provision to broad and, perhaps, fatal criticism. The Cajun opinion, premised on basic concepts of antitrust law, was issued at a time of substantial industry discussion on the concept of stranded investment and should greatly impact the decisions of both federal and state regulators on stranded investment.

Pembroke, J.D.

1994-10-01T23:59:59.000Z

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


141

KUB5/HERA: a dual acting protein that suppresses genomic instability and promotes DNA repair after low dose IR exposure  

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

KUB5/HERA: a dual acting protein that suppresses genomic instability and KUB5/HERA: a dual acting protein that suppresses genomic instability and promotes DNA repair after low dose IR exposure Julio C. Morales 1 , Amy Rommel 1 , Konstantin Leskov 2 , Walter M. Hittelman 3 , David A. Boothman 1# 1 Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 2 Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH 44106, USA. 3 Department of Experimental Therapeutics, M.D. Anderson Cancer Center, Houston, TX 77030, USA. # To whom correspondence should be addressed. E-mail: David.Boothman@utsouthwestern.edu Eukaryotic cells can respond to DNA double strand breaks created by low doses of IR by activating homologous recombination (HR) or non-homologous end- joining (NHEJ) pathways to repair DNA. A yeast two-hybrid screen using Ku70 as

142

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

DOE Patents [OSTI]

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

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

1995-01-01T23:59:59.000Z

143

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

DOE Patents [OSTI]

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

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

1995-04-11T23:59:59.000Z

144

DNA attachment to support structures  

SciTech Connect (OSTI)

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

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

2002-01-01T23:59:59.000Z

145

DNA walker circuits: computational potential, design, and verification  

E-Print Network [OSTI]

stochastic model of DNA walker `circuits' based on experimental data, and demonstrate the merit of using strands, the selected track becomes unblocked. (2) The nicking enzyme (E) attaches to the walker

Oxford, University of

146

Repair of Damaged DNA by Arabidopsis Cell Extract  

Science Journals Connector (OSTI)

...and irradiated at the doses indicated in figure legends...the repair of a model ionizing radiation-induced DNA strand...their genomes from a wide range of genotoxic stresses...Arabidopsis cytology genetics radiation effects Cell Extracts...

Anatoliy Li; David Schuermann; Francesca Gallego; Igor Kovalchuk; Bruno Tinland

147

Method for construction of normalized cDNA libraries  

DOE Patents [OSTI]

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

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

1998-01-01T23:59:59.000Z

148

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

SciTech Connect (OSTI)

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

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

2013-09-20T23:59:59.000Z

149

DNA-PK inhibition causes a low level of H2AX phosphorylation and homologous recombination repair in Medaka (Oryzias latipes) cells  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer We investigated the effect of DNA-PK inhibition on DSB repair using fish cells. Black-Right-Pointing-Pointer A radiation sensitive mutant RIC1 strain showed a low level of DNA-PK activity. Black-Right-Pointing-Pointer DNA-PK dysfunction leads defects in HR repair and DNA-PKcs autophosphorylation. Black-Right-Pointing-Pointer DNA-PK dysfunction leads a slight increase in the number of 53BP1 foci after DSBs. Black-Right-Pointing-Pointer DNA-PK dysfunction leads an alternative NHEJ that depends on 53BP1. -- Abstract: Nonhomologous end joining (NHEJ) and homologous recombination (HR) are known as DNA double-strand break (DSB) repair pathways. It has been reported that DNA-PK, a member of PI3 kinase family, promotes NHEJ and aberrant DNA-PK causes NHEJ deficiency. However, in this study, we demonstrate that a wild-type cell line treated with DNA-PK inhibitor and a mutant cell line with dysfunctional DNA-PK showed decreased HR efficiency in fish cells (Medaka, Oryzias latipes). Previously, we reported that the radiation-sensitive mutant RIC1 strain has a defect in the Histone H2AX phosphorylation after {gamma}-irradiation. Here, we showed that a DNA-PK inhibitor, NU7026, treatment resulted in significant reduction in the number of {gamma}H2AX foci after {gamma}-irradiation in wild-type cells, but had no significant effect in RIC1 cells. In addition, RIC1 cells showed significantly lower levels of DNA-PK kinase activity compared with wild-type cells. We investigated NHEJ and HR efficiency after induction of DSBs. Wild-type cells treated with NU7026 and RIC1 cells showed decreased HR efficiency. These results indicated that aberrant DNA-PK causes the reduction in the number of {gamma}H2AX foci and HR efficiency in RIC1 cells. We performed phosphorylated DNA-PKcs (Thr2609) and 53BP1 focus assay after {gamma}-irradiation. RIC1 cells showed significant reduction in the number of phosphorylated DNA-PKcs foci and no deference in the number of 53BP1 foci compared with wild-type cells. These results suggest that low level of DNA-PK activity causes aberrant DNA-PKcs autophosphorylation in RIC1 cells. It is known that 53BP1 is involved in both DNA-PK dependent and independent NHEJ. Therefore we suggest that DNA-PK independent NHEJ repair DSBs under the condition of decreased DNA-PK activity, which causes reduction of HR efficiency.

Urushihara, Yusuke [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan)] [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan); Kobayashi, Junya [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan)] [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan); Matsumoto, Yoshihisa [Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)] [Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Komatsu, Kenshi [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan)] [Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto 606-8501 (Japan); Oda, Shoji [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan)] [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan); Mitani, Hiroshi, E-mail: mitani@k.u-tokyo.ac.jp [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan)] [Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562 (Japan)

2012-12-14T23:59:59.000Z

150

Speeding up a single-molecule DNA device with a simple catalyst  

Science Journals Connector (OSTI)

Recently, several groups have designed and synthesized single-molecule devices based on DNA that can switch between different configurations in response to sequential addition of fuel DNA strands. There is considerable interest in improving the speed of these “nanomotors.” One approach is the use of rationally designed DNA catalysts to promote hybridization of complementary oligonucleotides. A particularly simple and robust DNA device reported by Li and Tan is comprised of a single-strand 17-base oligomer that folds into a chairlike quadruplex structure. We have identified the key rate-limiting barrier in this device as the tendency for one of the fuel strands B to fold into the quadruplex configuration of the device strand. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of B and shown that the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst remains effective even after repeated cycling.

Yufang Wang; Y. Zhang; N. P. Ong

2005-11-15T23:59:59.000Z

151

Magnetic instabilities in Nb3Sn strands and cables  

SciTech Connect (OSTI)

This paper describes a model for calculation of magnetic instabilities in superconducting wires with transport current and reports results of instability simulations in Nb{sub 3}Sn strands from different manufactures. The effect of magnetic instabilities on the strand and cable performance is presented and a criterion for the maximum effective sub-element size of strands for high field magnets is formulated.

Kashikhim, Vadim V.; Zlobin, Alexander V.; /Fermilab

2004-11-01T23:59:59.000Z

152

A DNA Nanostructure Platform for Directed Assembly of Synthetic Vaccines  

Science Journals Connector (OSTI)

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

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

2012-07-03T23:59:59.000Z

153

Microfluidic DNA sample preparation method and device  

DOE Patents [OSTI]

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

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

2002-01-01T23:59:59.000Z

154

Effect of silver nanoparticle and glycyrrhizic acid (SN-GLY) complex on repair of whole body radiation-induced cellular DNA damage and genomic instability in mice  

Science Journals Connector (OSTI)

Silver nanoparticles (SN) were redispersed in aqueous solution of Pluronic F127 and complexed with the phytoceutical, glycyrrhizic acid (GLY) to obtain SN-GLY complex. The ability of the SN-GLY complex to offer protection against ionising radiation in post-irradiation scenarios was evaluated in ex vivo and in vivo models using Swiss albino mice. Treatment of mouse blood leucocytes with SN-GLY immediately after 4 Gy gamma radiation exposure, ex vivo, enhanced the rate of repair of cellular DNA damages as revealed by comet assay. Exposure of mice to 4 Gy whole body gamma radiation induced formation of strand breaks in cellular DNA and the unrepaired double strand breaks eventually caused the formation of micronuclei. The post-irradiation administration of SN-GLY resulted in a faster decrease in the comet parameters indicating enhanced cellular DNA repair process and reduction in micronucleus formation. Thus the studies showed effective radiation protection by SN-GLY in post-irradiation conditions.

Dhanya K. Chandrasekharan; Cherupally Krishnan Krishnan Nair

2010-01-01T23:59:59.000Z

155

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

SciTech Connect (OSTI)

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.

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

2009-01-01T23:59:59.000Z

156

TileSoft: Sequence Optimization Software For Designing DNA Secondary Structures  

E-Print Network [OSTI]

as self-assembly, utilizing the Watson-Crick self-complementarity. During self- assembly, synthetic DNA- times invoked. In the first step, different sets of synthetic DNA strands are mixed to form small sTileSoft: Sequence Optimization Software For Designing DNA Secondary Structures Peng Yin* Bo Guo

Reif, John H.

157

Discrete Assembly of Synthetic Peptide-DNA Triplex Structures from Polyvalent Melamine-Thymine Bifacial Recognition  

E-Print Network [OSTI]

Discrete Assembly of Synthetic Peptide-DNA Triplex Structures from Polyvalent Melamine decadeoxyoligothymi- dine (dT10) tracts to form triplexes with a peptide-DNA strand ratio of 1:2. The synthetic, synthetic melamine-displaying peptide 1 induced assembly of a peptide-DNA triplex structures

Bong, Dennis

158

Self-assembly of three-dimensional prestressed tensegrity structures from DNA  

E-Print Network [OSTI]

Self-assembly of three-dimensional prestressed tensegrity structures from DNA Tim Liedl1,2,3 , Bjo DNA that act as tension-bearing cables. Our DNA ten- segrity structures can self-assemble against of oligodeoxyribonucleotide `staple strands' that self-assemble into tensed structures despite kinetic barriers imposed

Högberg, Björn

159

Nanotechnology with DNA DNA Nanodevices  

E-Print Network [OSTI]

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

Ludwig-Maximilians-Universität, München

160

E-Print Network 3.0 - amplified polymorphic dna-polymerase Sample...  

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

4 PROOFSMultiplex PCR Based on PCR Suppression High Multiplexity PCR Based Summary: -primer finds its target in the single-stranded regions of the stem-loop structures and DNA...

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


161

Structure of DNA-Bound FEN1 Reveals Mechanism of Action  

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

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

162

Monetizing stranded gas : economic valuation of GTL and LNG projects.  

E-Print Network [OSTI]

??Globally, there are significant quantities of natural gas reserves that lie economically or physically stranded from markets. Options to monetize such reserves include Gas to… (more)

Black, Brodie Gene, 1986-

2010-01-01T23:59:59.000Z

163

Aromatic Interactions in Proteins, DNA and Synthetic Receptors  

Science Journals Connector (OSTI)

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

1993-01-01T23:59:59.000Z

164

A Golden Ruler Used to Measure DNA Structure in Solution  

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

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

165

When DNA Needs to Stand Up and Be Counted  

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

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

166

When DNA Needs to Stand Up and Be Counted  

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

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

167

Design of a combinatorial dna microarray for protein-dnainteraction studies  

SciTech Connect (OSTI)

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

Mintseris, Julian; Eisen, Michael B.

2006-07-07T23:59:59.000Z

168

HIV-1 Tat depresses DNA-PK{sub CS} expression and DNA repair, and sensitizes cells to ionizing radiation  

SciTech Connect (OSTI)

Purpose There is accumulating evidence that cancer patients with human immmunodeficiency virus-1/acquired immunodeficency syndrome (HIV-1/AIDS) have more severe tissue reactions and often develop cutaneous toxic effects when subjected to radiotherapy. Here we explored the effects of the HIV-1 Tat protein on cellular responses to ionizing radiation. Methods and Materials Two Tat-expressing cell lines, TT2 and TE671-Tat, were derived from human rhabdomyosarcoma cells by transfecting with the HIV-1 tat gene. Radiosensitivity was determined using colony-forming ability. Gene expression was assessed by cDNA microarray and immunohybridization. The Comet assay and {gamma}-H2AX foci were use to detect DNA double-strand breaks (DSBs) and repair. Radiation-induced cell cycle changes were detected by flow cytometry. Results The radiosensitivity of TT2 and TE671-Tat cells was significantly increased as compared with parental TE671 cells or the control TE671-pCI cells. Tat also increased proliferation activity. The comet assay and {gamma}H2AX foci detection revealed a decreased capacity to repair radiation-induced DNA DSBs in Tat-expressing cells. Microarray assay demonstrated that the DNA repair gene DNA-PKcs, and cell cycle-related genes Cdc20, Cdc25C, KIF2C and CTS1 were downregulated in Tat-expressing cells. Depression of DNA-PKcs in Tat-expressing cells was further confirmed by RT-PCR and immuno-hybridization analysis. Tat-expressing cells exhibited a prolonged S phase arrest after 4 Gy {gamma}-irradiation, and a noticeable delay in the initiation and elimination of radiation-induced G{sub 2}/M arrest as compared with parental cells. In addition, the G{sub 2}/M arrest was incomplete in TT2 cells. Moreover, HIV-1 Tat resulted in a constitutive overexpression of cyclin B1 protein. Conclusion HIV-1 Tat protein sensitizes cells to ionizing radiation via depressing DNA repair and dysregulating cell cycle checkpoints. These observations provide new insight into the increased tissue reactions of AIDS cancer patients to radiotherapy.

Sun Yi [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Huang Yuechen [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Xu Qinzhi [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Wang Huiping [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Bai Bei [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Sui Jianli [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China); Zhou Pingkun [Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing (China)]. E-mail: zhoupk@nic.bmi.ac.cn

2006-07-01T23:59:59.000Z

169

ESR spectroscopy identifies inhibitory Cu2+ sites in a DNA-modifying enzyme to reveal determinants of catalytic specificity  

Science Journals Connector (OSTI)

...cuts, in preference to single-strand nicks that are readily repaired by DNA ligase...J-J.; a National Institutes of Health MERIT (5R37-GM029207) grant to...preference to readily repaired single-strand nicks. Nonlinear Poisson-Boltzmann calculations...

Zhongyu Yang; Michael R. Kurpiewski; Ming Ji; Jacque E. Townsend; Preeti Mehta; Linda Jen-Jacobson; Sunil Saxena

2012-01-01T23:59:59.000Z

170

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

SciTech Connect (OSTI)

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

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

2011-12-09T23:59:59.000Z

171

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

E-Print Network [OSTI]

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...

Lostak, Tracy Karon

2009-05-15T23:59:59.000Z

172

Sustainability Double Degree Double Degree Info  

E-Print Network [OSTI]

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

Grünwald, Niklaus J.

173

DOE Hydrogen Analysis Repository: Stranded Biogas Decision Tool for Fuel  

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

Stranded Biogas Decision Tool for Fuel Cell Co-Production Stranded Biogas Decision Tool for Fuel Cell Co-Production Project Summary Full Title: Stranded Biogas Decision Tool for Fuel Cell Co-Production Project ID: 257 Principal Investigator: Michael Ulsh Brief Description: This project will explore the feasibility and utility of using stranded biogas resources in fuel cell co-production networks as well as lay the basis for development of analysis and decision-making tools for potential biogas sources and energy end-users to evaluate the economic feasibility of deploying these systems. Performer Principal Investigator: Michael Ulsh Organization: National Renewable Energy Laboratory (NREL) Address: 1617 Cole Blvd. Golden, CO 80401 Telephone: 303-275-3842 Email: michael.ulsh@nrel.gov Website: http://www.nrel.gov

174

Characterizing marine mammal stranding events along the Texas coast  

E-Print Network [OSTI]

The Texas Marine Mammal Stranding Network (TMMSN) is a valuable data resource for the marine mammal community. Limitations of funding and personnel severely impact the ability of the Network to maintain impeccable databases. This research...

Mullins, Ruth Louise

2008-10-10T23:59:59.000Z

175

Characterization of Nb?Sn superconducting strand under pure bending  

E-Print Network [OSTI]

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 ...

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

2005-01-01T23:59:59.000Z

176

DNA-Repair Genetic Polymorphisms and Breast Cancer Risk  

Science Journals Connector (OSTI)

...auspices of US Department of Energy Contract #W-7405-ENG-48...double-strand break; FH, family history; HWE, Hardy-Weinberg...R., Perry H. R., Price F. M., Sanford K...adjustment for age, family history, age at menarche, age...North Carolina 27157, USA. | Journal Article Research...

Tasha R. Smith; Edward A. Levine; Nancy D. Perrier; Mark Steven Miller; Rita I. Freimanis; Kurt Lohman; L. Douglas Case; Jianfeng Xu; Harvey W. Mohrenweiser; and Jennifer J. Hu

2003-11-01T23:59:59.000Z

177

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

SciTech Connect (OSTI)

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

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

2012-07-17T23:59:59.000Z

178

Radiation induced strand breakage analyzed by tunel technique  

E-Print Network [OSTI]

RADIATION INDUCED STRAND BREAKAGE ANALYZED BY TUNEL TECHNIQUE A Thesis MAtuSSA DAWN REYNOLDS Submitted to the 015ce of Graduate Studies of Texas Ad. M University in partial fu1611ment of the requirements for the dree of MASTER OF SCIENCE May... 2003 Major Subject: Health Physics RADIATION INDUCED STRAND BREAKAGE ANALYZED BY TUNEL TECHNIQUE A Thesis MAtuSSA DAWN REYNOLDS Submitted to Texas %%:M University in partial fulfillmen of the requirements for the degree of MASTER OF SCIENCE...

Reynolds, Marissa Dawn

2003-01-01T23:59:59.000Z

179

Dissection of Double-Stranded RNA Binding Protein B2 from Betanodavirus  

Science Journals Connector (OSTI)

...ahead of print on 21 March 2007. Beau J. Fenner Winnie Goh Jimmy Kwang Corresponding author...Mol. Biol. 279: 1085-1099. 10 Fenner, B. J., Q. Du, W. Goh, R. Thiagarajan...ELISA. J. Fish Dis. 29: 423-432. 11 Fenner, B. J., W. Goh, and J. Kwang...

Beau J. Fenner; Winnie Goh; Jimmy Kwang

2007-03-21T23:59:59.000Z

180

Induction and Persistence of Large ?H2AX Foci by High Linear Energy Transfer Radiation in DNA-Dependent protein kinase–Deficient Cells  

SciTech Connect (OSTI)

Purpose: To evaluate the cell response to DNA double-strand breaks induced by low and high linear energy transfer (LET) radiations when the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), an essential protein of the nonhomologous end-joining repair pathway, lacks kinase activity. Methods and Materials: CHO10B2, a Chinese hamster ovary cell line, and its derived radiosensitive mutant cell line, irs-20, lacking DNA-PKcs activity, were evaluated after 0 to 3 Gy of ?-rays, plateau and Bragg peak protons, and lithium beams by clonogenic assay, and as a measurement of double-strand breaks, phosphorylated H2AX (?H2AX) foci number and size were quantified by immunocytofluorescence. Results: Irs-20 exhibited greater radiosensitivity and a higher amount of ?H2AX foci than CHO10B2 at 6 hours after irradiation for all types of radiations. Remarkably, CHO10B2 and irs-20 maintained their difference in radiosensitivity after high-LET radiation. Six hours after low-LET radiations, irs-20 did not reach basal levels of ?H2AX at high doses, whereas CHO10B2 recovered basal levels for all doses. After high-LET radiation, only CHO10B2 exhibited a reduction in ?H2AX foci, but it never reached basal levels. Persistent foci in irs-20 confirmed a repair deficiency. Interestingly, after 30 minutes of high-LET radiation both cell lines exhibited large foci (size >0.9 ?m{sup 2}) related to the damage nature, whereas at 6 hours irs-20 showed a higher amount of large foci than CHO10B2, with a 7-fold increase at 3 Gy, that could also be associated to radiosensitivity. Conclusions: We demonstrated, for the first time, an association between deficient DNA-PKcs activity and not only high levels of H2AX phosphorylation but also persistence and size increase of ?H2AX foci after high-LET irradiation.

Bracalente, Candelaria; Ibañez, Irene L. [Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires (Argentina); Molinari, Beatriz [Departamento de Radiobiología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires (Argentina); Palmieri, Mónica [Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires (Argentina); Kreiner, Andrés [Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires (Argentina); Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires (Argentina); Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires (Argentina); Valda, Alejandro [Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires (Argentina); and others

2013-11-15T23:59:59.000Z

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


181

DNA Extraction  

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

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

182

Identification of phosphotyrosine mimetic inhibitors of human tyrosyl-DNA phosphodiesterase I by a novel AlphaScreen high-throughput assay  

Science Journals Connector (OSTI)

...for the repair of topoisomerase I-mediated DNA lesions. DNA Repair (Amst) 2003;2:1087-100. 8 El-Khamisy SF, Saifi GM, Weinfeld M, et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1...

Christophe Marchand; Wendy A. Lea; Ajit Jadhav; Thomas S. Dexheimer; Christopher P. Austin; James Inglese; Yves Pommier; Anton Simeonov

2009-01-01T23:59:59.000Z

183

c) UNBUNDLING.- Any stranded cost recovery charge authorized by the  

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

c) UNBUNDLING.- Any stranded cost recovery charge authorized by the c) UNBUNDLING.- Any stranded cost recovery charge authorized by the Commission to be assessed by the Tennessee Valley Authority shall be unbundled from the otherwise applicable rates and charges to such customer and separately stated on the bill of such customer. The Tennessee Valley Authority shall not recover wholesale stranded costs from any customer through any other rate, charge, or mechanism. (d) REPORT.-Beginning in fiscal year 2001, as part of the annual management report submitted by the Tennessee Valley Authority to Congress, the Tennessee Valley Authority shall also specifically report: (1) the status of the Tennessee Valley Authority's long-range financial plans and the progress toward its goal of competitively priced electric power, and a general discussion of the Tennessee

184

Patterning quantum dot arrays using DNA replication principles.  

SciTech Connect (OSTI)

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

Crown, Kevin K.; Bachand, George David

2004-11-01T23:59:59.000Z

185

Targeting of single stranded oligonucleotides through metal induced cyclization of short complementary strands  

E-Print Network [OSTI]

manuscript #12;2 Abstract A new strategy to cyclize a short synthetic oligonucleotide on a DNA or a RNA of short synthetic oligonucleotides conjugated with two chelating 2,2':6',2"terpyridine moieties. Our protocol allows the efficient circularisation of synthetic oligonucleotides. Thereby

Paris-Sud XI, Université de

186

Method for fabricating multi-strand superconducting cable  

DOE Patents [OSTI]

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.

Borden, A.R.

1985-04-01T23:59:59.000Z

187

Purification and characterization of mouse DNA polymerase ? devoid of primase activity  

Science Journals Connector (OSTI)

A simple method was developed for the isolation of primase-free DNA polymerase-? from the DNA polymerase-?-primase complex of mouse FM3A cells. The polymerase was separated from primase submits by chromatography on a single-stranded DNA-cellulose column in the presence of 50% etylene glycol. The primase-free DNA polymerase-? contained two polypeptides with molecular masses of 180000 and 68000. Analysis of the DNA products with poly(dA)-oligo(dT)10 as template-primer revealed that both primase-free DNA polymerase-? and the DNA polymerase-?-primase complex predominantly synthesized short DNA with less than 30 nucleotides, but that the DNA polymerase-?-primase complex also synthesized some longer DNA with more than 300–400 nucleotides.

Ritsuko Takada-Takayama; Masashi Suzuki; Takemi Enomoto; Fumio Hanaoka; Michio Ui

1990-01-01T23:59:59.000Z

188

Theoretical description of a DNA-linked nanoparticle self-assembly  

E-Print Network [OSTI]

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.

Chia Wei Hsu; Francesco Sciortino; Francis W. Starr

2010-07-06T23:59:59.000Z

189

Molecular Mechanisms of Anthrax Toxin Assembly and Transport  

E-Print Network [OSTI]

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

Feld, Geoffrey Keith

2012-01-01T23:59:59.000Z

190

Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations  

Science Journals Connector (OSTI)

Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

2014-01-01T23:59:59.000Z

191

Boeing strike leaves satellites stranded on launch pad  

Science Journals Connector (OSTI)

... About 1,500 Boeing machinists and engineers walked off the job at facilities across the United States on 2 ... 5 November, leaving it stranded atop its Delta IV rocket in Cape Canaveral, Florida. Boeing officials are now assessing whether it will be possible to restart the countdown using non ...

Geoff Brumfiel

2005-11-09T23:59:59.000Z

192

The Arabidopsis SWR1 Chromatin-Remodeling Complex Is Important for DNA Repair, Somatic Recombination, and Meiosis  

Science Journals Connector (OSTI)

...either without or with a drug (doses ranging from 0.25 to 2 mug...additive roles in response to ionizing radiation. Plant J. 48 : 947-961...1999). DNA-PK activation by ionizing radiation-induced DNA single-strand...

Marisa Rosa; Mona Von Harder; Riccardo Aiese Cigliano; Peter Schlögelhofer; Ortrun Mittelsten Scheid

2013-06-18T23:59:59.000Z

193

RAP80 Acts Independently of BRCA1 in Repair of Topoisomerase II Poison-Induced DNA Damage  

Science Journals Connector (OSTI)

...Implications for the repair of topoisomerase I-mediated DNA damage. J Biol Chem 2004;279:37343-8. 15 El-Khamisy SF , Saifi GM, Weinfeld M, et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1...

Junko Iijima; Zhihong Zeng; Shunichi Takeda; Yoshihito Taniguchi

2010-11-01T23:59:59.000Z

194

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

E-Print Network [OSTI]

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

Gates, Kent. S.

195

HIV-1 integrase strand-transfer inhibitors: Design, synthesis and molecular modeling investigation  

Science Journals Connector (OSTI)

This study is focused on a new series of benzylindole derivatives with various substituents at the benzene-fused ring, suggested by our 3D pharmacophore model developed for HIV-1 integrase inhibitors (INIs). All synthesized compounds proved to be active in the nanomolar range (6–35 nM) on the strand-transfer step (ST). In particular, derivative 4-[1-(4-fluorobenzyl)-5,7-dimethoxy-1H-indol-3-yl]-2-hydroxy-4-oxobut-2-enoic acid (8e), presenting the highest best-fit value on pharmacophore model, showed a potency comparable to that of clinical \\{INSTIs\\} GS 9137 (1) and MK-0518 (2). The binding mode of our molecules has been investigated using the recently published crystal structure of the complex of full-length integrase from the prototype foamy virus in complex with its cognate DNA (PFV-IN/DNA). The results highlighted the ability of derivative 8e to assume the same binding mode of MK-0518 and GS 9137.

Laura De Luca; Sara De Grazia; Stefania Ferro; Rosaria Gitto; Frauke Christ; Zeger Debyser; Alba Chimirri

2011-01-01T23:59:59.000Z

196

DNA sequencing with pyrophosphatase  

DOE Patents [OSTI]

A kit or solution for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region homologous to the first single-stranded region, comprising a first agent able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture, and a second agent able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

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

1996-03-12T23:59:59.000Z

197

Mobile linkers on DNA-coated colloids: valency without patches  

E-Print Network [OSTI]

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.

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

2014-08-27T23:59:59.000Z

198

When DNA Needs to Stand Up and Be Counted  

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

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

199

Avarol-induced DNA Strand Breakage in Vitro and in Friend Erythroleukemia Cells  

Science Journals Connector (OSTI)

...Gesellschaft fur Kernenergieverwertung in Schiffbau und Schiffahrt Geesthacht. This paper is dedicated to Prof. Dr. Hamao Umezawa. Werner...roGesellschaft f rKernenergieverwertung in Schiffbau und Schif fahrt Geesthacht. This paper is dedicated to Prof. Dr. Hamao Umezawa...

Werner E. G. Müller; Dusan Sladi?; Rudolf K. Zahn; Karl-Heinz Bässler; Nikola Dogovi?; Horst Gerner; Miroslav J. Gasi?; Heinz C. Schröder

1987-12-15T23:59:59.000Z

200

Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1  

Science Journals Connector (OSTI)

... in spinocerebellar ataxia with axonal neuropathy-1 Sherif F. El-Khamisy SF Gulam M.Saifi GM Michael Weinfeld M Fredrik Johansson F Thomas Helleday T James R. Lupski JR ...

Sherif F. El-Khamisy; Gulam M. Saifi; Michael Weinfeld; Fredrik Johansson; Thomas Helleday; James R. Lupski; Keith W. Caldecott

2005-03-03T23:59:59.000Z

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


201

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA  

Science Journals Connector (OSTI)

...distribution function, PWLC (R,L,lp ), (19, 28) [2] and the FRET-averaged...3896 . 12 Kirmizialtin S Elber R ( 2010 ) Computational exploration...189 . 16 Chen AA Draper DE Pappu RV ( 2009 ) Molecular simulation studies of monovalent counterion-mediated...Crick SL Vitalis A Chicoine CL Pappu RV ( 2010 ) Net charge per residue...

Huimin Chen; Steve P. Meisburger; Suzette A. Pabit; Julie L. Sutton; Watt W. Webb; Lois Pollack

2012-01-01T23:59:59.000Z

202

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

Science Journals Connector (OSTI)

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

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

2014-09-01T23:59:59.000Z

203

Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon–helix–helix DNA-binding fold  

Science Journals Connector (OSTI)

...extending DNA strand separation to the nick site at the origin of transfer . Mol Microbiol...Z-score of 11.3 and a mean figure of merit of 0.37. Maximum likelihood density...phases, yielding an overall figure of merit of phasing of 0.66. Automatic building...

Jun Lu; Amke den Dulk-Ras; Paul J. J. Hooykaas; J. N. Mark Glover

2009-01-01T23:59:59.000Z

204

This booklet is brought to you by the AAAS/Science Business Office Sponsored by  

E-Print Network [OSTI]

: -Exonuclease binds to an end of double-stranded DNA and degrades one of the strands in a highly processive in their environment. Since humankind achieved an understanding of this muta- genesis process and its power, we have

Napp, Nils

205

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

SciTech Connect (OSTI)

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

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

2009-05-11T23:59:59.000Z

206

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)

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.

O'Neil, Peter

2009-05-15T23:59:59.000Z

207

Importance of EGFR/ERCC1 Interaction Following Radiation-Induced DNA Damage  

Science Journals Connector (OSTI)

...single-strand annealing and gene conversion in mammalian cells.Nucleic Acids Res 2008;36:1-9. 34. Houtsmuller AB , Rademakers S, Nigg AL, Hoogstraten D, Hoeijmakers JH Vermeulen W.Action of DNA repair endonuclease ERCC1/XPF in living cells...

Gianmaria Liccardi; John A. Hartley; Daniel Hochhauser

2014-07-01T23:59:59.000Z

208

DNA Activity  

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

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

209

Neutrinoless Double $?$-Decay  

E-Print Network [OSTI]

The neutrinoless double $\\beta$-decay is reviewed. Model independent evidence in favor of neutrino masses and mixing is briefly summarized. The data of the recent experiments on the search for $0\

S. M. Bilenky

2004-03-23T23:59:59.000Z

210

Double Beta Decay  

E-Print Network [OSTI]

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.

Steven R. Elliott; Petr Vogel

2002-02-27T23:59:59.000Z

211

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

E-Print Network [OSTI]

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

Martin, Jeffrey

2011-01-01T23:59:59.000Z

212

DNA nanotechnology: understanding and optimisation through simulation  

E-Print Network [OSTI]

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

Thomas E. Ouldridge

2014-11-07T23:59:59.000Z

213

Slow elimination of phosphorylated histone {gamma}-H2AX from DNA of terminally differentiated mouse heart cells in situ  

SciTech Connect (OSTI)

Phosphorylation of replacement histone H2AX occurs in megabase chromatin domains around double-strand DNA breaks (DSBs) and this modification (called {gamma}-H2AX) may serve as a useful marker of genome damage and repair in terminally differentiated cells. Here using immunohistochemistry we studied kinetics of {gamma}-H2AX formation and elimination in the X-irradiated mouse heart and renal epithelial tissues in situ. Unirradiated tissues have 3-5% {gamma}-H2AX-positive cells and in tissues fixed 1 h after X-irradiation {gamma}-H2AX-positive nuclei are induced in a dose-dependent manner approaching 20-30% after 3 Gy of IR. Analysis of mouse tissues at different times after 3 Gy of IR showed that maximal induction of {gamma}-H2AX in heart is observed 20 min after IR and then is decreased slowly with about half remaining 23 h later. In renal epithelium maximum of the {gamma}-H2AX-positive cells is observed 40 min after IR and then decreases to control values in 23 h. This indicates that there are significant variations between non-proliferating mammalian tissues in the initial H2AX phosphorylation rate as well as in the rate of {gamma}-H2AX elimination after X-irradiation, which should be taken into account in the analysis of radiation responses.

Gavrilov, Boris [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Vezhenkova, Irina [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Firsanov, Denis [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Solovjeva, Liudmila [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Svetlova, Maria [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Mikhailov, Vyacheslav [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation); Tomilin, Nikolai [Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg (Russian Federation)]. E-mail: nvtom@hotmail.com

2006-09-08T23:59:59.000Z

214

Numerical evidence for nucleated self-assembly of DNA brick structures  

E-Print Network [OSTI]

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever achieved the same degree of complexity. That failure seemed easy to rationalise: the larger the number of distinct building blocks, the higher the expected error rate for self-assembly. The experiments of Ke et al. have disproved this argument. Here, we report Monte Carlo simulations of the self-assembly of a DNA brick cube, comprising approximately 1000 types of DNA strand, using a simple model. We model the DNA strands as lattice tetrahedra with attractive patches, the interaction strengths of which are computed using a standard thermodynamic model. We find that, within a narrow temperature window, the target structure assembles with high probability. Our simulations suggest that mis-assembly is disfavoured because of a slow nucleation step. As our model incorporates no aspect of DNA other than its binding properties, these simulations suggest that, with proper design of the building blocks, other systems, such as colloids, may also assemble into truly complex structures.

Aleks Reinhardt; Daan Frenkel

2014-04-25T23:59:59.000Z

215

Factors affecting stranding of juvenile salmonids by wakes from ship passage in the Lower Columbia River  

SciTech Connect (OSTI)

The effects of deep-draft vessel traffic in confined riverine channels on shorelines and fish are of widespread concern. In the Pacific Northwest of the United States, wakes and subsequent beach run-up from ships transiting the Lower Columbia River have been observed to strand juvenile salmon and other fish. As part of a before-and-after study to assess stranding effects that may be associated with channel deepening, we measured 19 co-variables from observations of 126 vessel passages at three low-slope beaches and used multiple logistic regression to discern the significant factors influencing the frequency of stranding. Subyearling Chinook salmon were 82% of the fish stranded over all sites and seasons. Given a low-slope beach, stranding frequencies for juvenile salmon were significantly related to river location, salmon density in the shallows, a proxy for ship kinetic energy, tidal height, and two interactions. The beach types selected for our study do not include all the beach types along the Lower Columbia River so that the stranding probabilities described here cannot be extrapolated river-wide. A more sophisticated modeling effort, informed by additional field data, is needed to assess salmon losses by stranding for the entire lower river. Such modeling needs to include river-scale factors such as beach type, berms, proximity to navigation channel, and perhaps, proximity to tributaries that act as sources of out-migrating juvenile salmon. At both river and beach scales, no one factor produces stranding; rather interactions among several conditions produce a stranding event and give stranding its episodic nature.

Pearson, Walter H.; Skalski, John R.

2011-09-01T23:59:59.000Z

216

Double-Skin Façades  

Science Journals Connector (OSTI)

The double-skin façade is a system that consists of two building skins separated by a ventilated cavity (Fig. 9.1). The main aim of the cavity is to vary the physical properties of the façade throughout the ye...

2009-01-01T23:59:59.000Z

217

DOUBLE MAJORS Imaging Science + ...  

E-Print Network [OSTI]

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

Zanibbi, Richard

218

Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair  

Science Journals Connector (OSTI)

...high-throughput sequencing of DSB repair events in humans...conventional models of DSB repair are strained to predict...proposing that long patch base excision repair (BER) on complementary...in their short-read pipeline were true positives...

Justin N. Vaughn; Jeffrey L. Bennetzen

2014-01-01T23:59:59.000Z

219

WHY SEARCH FOR DOUBLE BETA DECAY?  

E-Print Network [OSTI]

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

Kayser, B.

2010-01-01T23:59:59.000Z

220

Double Flash | Open Energy Information  

Open Energy Info (EERE)

Flash Jump to: navigation, search Retrieved from "http:en.openei.orgwindex.php?titleDoubleFlash&oldid599606"...

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


221

Northwestern University Recombinant DNA  

E-Print Network [OSTI]

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

Shull, Kenneth R.

222

Domain walls and double bubbles  

Science Journals Connector (OSTI)

...5, which are never double bubbles, that is, none is the global...transverse cylinder, torus bubble, inner tube and double hydrant...transverse cylinder and the stability of the cylinder cross. The...three-dimensional double bubbles and show that the method can...

2009-01-01T23:59:59.000Z

223

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

Science Journals Connector (OSTI)

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

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

1984-01-01T23:59:59.000Z

224

Speeding up a single-molecule DNA motor with a simple catalyst  

E-Print Network [OSTI]

We demonstrate a catalytic control method for speeding up the single-molecule DNA motor introduced by Li and Tan [Nano Lett. {\\bf 2}, 315 (2002)]. A key rate-limiting barrier in the reaction part of the cycle is the tendency for the second fuel strand $B$ to fold into the chair-like configuration of the original motor strand $M$. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of $B$. Introduction of the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst shows robust behavior for more than one cycle. The experimental data can be understood with a model with intermediate products. This technique provides dynamic control of the restoration rate of the motor without affecting the straightening rate.

Yufang Wang; Y. Zhang; N. P. Ong

2004-12-10T23:59:59.000Z

225

Use of recombinant DNA (rDNA) and Biohazardous Materials  

E-Print Network [OSTI]

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

Danforth, Bryan Nicholas

226

Mutagenic properties of O/sup 6/-methylguanine in DNA in vivo and in vitro  

SciTech Connect (OSTI)

Among the many basic alkylated sites produced in DNA by simple alkylating mutagens, O/sup 6/-alkylguanine is believed to be the major promutagenic lesion. Using O/sup 6/-methyl dGTP as a substrate during in vitro synthesis of biologically active T7 DNA we have shown that the incorporation of the alkylated nucleotide leads to increased reversion of an amber mutation in the phage DNA. We have shown that O/sup 6/-methylguanine has a strong preference for pairing with thymine over cytosine during in vitro replication of synthetic DNA templates with T4 and T5 phage DNA polymerases and E. coli DNA polymerase I. The degree of preference depends not only on the DNA polymerase used but possibly on other factors as well, including the divalent metal ion cofactors. The alkylated base in the template DNA also inhibits chain elongation of the product strand. While O/sup 6/-methyl dGTP can act as a substrate for DNA polymerases, as an analog of dATP, the alkylated nucleotide is incorporated only infrequently and inhibits overall DNA synthesis at the same time. A much higher turnover of the alkylated nucleotide than that of the normal nucleotides suggests that O/sup 6/-methylguanine is not recognized as a normal base by the DNA polymerases in spite of the fact that it is predicted to form a stable base pair with thymine.

Snow, E.T.; Foote, R.S.; Dodson, L.A.; Masker, W.; Mitra, S.

1983-01-01T23:59:59.000Z

227

Asiakastyytyväisyystutkimus - DNA Kauppa Lappeenranta.  

E-Print Network [OSTI]

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

Pitkänen, Jesse

2013-01-01T23:59:59.000Z

228

GTL or LNG: which is the best way to monetize “stranded” natural gas?  

Science Journals Connector (OSTI)

A large portion of world’s natural gas reserves are “stranded” resources, the drive to monetize these resources leads to the development of gas-to-liquids (GTL) and liquefied natural gas (LNG) technologies. LNG h...

Lichun Dong; Shun’an Wei; Shiyu Tan; Hongjing Zhang

2008-11-01T23:59:59.000Z

229

Reactivity studies of antitumor active dirhodium compounds with DNA oligonucleotides  

E-Print Network [OSTI]

48 Circular dichroism (CD) spectropolarimetry spectra of double strands of revAA-revTT 12mer and dirhodium adducts-revTT 12mer..............113 49 An expansion of NOE correlation between aromatic protons of bases and H1? protons of sugar... of correlations between the H5 and H6 protons of cytosine...........117 51 A comparison of DQF-COSY spectra of the revAA 12mer and adduct D (top) or of the revAA 12mer and adduct E (bottom) in the area of correlations between the H5 and H6 protons...

Kang, Mijeong

2007-04-25T23:59:59.000Z

230

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands  

Science Journals Connector (OSTI)

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands ... We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. ... A target test tube is specified as a set of desired “on-target” complexes, each with a target secondary structure and target concentration, and a set of undesired “off-target” complexes, each with vanishing target concentration. ...

Brian R. Wolfe; Niles A. Pierce

2014-10-20T23:59:59.000Z

231

Using DNA to Build Nanomaterials | U.S. DOE Office of Science (SC)  

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

Using DNA to Build Nanomaterials Using DNA to Build Nanomaterials Stories of Discovery & Innovation Using DNA to Build Nanomaterials Enlarge Photo Photo courtesy of Brookhaven National Laboratory Oleg Gang, left, and Mircea Cotlet at Brookhaven's Center for Functional Nanomaterials. Enlarge Photo 05.09.11 Using DNA to Build Nanomaterials Scientists use complementary strands of synthetic DNA to build functional materials from the bottom up. Future applications include biosensors, optical nano-devices, and new kinds of solar cells. One central idea in the field of nanoscience is that if you can build things from the bottom up, atom-by-atom or molecule-by-molecule, you can rationally design materials to achieve desired functions. Taking a cue from how nature does this-using genetic code to instruct the

232

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

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.

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

1999-07-27T23:59:59.000Z

233

Method for introducing unidirectional nested deletions  

DOE Patents [OSTI]

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.

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

1999-07-27T23:59:59.000Z

234

E-Print Network 3.0 - adducts strand breaks Sample Search Results  

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

its complement... to its high reactivity toward DNA and cellular proteins. The major acrolein-DNA adduct, -hydrox- ypropano... -hy- droxynonenal, and acrolein, that readily form...

235

Comparison and Analysis of Twist Pitch Length Test Methods for ITER Nb3Sn and NbTi Strands  

E-Print Network [OSTI]

A twisted multifilamentary structure is needed for Nb3Sn and NbTi strands to be used in the International Thermonuclear Experimental Reactor (ITER) magnets. As important parameters for the superconducting strands design and production, the twist pitch length and direction of strands must meet the requirements according to ITER Procurement Arrangement (PA) and this must be verified. The technical requirements are 15mm+/-2mm for twist pitch length and right hand twist for direction. The strand twist pitch and the twist direction can be measured on straight sections of strand, which is recognized by the repetition of filament bundles or by the angle of the filaments. Several test methods and results are described and compared in this paper. The accuracy, uncertainty and feasibility of different methods are analyzed and recommended measurement methods are proposed for ITER strands verification.

Fang Liu; Feng Long; Chao Chen; Bo Liu; Yu Wu; Huajun Liu

2013-05-08T23:59:59.000Z

236

The scaling of transport AC losses in Roebel cables with varying strand parameters  

Science Journals Connector (OSTI)

A Roebel cable is a good candidate for low-voltage windings in a high-temperature superconductor (HTS) transformer because of its high current-carrying capability and low AC loss. Transport AC loss measurements were carried out in 1.8 m long 15/5 (fifteen 5 mm wide strands) and 15/4 Roebel cables. The results were compared with those in many Roebel cables composed of 2 mm wide Roebel strands. Comparison of the AC losses hinted that the intrinsic difference in normalized transport AC losses is due to differences in the g/w (ratio of the horizontal gap between the Roebel strands over the Roebel strand width) values. The intrinsic difference was confirmed by measuring transport AC loss in a series of horizontally arranged parallel conductor pairs with various g values. A method to scale transport AC losses in Roebel cables with varying strand parameters was developed. The scaling method will be useful for a rough assessment of AC loss in one-layer solenoid winding coils, such as in a HTS transformer.

Zhenan Jiang; Mike Staines; Nicholas J Long; Rodney A Badcock; Chris Bumby; Evgeny Talantsev; Kent Hamilton; Robert G Buckley; Naoyuki Amemiya

2014-01-01T23:59:59.000Z

237

Neutrinoless Double Phys 135c Spring 2007  

E-Print Network [OSTI]

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

Golwala, Sunil

238

DNA Nanotechnology- Architechtures Designed with DNA.  

E-Print Network [OSTI]

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

Han, Dongran

2012-01-01T23:59:59.000Z

239

The Monoclinic Double Sulphates Containing Ammonium. Completion of the Double Sulphate Series  

Science Journals Connector (OSTI)

...Double Sulphates Containing Ammonium. Completion of the Double Sulphate Series A. E...properties physical properties refractive index sulfates GeoRef, Copyright 2007, American...double sulphates containing ammonium; completion of the double sulphate series Tutton...

1916-01-01T23:59:59.000Z

240

Correlation of superconductor strand, cable, and dipole critical currents in CBA magnets  

SciTech Connect (OSTI)

A calibration between vendor critical current data for 0.0268'' diameter superconductor strand supplied to Fermilab, and the BNL 10/sup -12/..cap omega..cm critical current specification is presented. Vendor critical current data for over 400 Fermilab type billets are shown, both as supplied by the vendor and converted to BNL units. Predictions of cable critical current are made using the sum of the critical currents of the 23 strands, where all strands from the same half billet are assigned the same critical current. The measured critical current shows excellent correlation to the predicted value and is approximately 14 +- 2 percent below it. Colliding Beam Accelerator (CBA) full length dipoles reach the conductor critical current limit, essentially without training. Magnet performance is predictable from the measured critical current of a short sample of cable to within 2%.

Tannenbaum, M.J.; Garber, M.; Sampson, W.B.

1982-01-01T23:59:59.000Z

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


241

Single molecule techniques in DNA repair: A primer  

Science Journals Connector (OSTI)

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

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

2014-01-01T23:59:59.000Z

242

Double acting bit holder  

DOE Patents [OSTI]

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.

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

1994-01-01T23:59:59.000Z

243

The dependence of AC loss characteristics on the spacing between strands in YBCO Roebel  

Science Journals Connector (OSTI)

Transport AC loss in a short length of 9/2 YBCO Roebel cable, (i.e. with 9 ? 2 mm width strands), with 0.25 mm spacers between the strands is measured. The frequency varies from 59 to 354 Hz. The result is compared with the loss for a cable without spacers between the strands. Transport AC loss is decreased by the presence of the spacers. The AC loss reduction due to the extra spacing is more significant when the amplitude of the cable current is small compared to the cable Ic. The losses in the cable with spacers normalized by the square of the cable currents plotted against It/Ic approximately agree with those in a cable without spacers. Electromagnetic modelling was carried out for 9/2 and 8/2 cables, modelled as parallel stacks, to assist in understanding the above experimental results. The 8/2 configuration allows the greater use of symmetry to speed computations. Reasonable agreement between the numerical results and the measured results was obtained. This supports suggestions made in previous publications that the transport AC loss in a Roebel cable is roughly equivalent to the loss in two parallel stacks carrying the same current in each tape. The electromagnetic analysis in the 8/2 stacks shows the flux lines are more perpendicular to the strand face when the vertical space between strands is smaller, and this leads to a larger induced electrical field and larger AC loss. At small current amplitudes, the modelling shows the spacing has a strong effect on the AC loss in the surfaced part of the strands.

Zhenan Jiang; K P Thakur; Mike Staines; R A Badcock; N J Long; R G Buckley; A D Caplin; Naoyuki Amemiya

2011-01-01T23:59:59.000Z

244

APOBEC3G: a Double Agent in Defense Harold C. Smith  

E-Print Network [OSTI]

APOBEC3G: a Double Agent in Defense Harold C. Smith Department of Biochemistry and Biophysics to A3G having a requirement for a ssDNA Corresponding Author contacts: Harold C. Smith, Department and Dentistry, Rochester, NY 14642 USA, harold.smith@rochester.edu Voice: (585) 275-4267, FAX: (585) 275

Levin, Judith G.

245

Manganese oxide helices, rings, strands, and films, and methods for their preparation  

DOE Patents [OSTI]

Methods for the preparation of mixed-valence manganese oxide compositions with quaternary ammonium ions are described. The compositions self-assemble into helices, rings, and strands without any imposed concentration gradient. These helices, rings, and strands, as well as films having the same composition, undergo rapid ion exchange to replace the quaternary ammonium ions with various metal ions. And the metal-ion-containing manganese oxide compositions so formed can be heat treated to form semi-conducting materials with high surface areas.

Suib, Steven L. (Storrs, CT); Giraldo, Oscar (Storrs, CT); Marquez, Manuel (Wheeling, IL); Brock, Stephanie (Detroit, MI)

2003-01-07T23:59:59.000Z

246

Automating DNA processing  

E-Print Network [OSTI]

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

Wienen, Michael Jan

2012-06-07T23:59:59.000Z

247

Covalently Linked DNA Nanotubes  

Science Journals Connector (OSTI)

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

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

2010-03-17T23:59:59.000Z

248

DNA strand breaks measured within 100 milliseconds of irradiation of Escherichia coli by 4 MeV electrons  

Science Journals Connector (OSTI)

...Oslo, Blindern, Oslo, Norway; t Department of Biophysics, Norsk Hydros Institute for Cancer Research, Montebello, Oslo 3...data analysis. Technical assistance from the Linac crew at the Norsk Hydro's Institute for Cancer Research is gratefully acknowledged...

I Johansen; T Brustad; W D Rupp

1975-01-01T23:59:59.000Z

249

DNA nanotechnology: a future perspective  

Science Journals Connector (OSTI)

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

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

2013-03-01T23:59:59.000Z

250

Natural DNA sequencing by synthesis  

E-Print Network [OSTI]

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

Roller, Eric E.

2011-01-01T23:59:59.000Z

251

Neutrinoless Double Beta-Decay  

E-Print Network [OSTI]

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)

S. M. Bilenky

2010-01-12T23:59:59.000Z

252

Precisely Controlled Smart Polymer Scaffold for Nanoscale Manipulation of Biomolecules  

E-Print Network [OSTI]

for the next generation of nanomachines and biosensors. Synthetic molecular motors, and especially DNA motors for synthetic nanopores.8 Other platforms utilize orientation changes of surface immobilized DNA, termed "DNA double stranded DNA (dsDNA) and the conforma- tion of a polymer scaffold through variation in buffer p

253

Supplementary Materials: A Partition Function Algorithm for Interacting Nucleic Acid Strands  

E-Print Network [OSTI]

sets used for verification of our algorithm. 1 Preliminaries Throughout this paper, we denote the twoSupplementary Materials: A Partition Function Algorithm for Interacting Nucleic Acid Strands-Ludwigs-Universit¨at, Freiburg, Germany In this supplementary material, we describe in full the algorithm for computing

Will, Sebastian

254

Synthesis of Subgenomic RNAs by Positive-Strand RNA Viruses W. Allen Miller1  

E-Print Network [OSTI]

MINIREVIEW Synthesis of Subgenomic RNAs by Positive-Strand RNA Viruses W. Allen Miller1 is required for sgRNA synthesis, the RNA-dependent RNA polymerase (RdRp) is always translated first, directly, Tymovirus, Potexvirus, Hordeivirus, Tobamovirus, Sobemovirus, and Furovirus genera. Subgenomic RNA synthesis

Miller, W. Allen

255

Multi-strand coronal loop model and filter-ratio analysis  

E-Print Network [OSTI]

We model a coronal loop as a bundle of seven separate strands or filaments. Each of the loop strands used in this model can independently be heated (near their left footpoints) by Alfv\\'en/ion-cyclotron waves via wave-particle interactions. The Alfv\\'en waves are assumed to penetrate the strands from their footpoints, at which we consider different wave energy inputs. As a result, the loop strands can have different heating profiles, and the differential heating can lead to a varying cross-field temperature in the total coronal loop. The simulation of TRACE observations by means of this loop model implies two uniform temperatures along the loop length, one inferred from the 171:195 filter ratio and the other from the 171:284 ratio. The reproduced flat temperature profiles are consistent with those inferred from the observed EUV coronal loops. According to our model, the flat temperature profile is a consequence of the coronal loop consisting of filaments, which have different temperatures but almost similar e...

Bourouaine, S

2009-01-01T23:59:59.000Z

256

Stranded dolphin stomach contents represent the free-ranging population's diet  

Science Journals Connector (OSTI)

...Submitted posthumously. Diet is a fundamental aspect of animal ecology...foundation of consumer ecology and fundamental to empirical investigations...cause of death or stranding does not appear to significantly...ecology and conservation: a handbook of techniques (eds IL Boyd...

2013-01-01T23:59:59.000Z

257

Stranded Vehicles: How Gasoline Taxes Change the Value of Households' Vehicle Assets  

E-Print Network [OSTI]

Stranded Vehicles: How Gasoline Taxes Change the Value of Households' Vehicle Assets Meghan Busse pollution caused by the burning of fossil fuels. Argu- ments against energy taxes, and gasoline taxes more incidence of the tax. We study the effect of a gasoline tax using changes in vehicle values. We construct

Rothman, Daniel

258

Las Canteras Strand in Las Palmas Auslandssemester in Las Palmas de Gran Canaria: Welcome to Erasmus  

E-Print Network [OSTI]

Las Canteras Strand in Las Palmas Auslandssemester in Las Palmas de Gran Canaria: Welcome to Erasmus Spanien, Winter- und Sommersemester 2010/11 Gran Canaria hat die eindrucksvolle Eigenschaft nicht Gran Canaria (ULPGC). Für maximalen Genuss des Studienaufenthaltes gilt es einige Hinweise zu befolgen

Greifswald, Ernst-Moritz-Arndt-Universität

259

IMPORTANCE OF NEUTRINOLESS DOUBLE BETA DECAY Abstract  

E-Print Network [OSTI]

number violation in nature and what is its magnitude. The neutrinoless double beta decay experiment can

U. Sarkar; Utpal Sarkar

260

Radiosensitization of MDA-MB-231 breast tumor cells by adenovirus-mediated overexpression of a fragment of the XRCC4 protein  

Science Journals Connector (OSTI)

...Repair of DNA double strand breaks by non-homologous end joining. Biochimie 2003;85:1161-73. 9 El-Khamisy SF, Saifi GM, Weinfeld M, et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1...

Kara R. Jones; David A. Gewirtz; Steven M. Yannone; Shaoming Zhou; David G. Schatz; Kristoffer Valerie; Lawrence F. Povirk

2005-10-01T23:59:59.000Z

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


261

Structural investigations of platinum anticancer drugs with DNA  

SciTech Connect (OSTI)

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

Bellon, S.F.

1992-01-01T23:59:59.000Z

262

DNA: Building Blocks of Nanotechnology  

E-Print Network [OSTI]

is a powerful tool for nanotechnology. R eferences Andersen,q n 9 k / D N A % 2 0 Nanotechnology%20Staple%20Strands.jpgin the history of nanotechnology. In developing nanoscale

Powers, Alexander

2014-01-01T23:59:59.000Z

263

Mapping the binding site of aflatoxin B/sub 1/ in DNA: systematic analysis of the reactivity of aflatoxin B/sub 1/ with guanines in different DNA sequences  

SciTech Connect (OSTI)

The mutagenic and carcinogenic chemical aflatoxin B/sub 1/ (AFB/sub 1/) reacts almost exclusively at the N(7)-position of guanine following activation to its reactive form, the 8,9-epoxide (AFB/sub 1/ oxide). In general N(7)-guanine adducts yield DNA strand breaks when heated in base, a property that serves as the basis for the Maxam-Gilbert DNA sequencing reaction specific for guanine. Using DNA sequencing methods, other workers have shown that AFB/sub 1/ oxide gives strand breaks at positions of guanines; however, the guanine bands varied in intensity. This phenomenon has been used to infer that AFB/sub 1/ oxide prefers to react with guanines in some sequence contexts more than in others and has been referred to as sequence specificity of binding. Herein, data on the reaction of AFB/sub 1/ oxide with several synthetic DNA polymers with different sequences are presented, and (following hydrolysis) adduct levels are determine by high-pressure liquid chromatography. These results reveal that for AFB/sub 1/ oxide (1) the N(7)-guanine adduct is the major adduct found in all of the DNA polymers, (2) adduct levels vary in different sequences, and, thus, sequence specificity is also observed by this more direct method, and (3) the intensity of bands in DNA sequencing gels is likely to reflect adduct levels formed at the N(7)-position of guanine. Knowing this, a reinvestigation of the reactivity of guanines in different DNA sequences using DNA sequencing methods was undertaken. Methods are developed to determine the X (5'-side) base and the Y (3'-side) base are most influential in determining guanine reactivity. These rules in conjunction with molecular modeling studies were used to assess the binding sites that might be utilized by AFB/sub 1/ oxide in its reaction with DNA.

Benasutti, M.; Ejadi, S.; Whitlow, M.D.; Loechler, E.L.

1988-01-12T23:59:59.000Z

264

Comparison of two freshwater turtle species as monitors of radionuclide and chemical contamination: DNA damage and residue analysis  

SciTech Connect (OSTI)

Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of freshwater ecosystems where both low-level radioactive and nonradioactive contaminants are present. The pond slider (Trachemys scripta) and common snapping turtle (Chelydra serpentina) were analyzed for the presence of [sup 90]Sr, [sup 137]Cs, [sup 60]Co, and Hg, radionuclides and chemicals known to be present at the contaminated site, and single-strand breaks in liver DNA. The integrity of the DNA was examined by the alkaline unwinding assay, a technique that detects strand breaks as a biological marker of possible exposure to genotoxic agents. This measure of DNA damage was significantly increased in both species of turtles at the contaminated site compared with turtles of the same species at a reference site, and shows that contaminant-exposed populations were under more severe genotoxic stress than those at the reference site. The level of strand breaks observed at the contaminated site was high and in the range reported for other aquatic species exposed to deleterious concentrations of genotoxic agents such as chemicals and ionizing radiation. Statistically significantly higher concentrations of radionuclides and Hg were detected in the turtles from the contaminated area. Mercury concentrations were significantly higher in the more carnivorous snapping turtle compared with the slider; however, both species were effective monitors of the contaminants.

Meyers-Schoene, L. (Univ. of Tennessee, Knoxville, TN (United States)); Shugart, L.R.; Beauchamp, J.J.; Walton, B.T. (Oak Ridge National Lab., TN (United States))

1993-08-01T23:59:59.000Z

265

Controlling DNA Methylation  

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

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

266

DNA's Role with Proteins  

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

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

267

Decimal System and Double Digits  

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

Decimal System and Double Digits Decimal System and Double Digits Name: Ken Status: other Grade: other Country: Canada Date: April 2011 Question: If the origin of the decimal system reflects counting on ten fingers and if zero came into use after the decimal system had been established why did we not create a single symbol for our tenth digit rather than use the double digit 10? If T were to represent the tenth number this would have created a counting system where the number series 1,2...9,T is followed by the same series having a 1 to the left then followed by the same series having a 2 to the left, etc. The T would be the last number in a series of ten single digits rather than be the first number in a series of double digits. The symbol zero would be used only between negative one and positive one because it represents the existence of nothing and, therefore, would have no other function.

268

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

SciTech Connect (OSTI)

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

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

2013-10-15T23:59:59.000Z

269

DNA | Open Energy Information  

Open Energy Info (EERE)

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

270

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

E-Print Network [OSTI]

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 ...

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

2011-01-01T23:59:59.000Z

271

Mechanisms of liquid sheet breakup and the resulting drop size distributions; Part 2: strand breakup and experimental observations  

SciTech Connect (OSTI)

This paper reports that both a wave mechanism and a perforation mechanism have been proposed as the first step in the breakup of fluid sheets. For black liquor sprays, the dominant mechanism is the formation and growth of perforations according to either mechanism, cylindrical strands develop and subsequently break up to form drops. By combining the results of analyzing the breakup of both the sheet and strands, only a discrete number of drop sizes can be predicted from the wave mechanism.

Spielbauer, T.M.; Aidum, C.K. (Institute of Paper Science and Technology, Atlanta, GA (United States))

1992-03-01T23:59:59.000Z

272

NEUTRINOLESS DOUBLE BETA DECAY AND ITS “INVERSE”  

E-Print Network [OSTI]

subsequently published arguments, non-observation of neutrinoless double beta decay has, to date, no bearing on

Clemens A. Heusch; Peter Minkowski

1996-01-01T23:59:59.000Z

273

Neutrinoless Double Beta Decay and CP Violation  

E-Print Network [OSTI]

neutrinoless double beta decay in the case of two neutrino generations (or when the third generation leptons do

Patrick J. O’donnell; Utpal Sarkar

1993-01-01T23:59:59.000Z

274

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

E-Print Network [OSTI]

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

Aldaye, Faisal A., 1979-

2008-01-01T23:59:59.000Z

275

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

E-Print Network [OSTI]

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 ...

Wiktor-Brown, Dominika M

2007-01-01T23:59:59.000Z

276

MDM2 Is Required for Suppression of Apoptosis by Activated Akt1 in Salivary Acinar Cells  

Science Journals Connector (OSTI)

...serves to hydrolyze starches to simple sugars (97). Expression of amylase was analyzed in all...double-stranded DNA breaks (84), and gamma...suggest that the down-regulation of p53...Biochemistry of human alpha amylase isoenzymes. Crit...

Kirsten H. Limesand; Kathryn L. Schwertfeger; Steven M. Anderson

2006-09-18T23:59:59.000Z

277

E-Print Network 3.0 - adjacent pericarcinomatous foci Sample...  

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

p53 binding protein 1 foci as a biomarker of DNA double strand breaks induced by ionizing radiation... Radiation effect Bysta effect 53 BP1 a b s t r a c t Foci of p53 binding...

278

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system  

E-Print Network [OSTI]

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease ...

Zhang, Feng

279

Tools for Single-Molecule Sequence Detection and Manipulation.  

E-Print Network [OSTI]

??The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to double-stranded DNA is critical to a variety of single-molecule experiments. We… (more)

Zohar, Hagar

2011-01-01T23:59:59.000Z

280

Doubling of atmospheric methane supported  

SciTech Connect (OSTI)

Atmospheric methane over the past 27,000 years was measured by analyzing air trapped in glacial ice in Greenland and Antarctica. Atmospheric concentrations were stable over that period until about 200 years b.p. In the last 200 years they have more than doubled. This change in concentration is correlated with the increase in human population; the implications for climate modification are discussed. 1 figure, 3 references.

Kerr, R.A.

1984-11-23T23:59:59.000Z

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


281

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

Science Journals Connector (OSTI)

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

Rafael Giraldo; María Elena Fernández-Tresguerres

2010-01-01T23:59:59.000Z

282

Development of an Automated Microfluidic System for DNA Collection, Amplification, and Detection of Pathogens  

SciTech Connect (OSTI)

This project was focused on developing and testing automated routines for a microfluidic Pathogen Detection System. The basic pathogen detection routine has three primary components; cell concentration, DNA amplification, and detection. In cell concentration, magnetic beads are held in a flow cell by an electromagnet. Sample liquid is passed through the flow cell and bacterial cells attach to the beads. These beads are then released into a small volume of fluid and delivered to the peltier device for cell lysis and DNA amplification. The cells are lysed during initial heating in the peltier device, and the released DNA is amplified using polymerase chain reaction (PCR) or strand displacement amplification (SDA). Once amplified, the DNA is then delivered to a laser induced fluorescence detection unit in which the sample is detected. These three components create a flexible platform that can be used for pathogen detection in liquid and sediment samples. Future developments of the system will include on-line DNA detection during DNA amplification and improved capture and release methods for the magnetic beads during cell concentration.

Hagan, Bethany S.; Bruckner-Lea, Cynthia J.

2002-12-01T23:59:59.000Z

283

Strategic electricity sector assessment methodology under sustainability conditions: a Swiss case study on CO2 emissions, competition and stranded costs  

Science Journals Connector (OSTI)

Designing and implementing a sustainable energy sector will be a key element of defining and creating a sustainable society. In the electricity industry, the question of strategic planning for sustainability seems to conflict with the shorter time horizons associated with market forces as deregulation replaces vertical integration. In order to address such questions, a project called SESAMS (Strategic Electricity Sector Assessment Methodology under Sustainability) has been established to develop electricity sector planning methods related to sustainability. This effort is part of the Alliance for Global Sustainability (AGS) formed by the Massachusetts Institute of Technology (MIT), the Swiss Federal Institutes of Technology (ETHZ and EPFL), and the University of Tokyo (UT). The initial phase of SESAMS in 1997 created a methodology integrating multi-scenario simulation, life-cycle analysis and multi-criteria decision analysis. This 1998 case study has expanded the methodology to study the transitional effects of deregulation associated with the issues of stranded cost. This analysis has studied the inclusion of different classes of stranded assets, different recovery periods, and recovery of costs on a fixed vs. variable (per kWh) basis. On a societal basis, stranded costs are a zero-sum transfer payment, but the ownership patterns of stranded assets mean that compensation for stranded assets will produce relative winners and losers. These winners and losers shift according to the stranded cost and other options present in different scenarios. The results of the stranded cost analysis are integrated with updated multi-criteria trade-off analysis and life-cycle analysis results, based on expanded system boundaries.

W. Schenler; Adrian V. Gheorghe; Warren Stephen Connors; Stefan Hirschberg; Pierre-Andre Haldi

2002-01-01T23:59:59.000Z

284

Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces  

SciTech Connect (OSTI)

We study the effects of the presence of a hydrophilic and a hydrophobic surface on the conformations and interactions of a single-stranded DNA (ssDNA) oligomer using atomistic molecular dynamics, umbrella sampling, and temperature-replica exchange. Our simulations capture the expected interactions between the ssDNA and the two surfaces (e.g., hydrogen bonds, hydrophobic interactions), but we find that the surface chemistry does not strongly affect the exposure of the relatively hydrophobic nucleobases or the hydrophilic phosphate backbone in a 16-base ssDNA. Likewise, the surfaces do not strongly affect the preferred size of the ssDNA compared to bulk solution, although the hydrophilic surface does favor slightly more compact ssDNA conformations than the hydrophobic surface. In more compact conformations, the negative charge of the ssDNA is more concentrated, and the energetic interactions of the DNA and DNA-bound counterions with the hydrophilic surface are more favorable, which consequently favors smaller ssDNA sizes. Increasing temperature, regardless of the presence or chemistry of a surface, makes it less unfavorable for the ssDNA to assume both compact and extended conformations. With increasing temperature the free energy cost of assuming a compact conformation is reduced to a greater extent than the cost of assuming an extended conformation. The reason for this difference is the entropically favorable release of DNA-bound water molecules upon assuming a compact conformation. Increasing temperature decreases water-DNA interactions while surprisingly increasing counterion-DNA interactions, changes which are attributed to the relative balance of entropic and energetic contributions for water molecules and counterions bound to the ssDNA.

Elder, Robert M.; Jayaraman, Arthi, E-mail: arthi.jayaraman@colorado.edu [Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303 (United States)] [Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303 (United States)

2014-04-21T23:59:59.000Z

285

Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures  

E-Print Network [OSTI]

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

Reif, John H.

286

Recombinant Modified Vaccinia Virus Ankara Generating Excess Early Double-Stranded RNA Transiently Activates Protein Kinase R and Triggers Enhanced Innate Immune Responses  

Science Journals Connector (OSTI)

...interferon beta) were purchased from PBL Assay Science (Piscataway, NJ, USA). Murine IFN-alpha...adaptive immunity by the innate immune system. Science 327 :291-295. doi: 10.1126/science.1183021 . 6. Frenz, T , Z Waibler, J Hofmann...

Michael Wolferstätter; Marc Schweneker; Michaela Späth; Susanne Lukassen; Marieken Klingenberg; Kay Brinkmann; Ursula Wielert; Henning Lauterbach; Hubertus Hochrein; Paul Chaplin; Mark Suter; Jürgen Hausmann

2014-10-08T23:59:59.000Z

287

Ionizing Radiation Damage to the Folded Chromosome of Escherichia coli K-12: Repair of Double-Strand Breaks in Deoxyribonucleic Acid  

Science Journals Connector (OSTI)

...cell survival Dose (krad) % Recovery...it is in the range of sedimentation...that direct, radiation-induced cross-linking...during repair of ionizing radiation damage (3...is within the range ofsedimentation...biologically significant dose range. Unfortu...

Kevin M. Ulmer; Reinaldo F. Gomez; Anthony J. Sinskey

1979-05-01T23:59:59.000Z

288

Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus ?6 from De Novo Initiation to Elongation  

Science Journals Connector (OSTI)

...the interaction between heparin and a battery of mutant enzymes (Fig. 4A). Mutations...like WT) has a significantly lower thermal stability than WT even in the presence...and structure refinement.) Fig. S1 (Thermal denaturation curves.) Fig. S2 (Electron...

Sam Wright; Minna M. Poranen; Dennis H. Bamford; David I. Stuart; Jonathan M. Grimes

2011-12-28T23:59:59.000Z

289

Gene Conversion Is Strongly Induced in Human Cells by Double-strand Breaks and Is Modulated by the Expression of BCL-xL  

Science Journals Connector (OSTI)

...with the time of incubation. Factors responsible for the Pasteur...glycolytic and the respiratory energy. This appears to be a unique...date can use only respiratory energy for Pi transport. Rate-limiting factors in glycolysis and transport...

Claudia Wiese; Andrew J. Pierce; Stacey S. Gauny; Maria Jasin; and Amy Kronenberg

2002-03-01T23:59:59.000Z

290

Reversed Doppler effect in double negative metamaterials  

Science Journals Connector (OSTI)

Doppler shifts in double negative metamaterials have never been observed. This Rapid Communication presents experimental results on Doppler effect in a double negative acoustic metamaterial. We observed that frequency was downshifted when the source was approaching and upshifted when receding. Notably, while in ordinary media wavelengths corresponding to downshifted frequencies are longer, we demonstrate that in double negative metamaterials wavelengths increase as the frequencies increase. Consequently even though the frequencies were downshifted in front of the moving source, the wavelengths became shorter.

Sam Hyeon Lee; Choon Mahn Park; Yong Mun Seo; Chul Koo Kim

2010-06-14T23:59:59.000Z

291

Double perovskite catalysts for oxidative coupling  

DOE Patents [OSTI]

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.

Campbell, K.D.

1991-01-01T23:59:59.000Z

292

Review of double beta decay experiments  

E-Print Network [OSTI]

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

A. S. Barabash

2014-03-12T23:59:59.000Z

293

Review of double beta decay experiments  

E-Print Network [OSTI]

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

Barabash, A S

2014-01-01T23:59:59.000Z

294

Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI  

SciTech Connect (OSTI)

Restriction enzymes share little or no sequence homology with the exception of isoschizomers, or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not only the N- and C-terminal helices but also an internal 310 helix and containing {beta}-strands that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal 'arms' that appear to 'compete' for the minor groove. However, the arms are shorter than in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has higher star activity (at 37 C) compared to BamHI. Together, the OkrAI and BamHI structures offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA substrate.

Vanamee, Éva Scheuring; Viadiu, Hector; Chan, Siu-Hong; Ummat, Ajay; Hartline, Adrian M.; Xu, Shuang-yong; Aggarwal, Aneel K. (Mount Sinai Hospital); (NEB)

2011-11-18T23:59:59.000Z

295

Comparing Double String Theory Actions  

E-Print Network [OSTI]

Aimed to a deeper comprehension of a manifestly T-dual invariant formulation of string theory, in this paper a detailed comparison between the non-covariant action proposed by Tseytlin and the covariant one proposed by Hull is done. These are obtained by making both the string coordinates and their duals explicitly appear, on the same foot, in the world-sheet action, so "doubling" the string coordinates along the compact dimensions. After a discussion of the nature of the constraints in both the models and the relative quantization, it results that the string coordinates and their duals behave like "non-commuting" phase space type coordinates but their expressions in terms of Fourier modes generate the oscillator algebra of the standard bosonic string formulation. A proof of the equivalence of the two formulations is given. Furthermore, open-string solutions are also discussed.

Luca De Angelis; S. J. Gabriele Gionti; Raffaele Marotta; Franco Pezzella

2013-12-27T23:59:59.000Z

296

Review Paper. Ancient DNA  

Science Journals Connector (OSTI)

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

2005-01-01T23:59:59.000Z

297

Recognition of DNA by Synthetic Antibodies  

Science Journals Connector (OSTI)

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

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

1994-03-01T23:59:59.000Z

298

Nuclear DNA Amounts in Angiosperms  

Science Journals Connector (OSTI)

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

1976-01-01T23:59:59.000Z

299

DNA Structural Nanotechnology Duke University  

E-Print Network [OSTI]

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

Reif, John H.

300

Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly  

Science Journals Connector (OSTI)

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

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

2014-02-20T23:59:59.000Z

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


301

Double superexchange in quantum dot mesomaterials  

E-Print Network [OSTI]

as the critical obstacles to dramatic enhancements in the energy conversion efficiency of photovoltaic cells based.7­10 A low binding energy allows excitons to thermally dissociate and charge carriers hop from dot exhibits a double superexchange. In addition to enhancing carrier hopping rates, double superexchange plays

Wu, Zhigang

302

Double beta decay: experiments and theory review  

E-Print Network [OSTI]

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.

A. Nucciotti

2007-07-15T23:59:59.000Z

303

Received 12 Apr 2013 | Accepted 30 May 2013 | Published 2 Jul 2013 CRISPR-Cas and restrictionmodification systems  

E-Print Network [OSTI]

-Cas and restriction­modification systems are compatible and increase phage resistance Marie-E`ve Dupuis1,2, Manuela systems exist and at least two of them directly target the incoming DNA: restriction­modification (R plasticity. The most studied phages have double-stranded DNA (dsDNA) genome encapsidated in a protein capsid

Cai, Long

304

Role of Lon, an ATP-Dependent Protease Homolog, in Resistance of Pseudomonas aeruginosa to Ciprofloxacin  

Science Journals Connector (OSTI)

...in the pharmaceutical pipeline, resistance to the current...of SOS-mediated DNA repair mechanisms and cell filamentation...PA4763 recN RecN DNA repair protein H1121 6_G1...faithful recombinational repair of DNA double-strand...in the pharmaceutical pipeline, resistance to the current...

Michelle D. Brazas; Elena B. M. Breidenstein; Joerg Overhage; Robert E. W. Hancock

2007-09-24T23:59:59.000Z

305

Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers  

Science Journals Connector (OSTI)

...www.gene.com/gene/pipeline/status/oncology/apo2l...to broken chromosomes.DNA Repair (Amst) 2006;5:534-43...19. Lukas J Bartek J.DNA repair: New tales of an old tail...depends on nucleotide excision repair and not DNA double-strand...

Ellen V. Stevens; Satoshi Nishizuka; Smitha Antony; Mark Reimers; Sudhir Varma; Lynn Young; Peter J. Munson; John N. Weinstein; Elise C. Kohn; and Yves Pommier

2008-01-01T23:59:59.000Z

306

Self-assembly of hydrogen-bonded supramolecular strands from complementary melamine and barbiturate components with chiral  

E-Print Network [OSTI]

Self-assembly of hydrogen-bonded supramolecular strands from complementary melamine and barbiturate barbiturate 7 result in molecular recognition directed self-assembly in solution and in the solid state containing a dierent triazine enantiomer. Self-assembly takes place in biological systems with a high level

Rusell, K.C.

307

Fleet DNA (Presentation)  

SciTech Connect (OSTI)

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

Walkokwicz, K.; Duran, A.

2014-06-01T23:59:59.000Z

308

What can we learn from neutrinoless double beta decay experiments?  

E-Print Network [OSTI]

312 P. Vogel, “Limits From Neutrinoless Double-Beta Decay (Assumptions No detected neutrinoless double ?-decay lightestscale (1 ± 0.05 eV), No neutrinoless double ?-decay lightest

Bahcall, John N.

2009-01-01T23:59:59.000Z

309

A Search for Neutrinoless Double Beta Decay of Te-130  

E-Print Network [OSTI]

Bolometric experiments for neutrinoless double beta 3.2.1A Search for Neutrinoless Double Beta Decay of Te by AdamSpring 2010 A Search for Neutrinoless Double Beta Decay of

Bryant, Adam Douglas

2010-01-01T23:59:59.000Z

310

Neutrinoless Double Beta Decay in Light of SNO Salt Data  

E-Print Network [OSTI]

14] P. Vogel, “Limits From Neutrinoless Double-Beta Decay (Higgs, can also cause neutrinoless double-beta decay (seeLBNL-53996 Neutrinoless Double Beta Decay in Light of SNO

Murayama, Hitoshi

2009-01-01T23:59:59.000Z

311

Chiral Mesophases of DNA  

E-Print Network [OSTI]

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

Randall D. Kamien

1998-12-08T23:59:59.000Z

312

Radiation and viral DNA  

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

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

313

nAture methods | VOL.10 NO.7 | JULY2013 | 647 single-stranded oligonucleotides are important as research  

E-Print Network [OSTI]

relative to what biological systems produce. the number of errors in synthetic dnA increases- parison to what is produced in nature3. The number of errors in synthetic DNA increases with the number

Cai, Long

314

Structural design of double hull tankers  

SciTech Connect (OSTI)

After a brief introduction of structural design procedure for double hull tankers, their design features are firstly highlighted comparing with conventional single hull tankers. Next discussed are recent topics of double hull VLCC (Very Large Crude oil Carrier) including higher tensile steel and strut arrangement in transverse ring frames. Finally ultimate longitudinal strength of hull girder is analyzed through a simplified method under both sagging and hogging conditions. Making use of this result, some considerations are made on structural reliability of double hull VLCC.

Niho, O.; Yanagibayashi, S.; Akashi, T. [Mitsui Engineering and Shipbuilding Co., Ltd., Tokyo (Japan)

1994-12-31T23:59:59.000Z

315

Smectic Order in Double-Twist Cylinders  

E-Print Network [OSTI]

I propose a double-twist texture with local smectic order, which may have been seen in recent experiments. As in the Renn-Lubensky TGB phase, the smectic order is broken only through a lattice of screw dislocations. A melted lattice of screw dislocations can produce a double-twist texture as can an unmelted lattice. In the latter case I show that geometry only allows for certain angles between smectic regions. I discuss the possibility of connecting these double-twist tubes together to form a smectic blue phase.

Randall D. Kamien

1996-11-04T23:59:59.000Z

316

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)

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.

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

317

Photo double ionization of ethylene and acetylene near threshold  

E-Print Network [OSTI]

Photo double ionization of ethylene and acetylene nearcomplete measurements of the photo double ionization ofkinetic energy of the photo electrons and the nuclear

Gaire, B.

2014-01-01T23:59:59.000Z

318

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

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

National 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...

319

Photo double ionization of ethylene and acetylene near threshold  

E-Print Network [OSTI]

double ionization of ethylene and acetylene near thresholdphoto double ionization of ethylene (dou- ble CC bond) andsimilar yields of metastable ethylene dications produced by

Gaire, B.

2014-01-01T23:59:59.000Z

320

Molecular Dynamics Study of the Electrical Double Layer at Silver...  

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

Electrical Double Layer at Silver Chloride Electrolyte Interfaces. Molecular Dynamics Study of the Electrical Double Layer at Silver Chloride Electrolyte Interfaces. Abstract:...

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


321

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...

322

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

Science Journals Connector (OSTI)

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

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

1997-11-01T23:59:59.000Z

323

Double-Disk Dark Matter  

Science Journals Connector (OSTI)

Abstract Based on observational tests of large scale structure and constraints on halo structure, dark matter is generally taken to be cold and essentially collisionless. On the other hand, given the large number of particles and forces in the visible world, a more complex dark sector could be a reasonable or even likely possibility. This hypothesis leads to testable consequences, perhaps portending the discovery of a rich hidden world neighboring our own. We consider a scenario that readily satisfies current bounds that we call Partially Interacting Dark Matter (PIDM). This scenario contains self-interacting dark matter, but it is not the dominant component. Even if PIDM contains only a fraction of the net dark matter density, comparable to the baryonic fraction, the subdominant component’s interactions can lead to interesting and potentially observable consequences. Our primary focus will be the special case of Double-Disk Dark Matter (DDDM), in which self-interactions allow the dark matter to lose enough energy to lead to dynamics similar to those in the baryonic sector. We explore a simple model in which DDDM can cool efficiently and form a disk within galaxies, and we evaluate some of the possible observational signatures. The most prominent signal of such a scenario could be an enhanced indirect detection signature with a distinctive spatial distribution. Even though subdominant, the enhanced density at the center of the galaxy and possibly throughout the plane of the galaxy (depending on precise alignment) can lead to large boost factors, and could even explain a signature as large as the 130 GeV Fermi line. Such scenarios also predict additional dark radiation degrees of freedom that could soon be detectable and would influence the interpretation of future data, such as that from Planck and from the Gaia satellite. We consider this to be the first step toward exploring a rich array of new possibilities for dark matter dynamics.

JiJi Fan; Andrey Katz; Lisa Randall; Matthew Reece

2013-01-01T23:59:59.000Z

324

Characterizing the bending and flexibility induced by bulges in DNA duplexes  

E-Print Network [OSTI]

Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight and the bulge is on one side of the duplex, and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures.

John S. Schreck; Thomas E. Ouldridge; Flavio Romano; Ard A. Louis; Jonathan P. K. Doye

2014-12-19T23:59:59.000Z

325

Double Beta Decay Constraint on Composite Neutrinos  

Science Journals Connector (OSTI)

......Constraint on Composite Neutrinos Eiichi Takasugi Department of Physics, Osaka University, Toyonaka 560 Neutrinoless double beta decay (betabeta)0v occurs through the magnetic coupling of dimension five operator whose coupling constant is......

Eiichi Takasugi

1997-10-01T23:59:59.000Z

326

Phenomenology of single and double diffraction dissociation  

E-Print Network [OSTI]

Predictions of the gap-probability renormalization model for single and double diffraction dissociation cross sections in proton-proton collisions at the LHC are presented and compared with recent CMS measurements.

Konstantin Goulianos

2013-10-21T23:59:59.000Z

327

Phenomenology of neutrinoless double beta decay  

E-Print Network [OSTI]

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.

Gómez-Cadenas, J J

2015-01-01T23:59:59.000Z

328

Phenomenology of neutrinoless double beta decay  

E-Print Network [OSTI]

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.

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

2015-02-02T23:59:59.000Z

329

Double Pomeron Physics at the LHC  

E-Print Network [OSTI]

I discuss central exclusive production, otherwise known as Double Pomeron Exchange, DPE, from the ISR through the Tevatron to the LHC. There I emphasize the interest of exclusive Higgs and WW/ZZ production.

Michael G. Albrow

2005-07-25T23:59:59.000Z

330

Neutrinoless double beta decay with scalar bilinears  

E-Print Network [OSTI]

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.

H. V. Klapdor-Kleingrothaus; U. Sarkar

2002-11-18T23:59:59.000Z

331

Wavelength-doubling optical parametric oscillator  

DOE Patents [OSTI]

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.

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

2007-07-24T23:59:59.000Z

332

Double shell tank waste analysis plan  

SciTech Connect (OSTI)

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.

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

1994-12-15T23:59:59.000Z

333

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

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

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

334

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...

335

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

Science Journals Connector (OSTI)

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

Goran Pljevaljcic; Marc Pignot; Elmar Weinhold

2003-02-26T23:59:59.000Z

336

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

SciTech Connect (OSTI)

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

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

2013-02-01T23:59:59.000Z

337

Computer code for double beta decay QRPA based calculations  

E-Print Network [OSTI]

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

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

338

An analysis of tissues for total PCB and planar PCB concentrations in marine mammals stranded along the Gulf of Mexico  

E-Print Network [OSTI]

INTRODUCTION LITERATURE REVIEW Page v1 V111 1X Polychlorinated Biphenyls Transportation and Dispersal Planar PCB Congeners Bioaccumulation Marine Mammals as Bioindicators Recent Marine Mammal Mass Mortalities Considerations for Analyzing Stranded... comparison of the levels of PCBs containing 8, 9, and 10 chlorine atoms in the blubber of mature and immature female Tursiops truncatus 64 X LIST OF FIGURES (continued) Figure F age 14 A comparison of the levels of PCBs containing 4, 5, and 6 chlorine...

Davis, Joseph W.

2012-06-07T23:59:59.000Z

339

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

SciTech Connect (OSTI)

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.

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

340

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

SciTech Connect (OSTI)

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.

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

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


341

DNA Meta-Molecules: Synthe4c Biology via DNA Nanostructures &  

E-Print Network [OSTI]

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

Reif, John H.

342

Integrated Microfluidic Electrochemical DNA Sensor  

E-Print Network [OSTI]

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

Fygenson, Deborah Kuchnir

343

Single Molecule Studies of Telomere DNA  

E-Print Network [OSTI]

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

Long, Xi

2014-01-01T23:59:59.000Z

344

DNA Origami: A History and Current Perspective  

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

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

345

C4-Dicarboxylic acid metabolism in bundle-sheath chloroplasts, mitochondria and strands of Eriochloa borumensis Hack., a phosphoenolpyruvate-carboxykinase type C4 species  

Science Journals Connector (OSTI)

C4-acid metabolism by isolated bundlesheath chloroplasts, mitochondria and strands of Eriochloa borumensis Hack., a phosphoennolpyruvate-carboxykinase (PEP-CK)...4Cl. There was very little conversion of PEP to py...

C. K. M. Rathnam; G. E. Edwards

346

Effect of nanoclay on some applied properties of oriented strand board (OSB) made from underutilized low quality paulownia (Paulownia fortunei) wood  

Science Journals Connector (OSTI)

In this study, the effect of nanoclay on some applied properties of oriented strand ... of European Norm. With increasing 5 % nanoclay to UF resin, mechanical and physical properties ... electron microscope analy...

Ayoub Salari; Taghi Tabarsa; Abolghasem Khazaeian…

2012-12-01T23:59:59.000Z

347

DNA Single-Strand Breaks and Sister Chromatid Exchanges Induced by Treatment with Hematoporphyrin and Light or by X-Rays in Human NHIK 3025 Cells  

Science Journals Connector (OSTI)

...Biophysics [J. M., T. C.] and Genetics [H. W.], Norsk Hydro's Institute for Cancer Research, Montebello, Oslo...of Biophysics (J. M., T. C.Jand Genetics (H. W.j, Norsk Hydro s Institute for Cancer Research, Montebello, Oslo 3...

Johan Moan; Helga Waksvik; Terje Christensen

1980-08-01T23:59:59.000Z

348

Hyperthermia Activates a Subset of Ataxia-Telangiectasia Mutated Effectors Independent of DNA Strand Breaks and Heat Shock Protein 70 Status  

Science Journals Connector (OSTI)

...Figure 3. Effect of heat on cell cycle distribution in cells with and without...A, the cell cycle distribution after heat shock is identical...assay was carried out. Heat treatment of purified ATM resulted in the loss of its ability to phosphorylate...

Clayton R. Hunt; Raj K. Pandita; Andrei Laszlo; Ryuji Higashikubo; Manjula Agarwal; Tetsuya Kitamura; Arun Gupta; Nicole Rief; Nobuo Horikoshi; Rajeskaran Baskaran; Ji-Hoon Lee; Markus Löbrich; Tanya T. Paull; Joseph L. Roti Roti; and Tej K. Pandita

2007-04-01T23:59:59.000Z

349

Precision Muon Reconstruction in Double Chooz  

E-Print Network [OSTI]

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.

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

2014-01-01T23:59:59.000Z

350

The double-arm barn door tracker  

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

How to build a double-arm barn door tracker How to build a double-arm barn door tracker | Jefferson Lab Home Page | Science Education Home Page | Construction Notes/Photos Page | Sources: Sky & Telescope April 1989 (p436 - p441) [very good] Sky & Telescope February 1988 (p213 - p214) Original concept by Dave Trott A single-arm barn door tracker, driven by a straight screw, accumulates tangent error as time passes. Most of this error can be eliminated by adding a second hinged arm to the standard arrangement. There are four types of double-arm trackers, each with a different geometry. A comparison of accumulated error (in arc seconds) and construction parameters is given below: Error Chart [Apparently Type 1 is very bad and not worth constructing?? The two Type 4 drives vary in beta. This results in shifting the region of maximum error

351

Challenges and opportunities for structural DNA nanotechnology  

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

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

352

On the neutrinoless double ?{sup +}/EC decays  

SciTech Connect (OSTI)

The neutrinoless double positron-emission/electron-capture (0??{sup +}/EC) decays are studied for the magnitudes of the involved nuclear matrix elements (NMEs). Decays to the ground state, 0{sub gs}{sup +}, and excited 0{sup +} states are discussed. The participant many-body wave functions are evaluated in the framework of the quasiparticle random-phase approximation (QRPA). Effective, G-matrix-derived nuclear forces are used in realistic single-particle model spaces. The channels ?{sup +}?{sup +}, ?{sup +}EC, and the resonant neutrinoless double electron capture (R0?ECEC) are discussed.

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

2013-12-30T23:59:59.000Z

353

Nanotechnology Applications in Self-Assembly and DNA Computing  

E-Print Network [OSTI]

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

Akin, Hayri Engin

2011-01-01T23:59:59.000Z

354

Sequence independent amplification of DNA  

DOE Patents [OSTI]

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

Bohlander, S.K.

1998-03-24T23:59:59.000Z

355

Sequence independent amplification of DNA  

DOE Patents [OSTI]

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

Bohlander, Stefan K. (Chicago, IL)

1998-01-01T23:59:59.000Z

356

Unnatural nucleotides for DNA sequencing  

E-Print Network [OSTI]

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

Jacutin, Swanee E

2012-06-07T23:59:59.000Z

357

DNA UPTAKE BY TRANSFORMABLE BACTERIA  

SciTech Connect (OSTI)

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

LACKS,S.A.

1999-09-07T23:59:59.000Z

358

A Microscopic Double-Slit Experiment  

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

A Microscopic Double-Slit A Microscopic Double-Slit Experiment A Microscopic Double-Slit Experiment Print Wednesday, 29 February 2012 00:00 Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

359

Parameterized Algorithms for Double Hypergraph Dualization with  

E-Print Network [OSTI]

as Sperner families.) The support of a hypergraph is the set of all vertices covered by edges, the remaining sets in graphs are also known as vertex covers. We consider the following two operators on hypergraphsParameterized Algorithms for Double Hypergraph Dualization with Rank Limitation and Maximum Minimal

Damaschke, Peter

360

Double tracks test site characterization report  

SciTech Connect (OSTI)

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).

NONE

1996-05-01T23:59:59.000Z

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


361

Apparent Double SiO Maser Sources  

Science Journals Connector (OSTI)

......to 3 Jy with four 20-m antennas (Miyoshi 1998, a poster paper at JAS meeting). The double SiO sources found...Research (C) (No. 10640238) of the Ministry of Education, Science, Sports and Culture. One of authors (SD) received......

Shuji Deguchi; Takahiro Fujii; Hideyuki Izumiura; Shigeru Matsumoto; Yoshikazu Nakada; Peter R. Wood; Issei Yamamura

1999-06-01T23:59:59.000Z

362

Fatigue analysis for double hull VLCC  

SciTech Connect (OSTI)

This paper presents the procedure and the results of fatigue analysis forming a part of Dynamic Load Approach (DLA) applied for 280,000 DWT double hull VLCC, classed with DLA notation by American Bureau of Shipping. The spectral fatigue analysis is applied to the above vessel, and the fatigue strength is confirmed to be sufficient.

Kawachi, S.; Kushima, T.; Negayama, H.; Shigematsu, K. [Sumitomo Heavy Industries, Ltd., Yokosuka (Japan)

1994-12-31T23:59:59.000Z

363

Pion double charge exchange and hadron dynamics  

SciTech Connect (OSTI)

This paper will review theoretical results to show how pion double charge exchange is contributing to our understanding of hadron dynamics in nuclei. The exploitation of the nucleus as a filter is shown to be essential in facilitating the comparison between theory and experiment. 23 refs., 3 figs., 2 tabs.

Johnson, M.B.

1991-01-01T23:59:59.000Z

364

Neutrinoless Double $?$-Decay: Status and Future  

E-Print Network [OSTI]

A brief summary of the status of neutrino masses, mixing and oscillations is presented. Neutrinoless double $\\beta$-decay is considered. Predictions for the effective Majorana mass are reviewed. A possible test of the calculations of nuclear matrix elements of the $0\

S. M. Bilenky

2005-09-11T23:59:59.000Z

365

Double Tracks revegetation and monitoring plan  

SciTech Connect (OSTI)

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.

NONE

1997-07-01T23:59:59.000Z

366

Neutrinoless Double Beta Decay and ??Mass Determination  

Science Journals Connector (OSTI)

The search for Neutrinoless Double Beta Decay could improve our knowledge on neutrino properties. After a brief discussion on the implications of the observation of this rare process I will introduce the experimental approaches and review the prospects of the search for this nuclear transition.

M. Pedretti

2005-01-01T23:59:59.000Z

367

The Polymerase Chain Reaction and Branching Processes Fengzhu Sun  

E-Print Network [OSTI]

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

Sun, Fengzhu - Sun, Fengzhu

368

Modeling DNA Shuffling Fengzhu Sun  

E-Print Network [OSTI]

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

Sun, Fengzhu - Sun, Fengzhu

369

Designs of Autonomous Unidirectional Walking DNA Devices  

E-Print Network [OSTI]

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

Reif, John H.

370

Ancient DNA: the first three decades  

Science Journals Connector (OSTI)

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

2015-01-01T23:59:59.000Z

371

Molecular Computing with DNA Self-Assembly  

E-Print Network [OSTI]

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

Reif, John H.

372

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

Science Journals Connector (OSTI)

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

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

1994-04-01T23:59:59.000Z

373

Radiation-induced electron migration along DNA  

SciTech Connect (OSTI)

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

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

1994-04-01T23:59:59.000Z

374

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

Science Journals Connector (OSTI)

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

2012-01-01T23:59:59.000Z

375

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

E-Print Network [OSTI]

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

Rambaut, Andrew

376

BioMed Central Page 1 of 10  

E-Print Network [OSTI]

of neocarzinostatin-induced DNA double-strand breaks. Background Ionizing radiation induces multiple lesions in cell) in proportion to the radiation dose. Among the enzymes that have evolved for the repair of radiation damage-B activation and proper management of the oxidative stress inherent in radiation exposure. DNA

Boyer, Edmond

377

ATR Affecting Cell Radiosensitivity Is Dependent on Homologous Recombination Repair but Independent of Nonhomologous End Joining  

Science Journals Connector (OSTI)

...Toxicology, Maine Center for Toxicology and Environmental Health, Portland, ME, University of Bridgeport, Bridgeport, CT...DNA double strand breaks (DSBs) formation, one of the most dangerous types of DNA damage. The hMRE11-RAD50-NBS1 protein complex...

Hongyan Wang; Huichen Wang; Simon N. Powell; George Iliakis; and Ya Wang

2004-10-01T23:59:59.000Z

378

Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery  

Science Journals Connector (OSTI)

...by charged and polar patches. Figure 7 The human...essential for normal DNA repair, there is an advantage...structure determination pipeline. Proc. Natl Acad...double-strand-break-repair mutant mammalian cells...gene and its role in DNA repair and V(D)J recombination...

2006-01-01T23:59:59.000Z

379

Hanford Begins New Campaign to Remove Excess Water from Double...  

Energy Savers [EERE]

Hanford Begins New Campaign to Remove Excess Water from Double-Shell Tanks Hanford Begins New Campaign to Remove Excess Water from Double-Shell Tanks September 30, 2014 - 12:00pm...

380

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

SciTech Connect (OSTI)

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.

Kourbanis, ioanis

2014-06-01T23:59:59.000Z

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


381

Sensitivity of CUORE to Neutrinoless Double-Beta Decay  

E-Print Network [OSTI]

Sensitivity of CUORE to Neutrinoless Double-Beta Decay b c,:Results of the Search for Neutrinoless D o u b l e - B e t ah e i n a , Evidence for neutrinoless double beta decay, M o

Alessandria, F.

2013-01-01T23:59:59.000Z

382

Double photoionization of helium with synchrotron x-rays: Proceedings  

SciTech Connect (OSTI)

This report contains papers on the following topics: Overview and comparison of photoionization with charged particle impact; The ratio of double to single ionization of helium: the relationship of photon and bare charged particle impact ionization; Double photoionization of helium at high energies; Compton scattering of photons from electrons bound in light elements; Electron ionization and the Compton effect in double ionization of helium; Elimination of two atomic electrons by a single energy photon; Double photoionization of helium at intermediate energies; Double Photoionization: Gauge Dependence, Coulomb Explosion; Single and Double Ionization by high energy photon impact; The effect of Compton Scattering on the double to single ionization ratio in helium; and Double ionization of He by photoionization and Compton scattering. These papers have been cataloged separately for the database.

Not Available

1994-01-01T23:59:59.000Z

383

Cellular responses to environmental DNA damage  

SciTech Connect (OSTI)

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

Not Available

1994-08-01T23:59:59.000Z

384

NATURE PHYSICS | VOL 10 | JUNE 2014 | www.nature.com/naturephysics 413 news & views  

E-Print Network [OSTI]

shape assembled. In contrast, the DNA bricks were made using short strands of synthetic DNA, interlocked

Loss, Daniel

385

/ Search for Neutrinoless Double Beta Decay with CUORE  

E-Print Network [OSTI]

neutrinoless double beta decay (??0?) in 130 Te and other rare processes. The observation of ??0? would

Elena Ferri

386

Geothermal: Sponsored by OSTI -- Structure of the Electric Double...  

Office of Scientific and Technical Information (OSTI)

Structure of the Electric Double Layer in Hydrothermal Systems. Molecular Simulation Approach and Interpretation of Experimental Results...

387

The Majorana Neutrinoless Double-Beta Decay Experiment  

E-Print Network [OSTI]

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

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

388

Double K-Vacancy Production by X-Ray Photoionization  

E-Print Network [OSTI]

Double K-Vacancy Production by X-Ray Photoionization S. H. Southworth£ , R. W. Dunford£ , E. P Photon Source. Double K-vacancy production in Ne was observed by recording the KK-KLL Auger. For Mo, double K-vacancy production was observed by recording the K fluorescence hypersatellite

389

Sensitivity of CUORE to Neutrinoless Double-Beta Decay  

E-Print Network [OSTI]

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 .

Alessandria, F.

2013-01-01T23:59:59.000Z

390

Search for Neutrinoless Double-Beta Decay  

E-Print Network [OSTI]

After the pioneering work of the Heidelberg-Moscow (HDM) and International Germanium Experiment (IGEX) groups, the second round of neutrinoless double-$\\beta$ decay searches currently underway has or will improve the life-time limits of double-$\\beta$ decay candidates by a factor of two to three, reaching in the near future the $T_{1/2} = 3 \\times 10^{25}$ yr level. This talk will focus on the large-scale experiments GERDA, EXO-200, and KamLAND-Zen, which have reported already lower half-life time limits in excess of $10^{25}$ yr. Special emphasis is given to KamLAND-Zen, which is expected to approach the inverted hierarchy regime before future 1-ton experiments probe completely this life-time or effective neutrino-mass regime, which starts at $\\approx 2 \\times 10^{26}$ yr or $\\approx 50$ meV.

Tornow, Werner

2014-01-01T23:59:59.000Z

391

Double-clad nuclear fuel safety rod  

DOE Patents [OSTI]

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.

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

1984-01-01T23:59:59.000Z

392

A Microscopic Double-Slit Experiment  

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

A Microscopic Double-Slit Experiment Print A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

393

A Microscopic Double-Slit Experiment  

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

A Microscopic Double-Slit Experiment Print A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in establishing the validity of wave-particle duality, a puzzling concept that has ultimately become central to the interpretation of complementarity in quantum mechnanics. In a new twist on this classic experiment, the double slit (with light waves) has been replaced by a diatomic molecule (with electron waves). At ALS Beamline 10.0.1, researchers have shown that diatomic molecules can serve as two-center emitters of electron waves and that traces of electron-wave interference can be directly observed in precise measurements of vibrationally resolved photoionization spectra.

394

Vibration of Generalized Double Well Oscillators  

E-Print Network [OSTI]

We have applied the Melnikov criterion to examine a global homoclinic bifurcation and transition to chaos in a case of a double well dynamical system with a nonlinear fractional damping term and external excitation. The usual double well Duffing potential having a negative square term and positive quartic term has been generalized to a double well potential with a negative square term and a positive one with an arbitrary real exponent $q > 2$. We have also used a fractional damping term with an arbitrary power $p$ applied to velocity which enables one to cover a wide range of realistic damping factors: from dry friction $p \\to 0$ to turbulent resistance phenomena $p=2$. Using perturbation methods we have found a critical forcing amplitude $\\mu_c$ above which the system may behave chaotically. Our results show that the vibrating system is less stable in transition to chaos for smaller $p$ satisfying an exponential scaling low. The critical amplitude $\\mu_c$ as an exponential function of $p$. The analytical results have been illustrated by numerical simulations using standard nonlinear tools such as Poincare maps and the maximal Lyapunov exponent. As usual for chosen system parameters we have identified a chaotic motion above the critical Melnikov amplitude $\\mu_c$.

Grzegorz Litak; Marek Borowiec; Arkadiusz Syta

2006-10-20T23:59:59.000Z

395

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

SciTech Connect (OSTI)

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

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

1990-01-09T23:59:59.000Z

396

Mass Spectrometric Study of Genetic and Epigenetic DNA Modifications  

E-Print Network [OSTI]

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

Wang, Hongxia

2010-01-01T23:59:59.000Z

397

Low Dose Radiation Research Program: Quantification of Repair of  

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

Quantification of Repair of Low-Dose-Induced DNA Double-Strand Quantification of Repair of Low-Dose-Induced DNA Double-Strand Breaks in Diploid Human Cells Authors: David Schild,1 and Larry H. Thompson,2 Institutions: 1Life Sciences Division, Lawrence Berkeley National Laboratory; and 2BBR Program, Lawrence Livermore National Laboratory Double-strand breaks (DSBs) are the biochemical lesions of primary concern in radiation related health effects. Compelling evidence from rodent and chicken model systems indicates that homologous recombinational repair (HRR) plays an essential role for cell viability in the repair of spontaneous DSBs arising during DNA replication and an important role in the repair of IR-induced DSBs. IR-induced DSBs are also repaired by error-prone nonhomologous end joining (NHEJ). Using hTERT-immortalized

398

Repair of mismatched basepairs in mammalian DNA  

SciTech Connect (OSTI)

We have concentrated on three specific areas of our research plan. Our greatest emphasis is on the role of single strand nicks in influencing template strand selection in mismatch repair. We have found, that the ability of a nick in one strand to influence which strand is repaired is not a simple function of distance from the mismatched site but rather that an hot spot where a nick is more likely to have an influence can exist. The second line was production of single-genotype heteroduplexes in order to examine independently the repair of T/G and A/C mispairs within the same sequence context as in our mixed mispair preparations. We have shown preparations of supercoiled heteroduplex can be prepared that were exclusively T/G or exclusively A/C at the mispair site. The third effort has been to understand the difference in repair bias of different cell lines or different transfection conditions as it may relate to different repair systems in the cell. We have identified some of the sources of variation, including cell cycle position. We hope to continue this work to more precisely identify the phase of the cell cycle.

Taylor, J.H.; Hare, J.T.

1991-08-01T23:59:59.000Z

399

Frequency Doubling Nanocrystals for Cancer Theranostics  

E-Print Network [OSTI]

A novel bio-photonics approach based on the nonlinear optical process of second harmonic generation by non-centrosymmetric nanoparticles is presented and demonstrated on malignant human cell lines. The proposed method allows to directly interact with DNA in absence of photosensitizing molecules, to enable independent imaging and therapeutic modalities switching between the two modes of operation by simply tuning the excitation laser wavelength, and to avoid any risk of spontaneous activation by any natural or artificial light source.

Staedler, Davide; Passemard, Solène; Schwung, Sebastian; Dubled, Marc; Schneiter, Guillaume Stéphane; Rytz, Daniel; Gerber-Lemaire, Sandrine; Bonacina, Luigi; Wolf, Jean-Pierre

2013-01-01T23:59:59.000Z

400

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

E-Print Network [OSTI]

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

Hagiya, Masami

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


401

Nuclear matrix elements for neutrinoless double-beta decay and double-electron capture  

E-Print Network [OSTI]

A new generation of neutrinoless double beta decay experiments with improved sensitivity is currently under design and construction. They will probe inverted hierarchy region of the neutrino mass pattern. There is also a revived interest to the resonant neutrinoless double-electron capture, which has also a potential to probe lepton number conservation and to investigate the neutrino nature and mass scale. The primary concern are the nuclear matrix elements. Clearly, the accuracy of the determination of the effective Majorana neutrino mass from the measured 0\

Amand Faessler; Vadim Rodin; Fedor Simkovic

2012-06-03T23:59:59.000Z

402

The assessment of DNA-synthetic activity  

Science Journals Connector (OSTI)

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

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

1981-01-01T23:59:59.000Z

403

Fralin Life Science Institute DNA Biotechnology Kit  

E-Print Network [OSTI]

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

Virginia Tech

404

A DNA tweezer-actuated enzyme nanoreactor  

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

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

405

DNA Concentration By UV Spectrophotometry Measure Absorption  

E-Print Network [OSTI]

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

Aris, John P.

406

Towards Privacy Preserving of Forensic DNA Databases  

E-Print Network [OSTI]

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

Liu, Sanmin

2012-02-14T23:59:59.000Z

407

Energy Blog | Department of Energy  

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

April 4, 2012 April 4, 2012 The National Renewable Energy Lab's (NREL) utility rate database is a great resource for developers entering the Apps for Energy competition. | Map courtesy of NREL. Developer Resources for Apps for Energy Are you interested in participating in the Apps for Energy competition? Be sure to check out this list of resources that can help developers create energy apps. April 3, 2012 The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is proposed to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete and ready to load another protein onto the DNA. This last protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab.

408

Energy Blog | Department of Energy  

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

4, 2012 4, 2012 The National Renewable Energy Lab's (NREL) utility rate database is a great resource for developers entering the Apps for Energy competition. | Map courtesy of NREL. Developer Resources for Apps for Energy Are you interested in participating in the Apps for Energy competition? Be sure to check out this list of resources that can help developers create energy apps. April 3, 2012 The DNA replication origin recognition complex (ORC) is a six-protein machine with a slightly twisted half-ring structure (yellow). ORC is proposed to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete and ready to load another protein onto the DNA. This last protein (not shown) is the enzyme that unwinds the double stranded DNA so each strand can be replicated. | Illustration courtesy of Brookhaven Lab.

409

Neutrinoless Double Beta Decay with Composite Neutrinos.  

E-Print Network [OSTI]

We study in detail the contribution of heavy composite Majorana neutrinos to neutrino-less double beta decay (0???). Our analysis confirms the result of a previous estimate by two of the authors. Excited neutrinos couple to the electroweak gauge bosons through a magnetic type effective Lagrangian. The relevant nuclear matrix element is related to matrix elements available in the literature and current bounds on the half-life of 0??? are converted into bounds on the compositeness scale and/or the heavy neutrino mass. Our bounds are of the same order of magnitude as those available from accelerator experiments.

O. Panella (a; C. Carimalo (b; Y. N. Srivastava (a; A. Widom (c

1997-01-01T23:59:59.000Z

410

Double acting stirling engine phase control  

DOE Patents [OSTI]

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.

Berchowitz, David M. (Scotia, NY)

1983-01-01T23:59:59.000Z

411

Neutrino Oscillations, Neutrinoless Double Beta Decay  

Science Journals Connector (OSTI)

We review the experimental evidence for neutrino mixing and neutrino mass. Searches for possible branches into heavy neutrinos do not reveal evidence for static mixing with branching ratios larger than 10?4 to 10?6. Similarly neutrino oscillation experiments show no evidence for dynamic mixing in various oscillation channels. Stringent limits for ? e disappearance from a recent reactor experiment are presented. Results from neutrinoless double beta decay provide sensitive test for Majorana mass and right?hand couplings the present limits being 3–10 eV and 10?5 respectively.

F. Boehm

1982-01-01T23:59:59.000Z

412

Neutrinoless double beta decay and neutrino masses  

Science Journals Connector (OSTI)

Neutrinoless double beta decay (0???) 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??? 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??? from unknown nuclear background using only one isotope i.e. within one experiment.

Michael Duerr

2012-01-01T23:59:59.000Z

413

Neutrinoless double ? decay with composite neutrinos  

Science Journals Connector (OSTI)

We study in detail the contribution of heavy composite Majorana neutrinos to neutrinoless double beta decay (0???). Our analysis confirms the result of a previous estimate by two of the authors. Excited neutrinos couple to the electroweak gauge bosons through a magnetic-type effective Lagrangian. The relevant nuclear matrix element is related to matrix elements available in the literature and current bounds on the half-life of 0??? are converted into bounds on the compositeness scale and/or the heavy neutrino mass. Our bounds are of the same order of magnitude as those available from accelerator experiments.

O. Panella; C. Carimalo; Y. N. Srivastava; A. Widom

1997-11-01T23:59:59.000Z

414

Chromosome specific repetitive DNA sequences  

DOE Patents [OSTI]

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

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

1991-01-01T23:59:59.000Z

415

International Standards in Forensic DNA  

E-Print Network [OSTI]

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

416

DNA Hybridization Catalysts and Catalyst Circuits  

E-Print Network [OSTI]

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

Winfree, Erik

417

Amplification of chromosomal DNA in situ  

DOE Patents [OSTI]

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

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

2002-01-01T23:59:59.000Z

418

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

E-Print Network [OSTI]

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

Reif, John H.

419

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

Science Journals Connector (OSTI)

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

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

1999-07-01T23:59:59.000Z

420

DNA adsorption on synthetic and natural allophanes  

Science Journals Connector (OSTI)

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

Kazutoshi Saeki; Masao Sakai; Shin-Ichiro Wada

2010-01-01T23:59:59.000Z

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


421

Electromechanical Unzipping of Individual DNA Molecules Using  

E-Print Network [OSTI]

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

422

DNA Nanotechnology and its Biological Applications1  

E-Print Network [OSTI]

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

Reif, John H.

423

Self-assembled DNA Structures for Nanoconstruction  

E-Print Network [OSTI]

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

Yin, Peng

424

COMM-OPINION-ORDER, 76 FERC 61,347, Promoting Wholesale Competition Through Open-Access Non-discriminatory Transmission Services by Public Utilities, Docket No. RM95-8-000, Recovery of Stranded Costs by  

E-Print Network [OSTI]

-discriminatory Transmission Services by Public Utilities, Docket No. RM95-8-000, Recovery of Stranded Costs by Public Utilities and Transmitting Utilities, Docket No. RM94-7-001, (Sep. 27, 1996) COPYRIGHT 1999, CCH by Public Utilities, Docket No. RM95-8-000, Recovery of Stranded Costs by Public Utilities and Transmitting

Laughlin, Robert B.

425

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

Science Journals Connector (OSTI)

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

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

2013-01-16T23:59:59.000Z

426

Double pion photoproduction off 40Ca  

E-Print Network [OSTI]

The photoproduction of pi0pi0 and pi0pi+/- pairs off 40Ca has been investigated with the TAPS detector using the Glasgow photon tagging spectrometer at the Mainz MAMI accelerator. Data have been taken for incident photon energies in the energy range from 200 - 820 MeV. Total cross sections have been extracted from threshold up to the maximum photon energy and invariant mass distributions of the pion pairs have been obtained for incident photon energies between 400 - 500 MeV and 500 - 550 MeV. The double pi0 invariant mass distributions show some relative enhancement with respect to the mixed charge channel at small invariant masses. The effects are smaller than previously observed for lead nuclei and the distributions do not significantly deviate from carbon data. The data are in good agreement with the results of recent calculations in the framework of the BUU model, with careful treatment of final state interaction effects but without an explicit in-medium modification of scalar, iso-scalar pion pairs. This means that for Ca most of the experimentally observed effect can be explained by final state interactions. Only at low incident photon energies there is still a small low mass enhancement of the double pi0 data over the BUU results.

F. Bloch; J. Ahrens; J. R. M. Annand; R. Beck; L. S. Fog; D. Hornidge; S. Janssen; M. Kotulla; B. Krusche; J. C. McGeorge; I. J. D. MacGregor; J. G. Messchendorp; V. Metag; R. Novotny; R. O. Owens; M. Pfeiffer; M. Rost; R. Sanderson; S. Schadmand; A. Thomas; D. P. Watts

2007-03-24T23:59:59.000Z

427

Search For Neutrinoless Double Beta Decay  

E-Print Network [OSTI]

The HEIDELBERG-MOSCOW experiment, which is the most sensitive double beta decay experiment since ten years has been regularly continued until end of November 2003. An analysis of the data has been performed already until May 20, 2003. The experiment yields now, on a 4? level, evidence for lepton number violation and proves that the neutrino is a Majorana particle. It further shows that neutrino masses are degenerate. In addition it puts several stringent constraints on other physics beyond the Standard Model. Among others it opens the door to test various supersymmetric theory scenarios, for example it gives the sharpest in the R-parity violating part of the superpotential, and limit on the parameter ? ? 111 gives information on the splitting of the sneutrino-antisneutrino system. The result from the HEIDELBERG-MOSCOW experiment is consistent with recent results from CMB investigations, with high energy cosmic rays, with the result from the g-2 experiment and with recent theoretical work. It is indirectly supported by the analysis of other Ge double beta experiments. Recent criticism of various kind has been shown to be wrong, among others by measurements performed in 2003 with a 214Bi source ( 226Ra), by simulation of the background in the range of Q?? by GEANT4, and by deeper investigation of statistical features such as sensitivity of peak search, and relevance of width of window of analysis. 1

H. V. Klapdor-kleingrothaus *a; I. V. Krivosheina A; A. Dietz A

2004-01-01T23:59:59.000Z

428

Particle acceleration in double radio sources  

Science Journals Connector (OSTI)

Further study has been made of a model of extragalactic double radio sources in which the magnetized accretion disc of a massive black hole acts as an electric dynamo producing oppositely directed beams of relativistic particles. An empty region of small angular size—a vortice core—is shown to be a possible consequence of the hydrodynamics of accretion of gas with angular momentum. An ambient magnetic field in the gas tends to accumulate in the core region. The acceleration of electrons in the dynamo electric field gives rise to oppositely directed electron beams which in turn produce synchroton gamma rays collimated along the core. Collisions between the gamma rays and low energy photons caN initiate an electromagnetic cascade shower. The cascade acts to produce a collimated relativistic electron?positron beam. If the current flow in the dynamo occurs in surges then the outward propagation of the head of the electron–positron beams may produce expanding compact radio components. The electron–positron beam is ballistic in nature and it is electrically neutral and carries no current. Such a beam appears to have favorable stability properties. The beam is eventually stopped and spread out in pitch angle by the ram pressure of the external medium. Synchrotron radiated lobes of double radio sources.

R. V. E. Lovelace; J. MacAuslan; M. Burns

1979-01-01T23:59:59.000Z

429

Double Retort System for Materials Compatibility Testing  

SciTech Connect (OSTI)

With Naval Reactors (NR) approval of the Naval Reactors Prime Contractor Team (NRPCT) recommendation to develop a gas cooled reactor directly coupled to a Brayton power conversion system as the Space Nuclear Power Plant (SNPP) for Project Prometheus (References a and b) there was a need to investigate compatibility between the various materials to be used throughout the SNPP. Of particular interest was the transport of interstitial impurities from the nickel-base superalloys, which were leading candidates for most of the piping and turbine components to the refractory metal alloys planned for use in the reactor core. This kind of contamination has the potential to affect the lifetime of the core materials. This letter provides technical information regarding the assembly and operation of a double retort materials compatibility testing system and initial experimental results. The use of a double retort system to test materials compatibility through the transfer of impurities from a source to a sink material is described here. The system has independent temperature control for both materials and is far less complex than closed loops. The system is described in detail and the results of three experiments are presented.

V. Munne; EV Carelli

2006-02-23T23:59:59.000Z

430

Direct Inhibition of Tombusvirus Plus-Strand RNA Synthesis by a Dominant Negative Mutant of a Host Metabolic Enzyme, Glyceraldehyde-3-Phosphate Dehydrogenase, in Yeast and Plants  

Science Journals Connector (OSTI)

...assay based on yeast cell-free extracts (CFE) that are prepared from yeast mutant strains...positive-strand viral RNAs in the GAPDH-depleted CFE, resulting in symmetric replication of...recombinant GAPDH to the GAPDH-depleted CFE restored asymmetric RNA synthesis by producing...

Tyng-Shyan Huang; Peter D. Nagy

2011-06-22T23:59:59.000Z

431

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

Science Journals Connector (OSTI)

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

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

2009-01-01T23:59:59.000Z

432

Development of Novel Diagnostic Tools and beyond for Targets of Human Significance: Metabolites, Toxins & Viruses  

E-Print Network [OSTI]

selection: The synthetic DNA library of 40 randomfrom a synthetic library of single stranded DNA (ssDNA)

Cella, Lakshminarasamamba

2012-01-01T23:59:59.000Z

433

Neutrinoless double beta decay search with the NEMO 3 experiment  

Science Journals Connector (OSTI)

The NEMO 3 experiment searches for neutrinoless double beta decay and makes precision measurements of two?neutrino double beta decay in seven isotopes. The latest two?neutrino half?life results are presented together with the limits on neutrinoless half?lives and the corresponding effective Majorana neutrino masses. Also given are the limits obtained on neutrinoless double beta decay mediated by R p ?violating SUSY right?hand currents and different Majoron emission modes.

Irina Nasteva; NEMO collaboration

2008-01-01T23:59:59.000Z

434

[http://ocw.mit.edu/OcwWeb/Mechanical-Engineering/2-76Fall-2004/LectureNotes/index.htm] We are here  

E-Print Network [OSTI]

;#12;#12;Single-stranded DNA #12;Single-stranded DNA Synthetic DNA #12;Single-stranded DNA Synthetic DNA Hydrogen bond #12;Single-stranded DNA Synthetic DNA Hydrogen bond 424nm =29 blocks Repeating motif #12;Synthetic DNA M13mp18 Mg2+ buffer 170 synthetic short DNA strands in Mg2+ buffer #12;#12;#12;#12;#12;418nm 100nm

Reif, John H.

435

Thermal Performance of a Double-Tube Type Lng Vaporizer  

Science Journals Connector (OSTI)

This report concerns the confirmed test results and method of analysis of the thermal performance of a double-tube type LNG vaporizer (DTV). The DTV is a...

Y. Miyata; T. Miura; S. Kasahara; H. Shohtani…

1994-01-01T23:59:59.000Z

436

Majorana Neutrino Masses from Neutrinoless Double Beta Decay and Cosmology  

E-Print Network [OSTI]

When three Majorana neutrinos describe the solar and atmospheric neutrino data via oscillations, a nonzero measurement of neutrinoless double beta ($0\

V. Barger; K. Whisnant

1999-04-08T23:59:59.000Z

437

Electromagnetically Induced Transparency in a Double Well Atomic Josephson Junction  

E-Print Network [OSTI]

observation of these Josephson junction resonances. 2.dressed Bose condensed Josephson junction Let us consider ain a Double Well Atomic Josephson Junction J.O. Weatherall

Weatherall, J. O.; Search, C. P.

2009-01-01T23:59:59.000Z

438

Neutrinoless double beta decay can constrain neutrino dark matter  

E-Print Network [OSTI]

We examine how constraints can be placed on the neutrino component of dark matter by an accurate measurement of neutrinoless double beta ($0\

V. Barger; S. L. Glashow; D. Marfatia; K. Whisnant

2002-02-26T23:59:59.000Z

439

The complex Doppler effect in double negative media  

Science Journals Connector (OSTI)

The Doppler effect in doubly double negative acoustic media is ... ’s functions. It is shown that several Doppler modes can be generated by a monochromatic...

I. V. Lisenkov; S. A. Nikitov

2011-06-01T23:59:59.000Z

440

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

E-Print Network [OSTI]

??This dissertation describes an experimental search for neutrinoless double beta (0???) decay of 130Te. An observation of 0??? decay would establish that neutrinos are Majorana… (more)

Bryant, Adam Douglas

2010-01-01T23:59:59.000Z

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


441

Human Genome Research: Decoding DNA  

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

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

442

Electromagnetic Signals from Bacterial DNA  

E-Print Network [OSTI]

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

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

2012-02-09T23:59:59.000Z

443

2005 Double white lines on bills of Razorbill 103 DOUBLE WHITE LINES ON THE BILL OF THE  

E-Print Network [OSTI]

2005 Double white lines on bills of Razorbill 103 DOUBLE WHITE LINES ON THE BILL OF THE RAZORBILL.L., MUZAFFAR S.B. & JONES I.L. Lavers J.L., Muzaffar S.B. & Jones I.L. 2006. Double white lines on the bill Seabirds 7(3): 103-108. One of the diagnostic features of the Razorbill Alca torda is the distinct white

Jones, Ian L.

444

A hybrid double-dot in silicon  

SciTech Connect (OSTI)

We report electrical measurements of a single arsenic dopant atom in the tunnel barrier of a silicon single-electron transistor (SET). In addition to performing the electrical characterisation of the individual dopants, we study the series electrical transport through the dopant and SET. We measure the bias triangles of this hybrid double-dot and show that we can tune the electrostatic coupling between the two sub-systems. Additionally, we measured SET in which an additional plunger gate allows the reduction of the electron number in the SET down to the few-electron regime where the dot presents well-defined spin configurations. Finally, we discuss the challenges of operating a dopant-dot hybrid system in the few-electron regime.

Gonzalez-Zalba, M. F.; Heiss, D.; Ferguson, A. J. [Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge (United Kingdom)

2013-12-04T23:59:59.000Z

445

Efficient jitter compensation using double exponential smoothing  

Science Journals Connector (OSTI)

This paper proposes a new jitter reduction scheme based on double exponential smoothing (DES). We compare this DES-based method to jitter reduction methods based on the Kalman filter (KF) and extended Kalman filter (EKF), two well-known methods of jitter reduction. To evaluate the jitter reduction performance, we used a laser pointer interaction system with a known problem with jittery laser spot movements caused by natural hand tremors. We show that the DES-based scheme runs approximately 100 times faster than the EKF-based method and 19 times faster than the KF-based method. Furthermore, in terms of jitter reduction, the proposed DES-based method yields approximately 18% better results than the EKF-based method and 20% better results than the KF-based method.

Min Gyo Chung; Sang-Kyun Kim

2013-01-01T23:59:59.000Z

446

Range Separated Brueckner Coupled Cluster Doubles Theory  

E-Print Network [OSTI]

We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel with the long-range ring channel in the presence of a Bruckner renormalized one-body interaction and obtain ground-state energies with an accuracy of 0.001 a.u./electron across a wide range of density regimes. Our scheme is particularly useful in the low-density and strongly-correlated regimes, where regular CCD has serious drawbacks. Moreover, we cure the infamous overcorrelation of approaches based on ring diagrams (i.e. the particle-hole random phase approximation). Our energies are further shown to have appropriate basis set and thermodynamic limit convergence, and overall this scheme promises energetic properties for realistic periodic and extended systems which existing methods do not possess.

Shepherd, James J; Scuseria, Gustavo E

2013-01-01T23:59:59.000Z

447

Experimental searches of neutrinoless double beta decay  

E-Print Network [OSTI]

Neutrinoless double decay is a unique probe for lepton number conservation and neutrino properties. It allows to investigate the Dirac/Majorana nature of the neutrinos and their absolute mass scale (hierarchy problem) with unprecedented sensitivity. A number of experiments are presently under preparation to cover the quasi-degenerate region of the neutrino mass spectrum. Improved sensitivities are however required to sound the so-called inverted hierarchy region. This is a real challenge faced by a number of new proposed projects, based either on large expansions of the present experiments or on new ideas top improve the technical performance or reduce the background contributions. A review of the most relevant ongoing experiments is given. The most relevant parameters contributing to the experimental sensitivity are discussed and a critical comparison of the future projects is proposed.

Oliviero Cremonesi

2012-12-19T23:59:59.000Z

448

Double Shell Tank (DST) Utilities Specification  

SciTech Connect (OSTI)

This specification establishes the performance requirements and provides the references to the requisite codes and standards to he applied during the design of the Double-Shell Tank (DST) Utilities Subsystems that support the first phase of waste feed delivery (WFD). The DST Utilities Subsystems provide electrical power, raw/potable water, and service/instrument air to the equipment and structures used to transfer low-activity waste (LAW) and high-level waste (HLW) to designated DST staging tanks. The DST Utilities Subsystems also support the equipment and structures used to deliver blended LAW and HLW feed from these staging tanks to the River Protection Project (RPP) Privatization Contractor facility where the waste will be immobilized. This specification is intended to be the basis for new projects/installations. This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

SUSIENE, W.T.

2000-04-27T23:59:59.000Z

449

Correlations and the neutrinoless double beta decay  

Science Journals Connector (OSTI)

We explore the influence of the deformation on the nuclear matrix elements of the neutrinoless double beta decay (NME) concluding that the difference in deformation ?or more generally on the amount of quadrupole correlations? between parent and grand daughter nuclei quenchs strongly the decay. We discuss how varies the nuclear matrix element of 76 Ge decay when the wave functions of the two nuclei involved in the transition are constrained to reproduce the experimental occupancies. In the Interacting Shell Model description the value of the NME is enhanced about 15% compared to previous calculations whereas in the QRPA the NME’s are reduced by 20%–30% thus the discrepancies between both approaches diminish.

J. Menéndez; A. Poves; E. Caurier; F. Nowacki

2009-01-01T23:59:59.000Z

450

Deep subwavelength plasmonic waveguide switch in double graphene layer structure  

E-Print Network [OSTI]

Deep subwavelength plasmonic waveguide switch in double graphene layer structure Hideo Iizuka in double graphene layer structure Hideo Iizuka1,a) and Shanhui Fan2,b) 1 Toyota Central Research December 2013) Graphene provides excellent prospects of the dynamic tunability, low propagation loss

Fan, Shanhui

451

Double quantum dot as a minimal thermoelectric generator  

Science Journals Connector (OSTI)

Based on numerical renormalization group calculations, we demonstrate that experimentally realized double quantum dots constitute a minimal thermoelectric generator. In the Kondo regime, one quantum dot acts as an n-type and the other one as a p-type thermoelectric device. Properly connected, a capacitively coupled double quantum dot provides a miniature power supply utilizing the thermal energy of the environment.

S. Donsa; S. Andergassen; K. Held

2014-03-05T23:59:59.000Z

452

Strategies for Next Generation Neutrinoless Double-Beta Decay Experiments  

E-Print Network [OSTI]

Strategies for Next Generation Neutrinoless Double-Beta Decay Experiments F. T. Avignone III A brief discussion of the connection between neutrino oscillation data and predictions of neutrinoless the necessary tools for comparative evaluation. 1. INTRODUCTION Neutrinoless double-beta (0)-decay has been

453

Neutrinoless double-beta decay. A brief review  

E-Print Network [OSTI]

In this brief review we discuss the generation of Majorana neutrino masses through the see-saw mechanism, the theory of neutrinoless double-beta decay, the implications of neutrino oscillation data for the effective Majorana mass, taking into account the recent Daya Bay measurement of theta_13, and the interpretation of the results of neutrinoless double-beta decay experiments.

S. M. Bilenky; C. Giunti

2012-03-23T23:59:59.000Z

454

The fraction of double degenerates among DA white dwarfs  

E-Print Network [OSTI]

We present the results of a radial velocity survey designed to measure the fraction of double degenerates among DA white dwarfs. The narrow core of the H-alpha line was observed twice or more for 46 white dwarfs yielding radial velocities accurate to a few km/s. This makes our survey the most sensitive to the detection of double degenerates undertaken to date. We found no new double degenerates in our sample, though H-alpha emission from distant companions is seen in two systems. Two stars known to be double degenerates prior to our observations are included in the analysis. We find a 95% probability that the fraction of double degenerates among DA white dwarfs lies in the range [0.017,0.19].

P. F. L. Maxted; T. R. Marsh

1999-01-20T23:59:59.000Z

455

Single- and double-charge exchange at low pion energies  

SciTech Connect (OSTI)

A review is given of pion single- and double-charge exchange reactions at incident energies of 25 to 65 MeV leading to isobaric analog states, and in the case of double-charge exchange leading to the ground state of the residual nucleus. The crucial role of the higher nuclear transparency at low pion energies for the analysis of the data in terms of single and double scattering is demonstrated. The large effects on double-charge exchange produced by the spatial correlations in nuclear wave functions are evident. The data on 1f{sub 7/2} nuclei at 35 MeV are used to establish the general validity of a shell-model-based two-amplitude model for these transitions. Recent measurements of the energy dependence between 25 and 65 MeV of double-charge exchange cross sections at forward angles are presented and discussed. 33 refs., 19 figs.

Baer, H.W.

1991-01-01T23:59:59.000Z

456

Single molecule studies of DNA mismatch repair  

Science Journals Connector (OSTI)

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

Dorothy A. Erie; Keith R. Weninger

2014-01-01T23:59:59.000Z

457

Enhancing the DNA Patent Database  

SciTech Connect (OSTI)

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

Walters, LeRoy B.

2008-02-18T23:59:59.000Z

458

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

Science Journals Connector (OSTI)

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

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

2011-01-01T23:59:59.000Z

459

A Synthetic DNA Walker for Molecular Transport  

Science Journals Connector (OSTI)

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

Jong-Shik Shin; Niles A. Pierce

2004-08-17T23:59:59.000Z

460

IT for synthetic biology and DNA nanotechnology  

Science Journals Connector (OSTI)

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

Masami Hagiya; Fumiaki Tanaka; Ibuki Kawamata

2010-09-01T23:59:59.000Z

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


461

j5 DNA Assembly Design Automation Software  

Science Journals Connector (OSTI)

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

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

2011-12-07T23:59:59.000Z

462

First results on neutrinoless double beta decay of Te-130 with the calorimetric cuoricino experiment  

E-Print Network [OSTI]

Evidence for Neutrinoless Double Beta Decay” arXiv:hep-on “Evidence for neutrinoless double beta decay”- arXiv:hep-Results on Neutrinoless Double Beta Decay of 130 Te with the

2003-01-01T23:59:59.000Z

463

Codeword design and information encoding in DNA ensembles  

Science Journals Connector (OSTI)

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

Max H. Garzon; Russell J. Deaton

2004-08-01T23:59:59.000Z

464

Half-lives of Double $\\beta ^+$-decay with Two Neutrinos  

E-Print Network [OSTI]

Nuclear double $\\beta ^-$-decays with two neutrinos were observed for many years and a systematic law describing the relation between their half-lives and decay energies was also proposed recently [Phys. Rev. C89, 064603 (2014)]. However, double $\\beta ^+$-decay ($\\beta ^+\\beta^+)$ with emission of both two positrons and two neutrinos has not been observed up to date. In this article, we perform a systematic analysis on the candidates of double $\\beta ^+$-decay, based on the 2012 nuclear mass table. Eight nuclei are found to be the good candidates for double $\\beta ^+$-decay and their half-lives are predicted according to the generalization of the systematic law to double $\\beta ^+$-decay. As far as we know, there is no theoretical result on double $\\beta ^+$-decay of nucleus $^{154}Dy$ and our result is the first prediction on this nucleus. This is also the first complete research on eight double $\\beta ^+$-decay candidates based on the available data of nuclear masses. It is expected that the calculated hal...

Ren, Yuejiao

2015-01-01T23:59:59.000Z

465

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

Science Journals Connector (OSTI)

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

G L McLaughlin; W E Collins; G H Campbell

1987-05-01T23:59:59.000Z

466

Experimental research of double beta decay of atomic nuclei  

E-Print Network [OSTI]

Results of several double beta decay experiments, performed with the help of low background crystal scintillators, are presented. In particular, the half-life value of the two-neutrino double beta decay of 116-Cd has been measured as 2.9 10^{19} yr, and the new half-life limit on the neutrinoless double beta decay of 116-Cd has been established as >1.7 10^{23} yr at 90%, which corresponds to a restriction on the neutrino mass <1.7 eV. New half-life bounds on the level of 10^{17}-10^{21} yr were set for double beta processes in 64-Zn, 70-Zn, 106-Cd, 108-Cd, 114-Cd, 136-Ce, 138-Ce, 142-Ce, 160-Gd, 180-W, and 186-W by using low-background CdWO4, GSO, and ZnWO4 crystal scintillators. The claim of discovery of the neutrinoless double beta decay of 76-Ge [Mod. Phys. Lett. A 16 (2001) 2409] was analyzed. The demands of the future high sensitivity double beta decay experiments, aiming to observe the neutrinoless double beta decay or to advance restrictions on the neutrino mass to < 0.01 eV, were considered. Requirements for their sensitivity and discovery potential were formulated. Two projects of double beta experiments with a sensitivity on the level of 10^{26}-10^{27} yr (CAMEO and CARVEL projects) were discussed. Scintillation properties and radioactive contamination of CaWO4, ZnWO4, CdWO4, PbWO4, GSO(Ce), CeF3, yttrium-aluminum garnet doped with neodymium (YAG:Nd) crystal scintillators were studied. Applicability of these scintillators to search for double beta decay was discussed.

F. A. Danevich

2011-12-26T23:59:59.000Z

467

Man-made marine debris and sea turtle strandings on beaches of the upper Texas and southwestern Louisiana coasts, June 1987 through September 1989. Technical memo  

SciTech Connect (OSTI)

The upper Texas and southwestern Louisiana coastlines were divided into six sampling zones to survey the amounts, types and rates of accumulation of man-made marine debris, the number of sea turtle strandings, the incidence of sea turtle entanglements in marine debris and the incidence of ingestion of such debris by sea turtles. From June 1987 through September 1989, 473 sample plots were examined for marine debris. Significant differences were detected in mean number of debris items per 100 sq m of beach sampled by year, zone and month. Significant differences in mean weight of debris items per 100 sq m of beach sampled were detected by month and zone. Both number and weights (per 100 sq m) of debris were lowest in the winter months. Number per 100 sq m was greatest in August while weight per 100 sq m peaked in May. Tar balls and plastic items were the most frequently encountered marine debris items. Wooden items had the highest average weights while tar balls and polystyrene foam were the lightest items collected. A total of 171 sea turtles stranded on the surveyed beaches during the study. Of 26 gastrointestinal tracts examined, 16 had ingested some form of man-made debris. Six turtles were entangled in man-made debris and 9 were live stranded.

Duronslet, M.J.; Revera, D.B.; Stanley, K.M.

1991-02-01T23:59:59.000Z

468

HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles  

SciTech Connect (OSTI)

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.

Sherman W. B.

2012-06-05T23:59:59.000Z

469

Superconvergence of period doubling cascade in trapezoid maps  

E-Print Network [OSTI]

In the symmetric and the asymmetric trapezoid maps, as a slope of the trapezoid is increased, the period doubling cascade occurs and the symbolic sequence of periodic points is the Metropolis-Stein-Stein sequence and the convergence of the onset point of the period 2^m solution to the accumulation point is exponentially fast. We reported these results previously. In this paper, we give the detailed description of the proof on the results. Further, we study the period doubling cascade starting from period p solution and show the superconvergence of the period doubling cascade.

T. Uezu

2000-01-12T23:59:59.000Z

470

Photo-double-ionization of the nitrogen molecule  

Science Journals Connector (OSTI)

The triple differential cross sections of the photo-double-ionization of the nitrogen molecule to the X 1?+g and a3?u N22+ states have been measured at about 20 eV above their respective ionization thresholds in the equal energy sharing kinematics and calculated using a model which makes use of correlated two-center double continuum wave functions. The comparison of the results with those obtained by the Gaussian parametrization method applied in the past with success to heliumlike targets shows the influence of the molecular nature of the N2 target in the photo-double-ionization.

P. Bolognesi; B. Joulakian; A. A. Bulychev; O. Chuluunbaatar; L. Avaldi

2014-05-07T23:59:59.000Z

471

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

E-Print Network [OSTI]

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

Mizoguchi, Kenji

472

E-Print Network 3.0 - aligned double-walled carbon Sample Search...  

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

Summary: , and H. M. Cheng. Polarized raman analysis of aligned double- walled carbon nanotubes. Physical Review B... Nonlinear Oscillations of a Double-Walled Carbon Nanotube...

473

Neutrinoless double beta decay in deformed nuclei: its implications in particle and nuclear physics .  

E-Print Network [OSTI]

??In my thesis, we calculated the Nuclear Matrix Elements (NME) for neutrinoless double beta decay (0??? decay). Neutrinoless double beta decay is a rare nuclear… (more)

Fang, DongLiang

2011-01-01T23:59:59.000Z

474

SciTech Connect: What can we learn from neutrinoless double beta...  

Office of Scientific and Technical Information (OSTI)

What can we learn from neutrinoless double beta decay experiments? Citation Details In-Document Search Title: What can we learn from neutrinoless double beta decay experiments?...

475

A Search for Neutrinoless Double-Beta Decay with EXO-200 .  

E-Print Network [OSTI]

??This work presents a search for neutrinoless double beta decay of 136Xe using data from the EXO-200 detector collected between 2011 and 2012. Neutrinoless double… (more)

Slutsky, Simon

2013-01-01T23:59:59.000Z

476

Property:NEPA DNA Worksheet | Open Energy Information  

Open Energy Info (EERE)

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

477

Mass Transfer between Double White Dwarfs  

E-Print Network [OSTI]

Three periodically variable stars have recently been discovered (V407 Vul, P=9.5 min; ES Cet, P=10.3 min; RX J0806.3+1527, P=5.3 min) with properties that suggest that their photometric periods are also their orbital periods, making them the most compact binary stars known. If true, this might indicate that close, detached, double white dwarfs are able to survive the onset of mass transfer caused by gravitational wave radiation and emerge as the semi-detached, hydrogen-deficient stars known as the AM CVn stars. The accreting white dwarfs in such systems are large compared to the orbital separations. This has two effects: first it makes it likely that the mass transfer stream can hit the accretor directly, and second it causes a loss of angular momentum from the orbit which can destabilise the mass transfer unless the angular momentum lost to the accretor can be transferred back to the orbit. The effect of the destabilisation is to reduce the number of systems which survive mass transfer by as much as one hundred-fold. In this paper we analyse this destabilisation and the stabilising effect of a dissipative torque between the accretor and the binary orbit. We obtain analytic criteria for the stability of both disc-fed and direct impact accretion, and carry out numerical integrations to assess the importance of secondary effects, the chief one being that otherwise stable systems can exceed the Eddington accretion rate. We show that to have any effect upon survival rates, the synchronising torque must act on a timescale of order 1000 years or less. If synchronisation torques are this strong, then they will play a significant role in the spin rates of white dwarfs in cataclysmic variable stars as well.

T. R. Marsh; G. Nelemans; D. Steeghs

2003-12-22T23:59:59.000Z

478

Carbon Nanotube DNA Sensor and Sensing Mechanism  

E-Print Network [OSTI]

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

Le Roy, Robert J.

479

A Statistical Model of the Inhomogeneous Corona Constrained by Triple-Filter Measurements of Elementary Loop Strands with TRACE  

Science Journals Connector (OSTI)

Here we present the first quantitative model of the inhomogeneous solar corona, which we call the composite and elementary loops in a thermally inhomogeneous corona (CELTIC) model. We develop a self-consistent statistical model that quantifies the distributions of physical parameters, i.e., the distributions of loop widths, N(w,Te), electron densities, N(ne,Te), electron temperatures, N(Te), and statistical correlations between them. The parameterized distributions are constrained by the observed triple-filter fluxes of the EUV corona measured at some 18,000 loop positions with TRACE in the temperature range of Te ? 0.7-2.7 MK, as well as by the individual loop parameters (w,ne,Te) measured at these positions in ?240 detected loops, mostly sampled in active regions. The CELTIC model is inverted from the TRACE data and reproduces both the fluxes of the composite (active region and quiet Sun) background corona and the distributions of loop parameters in a self-consistent way. The best-fit values constrain a statistical correlation between the density and temperature, i.e., ne ? Te?, with ? = 0.9 ± 0.6, and between the loop width and temperature, i.e., w ? Te?, with ? = 1.3 ± 0.7, which can be related to the thermal pressure in a regime with a high plasma-? parameter. A possible explanation is a heating process located in the lower transition region or the upper chromosphere (e.g., as reproduced in the recent MHD simulations of Gudiksen and Nordlund), which produces sufficiently high electron densities, high plasma-? parameters, and thermally homogeneous loop cross sections as observed in elementary loop strands.

Markus J. Aschwanden; Richard W. Nightingale; Paul Boerner

2007-01-01T23:59:59.000Z

480

Mass Spectrometry and Density Functional Theory Characterizations of DNA Modifications  

E-Print Network [OSTI]

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

Williams, Renee Therese

2012-01-01T23:59:59.000Z

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


481

Stabilizing synthetic data in the DNA of living organisms  

Science Journals Connector (OSTI)

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

Nozomu Yachie; Yoshiaki Ohashi; Masaru Tomita

2008-06-01T23:59:59.000Z

482

Single-molecule studies of DNA dynamics and intermolecular forces  

E-Print Network [OSTI]

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

Robertson, Rae Marie

2007-01-01T23:59:59.000Z

483

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

Science Journals Connector (OSTI)

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

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

1982-07-01T23:59:59.000Z

484

Mass Spectrometry and Density Functional Theory Characterizations of DNA Modifications  

E-Print Network [OSTI]

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

Williams, Renee Therese

2012-01-01T23:59:59.000Z

485

Electric DNA chips for determination of pathogenic microorganisms  

E-Print Network [OSTI]

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

Enfors, Sven-Olof

486

Single molecule analysis of DNA electrophoresis in microdevices  

E-Print Network [OSTI]

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

Randall, Greg C

2006-01-01T23:59:59.000Z

487

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

E-Print Network [OSTI]

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

Halbert, Natalie Rose

2013-02-22T23:59:59.000Z

488

Allosteric Modulation of DNA by Small Molecules  

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

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

489

DNA nanotechnology: understanding and optimisation through simulation  

E-Print Network [OSTI]

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

Ouldridge, Thomas E

2014-01-01T23:59:59.000Z

490

DUF6 Project Doubles Production in 2013 | Department of Energy  

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

DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 November 26, 2013 - 12:00pm Addthis LEXINGTON, Ky. - The conversion plants at EM's Paducah and Portsmouth sites surpassed a fiscal year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office (PPPO) and contractor Babcock & Wilcox Conversion Services LLC (BWCS) began operations in 2011 to convert the nation's 800,000-metric-ton inventory of DUF6 to more benign forms for sale, ultimate disposal or long-term storage. "Since 2011, we have been ramping up production to determine and achieve the safe, sustainable operating rate of the plants," said George E.

491

Non-Double-Couple Microearthquakes At Long Valley Caldera, California,  

Open Energy Info (EERE)

Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Provide Evidence For Hydraulic Fracturing Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Journal Article: Non-Double-Couple Microearthquakes At Long Valley Caldera, California, Provide Evidence For Hydraulic Fracturing Details Activities (1) Areas (1) Regions (0) Abstract: Most of 26 small (0.4<~M<~3.1) microearthquakes at Long Valley caldera in mid-1997, analyzed using data from a dense temporary network of 69 digital three-component seismometers, have significantly non-double-couple focal mechanisms, inconsistent with simple shear faulting. We determined their mechanisms by inverting P- and S-wave polarities and amplitude ratios using linear-programming methods, and

492

DUF6 Project Doubles Production in 2013 | Department of Energy  

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

DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 DUF6 Project Doubles Production in 2013 November 26, 2013 - 12:00pm Addthis LEXINGTON, Ky. - The conversion plants at EM's Paducah and Portsmouth sites surpassed a fiscal year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office (PPPO) and contractor Babcock & Wilcox Conversion Services LLC (BWCS) began operations in 2011 to convert the nation's 800,000-metric-ton inventory of DUF6 to more benign forms for sale, ultimate disposal or long-term storage. "Since 2011, we have been ramping up production to determine and achieve the safe, sustainable operating rate of the plants," said George E.

493

Kinetic Alfven double layer formed by electron viscosity  

SciTech Connect (OSTI)

The effect of the electron viscosity on the kinetic Alfven solitary wave is investigated. It is found that small electron viscosity changes the electron motion along the magnetic field producing a boundary layer, and thus that in a low beta electron-ion plasma({beta} Much-Less-Than m{sub e}/m{sub i}), an obliquely propagating kinetic solitary Alfven wave can become a double layer. This double layer can exist in the sub-Alfvenic and super-Alfvenic regimes. The length scale of density drop for this double layer is on the order of that of the conventional kinetic solitary Alfven wave, and thus this double layer can accelerate electrons on a very short length scale.

Woo, M. H.; Ryu, C.-M. [Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of); Choi, C. R. [Department of Physics, Korea Advanced Institute of Science and Technology, Taejon 305-701 (Korea, Republic of)

2012-07-15T23:59:59.000Z

494

Superconductivity in Bundles of Double-Wall Carbon Nanotubes  

E-Print Network [OSTI]

We present electrical and thermal specific heat measurements that show superconductivity in double-wall carbon nanotube (DWCNT) bundles. Clear evidence, comprising a resistance drop as a function of temperature, magnetoresistance ...

Shi, Wu

495

Characterization of double walled carbon nanotubes-polyvinylidene fluoride nanocomposites  

E-Print Network [OSTI]

One of the main objectives of this thesis is to disperse double-walled carbon nanotubes (DWNT) in a polyvinylidene fluoride (PVDF) matrix, and to characterize the resulting composite using electrical, thermal, and mechanical characterization...

Almasri, Atheer Mohammad

2007-04-25T23:59:59.000Z

496

Student's difficulties with the theory of double-slit interference  

E-Print Network [OSTI]

developed abstract thinking abilities [3, 4]. The remainder are unable to learn physics by listening arrangement for theoretical treatment of double-slit interference. Figure 2. The mechanical device

Planin�iè, Gorazd

497

Young’s double-slit interference experiment with electrons  

Science Journals Connector (OSTI)

In this short Note we report a method for producing samples containing two nano-sized slits suitable for demonstrating to undergraduate and graduate students the double-slit electron interference experiment in a conventional transmission electron microscope.

S. Frabboni; G. C. Gazzadi; G. Pozzi

2007-01-01T23:59:59.000Z

498

Comment on "Evidence for Neutrinoless Double Beta Decay"  

E-Print Network [OSTI]

We comment on the recent claim for the experimental observation of neutrinoless double-beta decay. We discuss several limitations in the analysis provided in that paper and conclude that there is no basis for the presented claim.

C. E. Aalseth; F. T. Avignone III; A. Barabash; F. Boehm; R. L. Brodzinski; J. I. Collar; P. J. Doe; H. Ejiri; S. R. Elliott; E. Fiorini; R. J. Gaitskell; G. Gratta; R. Hazama; K. Kazkaz; G. S. King III; R. T. Kouzes; H. S. Miley; M. K. Moe; A. Morales; J. Morales; A. Piepke; R. G. H. Robertson; W. Tornow; P. Vogel; R. A. Warner; J. F. Wilkerson

2002-05-22T23:59:59.000Z

499

Double Auction experiments and their relevance for emissions trading  

Science Journals Connector (OSTI)

In this article, we discuss selected methodological problems from previous Double Auction (DA) experiments and analyze the two following questions experimentally. Firstly, does the framing of the decision situati...

Bodo Sturm

2008-01-01T23:59:59.000Z

500

Glass Does a Double-Take | Advanced Photon Source  

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

| 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Glass Does a Double-Take APRIL 4, 2008 Bookmark and Share Predicted phase diagram as a...