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1

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

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

2

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

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

3

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

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

4

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

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

5

Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA cleavage chemistry used to resolve these altered DNA structures can also operate as a weak link that can be exploited to kill cells-in a good way. A variety of small molecules...

6

Specific DNA cleavage mediated by [SalenMn(III)][sup +  

Science Conference Proceedings (OSTI)

The combination of [SalenMn(III)][sup +] and a terminal oxidant affords efficient and specific cleavage of right-handed double-helical DNA in regions rich in A:T base pairs. Metal complexes of the tetradentate chelating ligands Salen (Salen = N,N[prime]-ethylenebis(salicylideneaminato)) have been part of the inorganic chemistry literature for several decades. The cationic manganese(III) complex [SalenMn(III)][sup +] (1) is an efficient catalyst for the epoxidation of olefins with terminal oxidants such as iodosylbenzene. 1 also catalyzes oxidative C-H bond activation. The flat, crescent shape of 1, its aromatic and cationic nature, and its ability to catalyze hydrocarbon oxidation are features shared in whole or in part by metal complexes which bind to DNA and cleave it via oxidative processes. These similarities prompted the authors to evaluate the DNA-cleaving properties of 1, and they now report that 1 mediates specific cleavage of right-handed double-helical DNA in a reaction requiring a terminal oxidant. 20 refs., 3 figs., 1 tab.

Gravert, D.J.; Griffin, J.H. (Stanford Univ., CA (United States))

1993-02-12T23:59:59.000Z

7

Etoposide Metabolites Enhance DNA Topoisomerase II Cleavage near Leukemia-Associated MLL Translocation Breakpoints  

E-Print Network (OSTI)

ABSTRACT: Chromosomal breakage resulting from stabilization of DNA topoisomerase II covalent complexes by epipodophyllotoxins may play a role in the genesis of leukemia-associated MLL gene translocations. We investigated whether etoposide catechol and quinone metabolites can damage the MLL breakpoint cluster region in a DNA topoisomerase II-dependent manner like the parent drug and the nature of the damage. Cleavage of two DNA substrates containing the normal homologues of five MLL intron 6 translocation breakpoints was examined in vitro upon incubation with human DNA topoisomerase IIR, ATP, and either etoposide, etoposide catechol, or etoposide quinone. Many of the same cleavage sites were induced by etoposide and by its metabolites, but several unique sites were induced by the metabolites. There was a preference for G(-1) among the unique sites, which differs from the parent drug. Cleavage at most sites was greater and more heat-stable in the presence of the metabolites compared to etoposide. The MLL translocation breakpoints contained within the substrates were near strong and/or stable cleavage sites. The metabolites induced more cleavage than etoposide at the same sites within a 40 bp double-stranded oligonucleotide containing two of the translocation breakpoints, confirming the results

Brian D. Lovett; Dirk Strumberg; Ian A. Blair; Shaokun Pang; O Donald; A. Burden; Maureen D. Megonigal; Timothy R. Rebbeck; Neil Osheroff; Yves G. Pommier; Carolyn A. Felix

2000-01-01T23:59:59.000Z

8

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

E-Print Network (OSTI)

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

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

2006-01-01T23:59:59.000Z

9

Mechanism of DNA Translocation in a Replicative Hexameric Helicase  

Science Conference Proceedings (OSTI)

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.

Enemark,E.; Joshua-Tor, L.

2006-01-01T23:59:59.000Z

10

Helicase on DNA: A Phase coexistence based mechanism  

E-Print Network (OSTI)

We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.

Somendra M. Bhattacharjee; Flavio Seno

2002-05-13T23:59:59.000Z

11

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

NLE Websites -- All DOE Office Websites (Extended Search)

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

12

Diffusion-based DNA target colocalization by thermodynamic mechanisms  

E-Print Network (OSTI)

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

Antonio Scialdone; Mario Nicodemi

2011-05-04T23:59:59.000Z

13

Structure of DNA-Bound FEN1 Reveals Mechanism of Action  

NLE Websites -- All DOE Office Websites (Extended Search)

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

14

Structure of DNA-Bound FEN1 Reveals Mechanism of Action  

NLE Websites -- All DOE Office Websites (Extended Search)

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

15

Statistical-mechanical lattice models for protein-DNA binding in chromatin  

E-Print Network (OSTI)

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quant...

Teif, Vladimir B

2010-01-01T23:59:59.000Z

16

A Newly Discovered DNA Repair Mechanism | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

scanning for these lesions. When they encounter one, they break the base pair bond and flip the deformed base out of the DNA double helix. The enzyme contains a specially shaped...

17

WRN Exonuclease Structure, Molecular Mechanism, and DNA EndProcessing Role  

Science Conference Proceedings (OSTI)

WRN is unique among the five human RecQ DNA helicases by having a functional exonuclease domain (WRN-exo) and being defective in the premature aging and cancer-related disorder Werner syndrome. Here, we characterize WRN-exo crystal structures, biochemical activity and participation in DNA end-joining. Metal ion complex structures, active site mutations and activity assays reveal a two-metal-ion mediated nuclease mechanism. The DNA end-binding Ku70/80 complex specifically stimulates WRN-exo activity, and structure-based mutational inactivation of WRN-exo alters DNA end-joining in human cells. We furthermore establish structural and biochemical similarities of WRN-exo to DnaQ family replicative proofreading exonucleases, with WRN-specific adaptations consistent with dsDNA specificity and functionally important conformational changes. These results indicate WRN-exo is a human DnaQ family member and support analogous proof-reading activities that are stimulated by Ku70/80 with implications for WRN functions in age related pathologies and maintenance of genomic integrity.

Perry, J. Jefferson P.; Yannone, Steven M.; Holden, Lauren G.; Hitomi, Chiharu; Asaithamby, Aroumougame; Han, Seungil; Cooper, PriscillaK.; Chen, David J.; Tainer, John A.

2006-02-15T23:59:59.000Z

18

A model for DNA helicase mechanism based on a flashing ratchet  

E-Print Network (OSTI)

Helicases are molecular motors that consume energy supplied by chemical reactions to unwind double-stranded nucleic acids (like DNA and RNA) and to translocate along one of the single-strands. Motivated by the recent claims, based on experimental observations on the helicase NS3 of hepatitis C virus (HCV), that monomeric helicases are governed by a Brownian ratchet mechanism, here we develope a quantitative model. Our Brownian ratchet model, which is a somewhat new reformulation of the Betterton-J\\"ulicher theory of helicases, is generic two-state model and is applicable to all helicases which follow the Brownian ratchet mechanism. We illustrate the predictive power of the model by calculating some experimentally testable motor properties of a few monomeric helicases. Speficically, we predict the speed of unwinding of the double-stranded DNA and fluctuations around the average drift of the helicase. Our predictions are in excellent quantitative agreement with the corresponding experimental data.

Garai, Ashok; Chowdhury, Debashish

2007-01-01T23:59:59.000Z

19

DNA  

NLE Websites -- All DOE Office Websites (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

20

Application of chemical probes to study the kinetic mechanism of DNA polymerases.  

E-Print Network (OSTI)

??Kinetic and structural basis of high-fidelity DNA replication by DNA polymerases has been the subject of extensive studies for several decades; however, it is still (more)

Bakhtina, Marina M.

2006-01-01T23:59:59.000Z

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


21

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif  

E-Print Network (OSTI)

We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale up to 10 ns. Two unfolding mechanisms with decreasing connectivity between the initially interacting nucleobases can be identified where one pathway is characterized as entropically more favorable. The entropic preference can be mainly explained by strong water ordering effects due to hydrogen bonds for several occurring structures along the pathways. Finally we are able to indicate via free energy calculations the most stable configurations belonging to distinct hairpin structures in good agreement to experimental results.

Smiatek, Jens; Liu, Dongsheng; Heuer, Andreas

2011-01-01T23:59:59.000Z

22

DNA folding: structural and mechanical properties of the two-angle model for chromatin  

E-Print Network (OSTI)

We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N. Whitaker. 1993. PNAS 90:9021-9025) that describes the chromatin fiber geometry in terms of the entry-exit angle of the nucleosomal DNA and the rotational setting of the neighboring nucleosomes with respect to each other. We explore analytically the different structures that arise from this building principle, and demonstrate that the geometry with the highest density is close to the one found in native chromatin fibers under physiological conditions. On the basis of this model we calculate mechanical properties of the fiber under stretching. We obtain expressions for the stress-strain characteristics which show good agreement with the results of recent stretching experiments (Cui, Y., and C. Bustamante. 2000. PNAS 97:127-132) and computer simulations (Katritch, V., C. Bustamante, and W. K. Olson. 2000. J. Mol. Biol. 295:29-40), and which provide simple physical insights into correlations between the structural and elastic properties of chromatin.

H. Schiessel; W. M. Gelbart; R. Bruinsma

2001-02-07T23:59:59.000Z

23

Modelling cleavage fracture of bainitic steels  

Science Conference Proceedings (OSTI)

The origin of brittle fracture of polycrystalline metals failing by cleavage is most frequently associated to slip-induced cracking of some non-metallic brittle particle or inclusion (a carbide in ferritic steels). When the size of the particles is smaller than the grain size of the metallic matrix, the nucleating event of a macroscopic failure results from the successive occurrence of three simple events: slip-induced cleavage of a particle, transmission of the microcrack to the neighboring grain across the particle/matrix interface and propagation of the grain-size microcrack to the neighboring grains across the grain boundary. On the basis of this scheme, a statistical weakest link'' fracture model has been developed which takes into account the presence of two independent distributions of structural elements (isolated particles and matrix grains) with two barriers for cleavage propagation (the particle/matrix interfaces and the grain boundaries), characterized by a crack arrest capability well over the crack propagation resistance of the cleavage planes of the crystalline lattices of the two planes. An application of the model to the prediction of the fracture stress and the critical stress intensity factor as a function of the temperature of a bainitic steel is presented.

Martin-Meizoso, A.; Ocana-Arizcorreta, I.; Gil-Sevillano, J.; Fuentes-Perez, M. (Univ. de Navarra, San Sebastian (Spain). Escuela Superior de Ingenieros Centro de Estudios e Investigaciones Tecnicas de Guipuzcoa, San Sebastian (Spain))

1994-06-01T23:59:59.000Z

24

Enzymological and Structural Studies of the Mechanism of Promiscuous Substrate Recognition by the Oxidative DNA Repair Enzyme AlkB  

SciTech Connect

Promiscuous substrate recognition, the ability to catalyze transformations of chemically diverse compounds, is an evolutionarily advantageous, but poorly understood phenomenon. The promiscuity of DNA repair enzymes is particularly important, because it enables diverse kinds of damage to different nucleotide bases to be repaired in a metabolically parsimonious manner. We present enzymological and crystallographic studies of the mechanisms underlying promiscuous substrate recognition by Escherichia coli AlkB, a DNA repair enzyme that removes methyl adducts and some larger alkylation lesions from endocyclic positions on purine and pyrimidine bases. In vitro Michaelis-Menten analyses on a series of alkylated bases show high activity in repairing N1-methyladenine (m1A) and N3-methylcytosine (m3C), comparatively low activity in repairing 1,N6-ethenoadenine, and no detectable activity in repairing N1-methylguanine or N3-methylthymine. AlkB has a substantially higher kcat and Km for m3C compared with m1A. Therefore, the enzyme maintains similar net activity on the chemically distinct substrates by increasing the turnover rate of the substrate with nominally lower affinity. Cocrystal structures provide insight into the structural basis of this 'kcat/Km compensation,' which makes a significant contribution to promiscuous substrate recognition by AlkB. In analyzing a large ensemble of crystal structures solved in the course of these studies, we observed 2 discrete global conformations of AlkB differing in the accessibility of a tunnel hypothesized to control diffusion of the O2 substrate into the active site. Steric interactions between a series of protein loops control this conformational transition and present a plausible mechanism for preventing O2 binding before nucleotide substrate binding.

Yu, B.; Hunt, J

2009-01-01T23:59:59.000Z

25

Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage  

Science Conference Proceedings (OSTI)

In this chapter, we summarize recent work from our laboratory and provide new perspective on two important aspects of bacterial mercury resistance: the molecular mechanism of transcriptional regulation by MerR, and the enzymatic cleavage of the Hg-C bond in methylmercury by the organomercurial lyase, MerB. Molecular dynamics (MD) simulations of MerR reveal an opening-and-closing dynamics, which may be involved in initiating transcription of mercury resistance genes upon Hg(II) binding. Density functional theory (DFT) calculations on an active-site model of the enzyme reveal how MerB catalyzes the Hg-C bond cleavage using cysteine coordination and acid-base chemistry. These studies provide insight into the detailed mechanisms of microbial gene regulation and defense against mercury toxicity.

Guo, Hao-Bo [ORNL; Parks, Jerry M [ORNL; Johs, Alexander [ORNL; Smith, Jeremy C [ORNL

2011-01-01T23:59:59.000Z

26

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

SciTech Connect

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

None

2013-05-15T23:59:59.000Z

27

Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein  

E-Print Network (OSTI)

Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein Eco two motors to translocate DNA before carrying out DNA cleavage. The motor func- tion is accomplished unit of the enzyme loads the motor subunits onto adjacent DNA by allowing them to bind and initiate

Seidel, Ralf

28

George R. Irwin Symposium on Cleavage Fracture TABLE OF ...  

Science Conference Proceedings (OSTI)

L.P. Zhang, C.L. Davis, and M. Strangwood. A New Tool for Crystallographic ... J.I. Dickson, J.-B. Vogt, A.H. Messai, and J. Foct. Oxide Film Effects on Cleavage

29

X-ray Crystallographic Observation of 'In-line' and 'Adjacent' Conformations in a Bulged Self-Cleaving RNA/DNA Hybrid  

Science Conference Proceedings (OSTI)

The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Husken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line ) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.

Tereshko, V.; Wallace, S.T.; Usman, N.; Wincott, F.; Egli, M. (Northwestern)

2010-03-08T23:59:59.000Z

30

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

DOE Green Energy (OSTI)

The objective of the project was to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically, the development of a novel biochemical pathway for the selective cleavage of C-N bonds in carbazole was the focus of research in this project. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. Obtaining an enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl-2,3-diol was the focus of much of the research in this project, however; no suitable enzyme was found. Project accomplishments included expressing the genes for carbazole dioxygenase in Rhodococcus erythropolis and Escherichia coli, development of gene expression vectors for Rhodococcus, and isolation of a Pseudomonas sp. strain GTIN-G4 that has the novel biochemical ability to replace one of the nitrogen-associated hydrogen atoms in 2-aminobiphenyl with formaldehyde. Rhodococcus cultures are capable of metabolizing a wide range of substrates, including hydrophobic substrates like petroleum, and may find widespread use in the development of biotechnology processes in the future. The results of this project will directly benefit the development of future biotechnology processes/projects employing Rhodococcus hosts. Three manuscripts were prepared and submitted for publication based on the data obtained in this project: (1) ''Formylation of 2-aminobiphenyl by Pseudomonas sp. strain GTIN-G4''; (2) ''Screening and Analysis of DNA Fragments that Show Promoter Activities in Rhodococcus erythropolis''; and (3) ''Microbial Biocatalyst Developments to Upgrade Fossil Fuels''.

John J. Kilbane II

2006-04-01T23:59:59.000Z

31

Fundamental Interaction Mechanisms of Engineered ...  

Science Conference Proceedings (OSTI)

Fundamental Interaction Mechanisms of Engineered Nanomaterials with DNA. Summary: We utilized isotope-dilution liquid ...

2012-10-01T23:59:59.000Z

32

[Vertically intergrated analysis of human DNA]. Progress report, [April 1, 1993--February 28, 1994  

Science Conference Proceedings (OSTI)

Progress is reported on several fronts aimed at DNA sequencing using cosmids-contigs. Specifically results gained in exploiting RARE (recA-assisted-restriction enzyme) cleavage, in clone isolation by flow cytometry, in cosmid-DNA preparations, in automated interpretation of digitized gel images and in contig building via multiple complete digest (MCD) mapping are briefly described.

Olson, M.V.

1994-03-01T23:59:59.000Z

33

DNA Record  

Science Conference Proceedings (OSTI)

... 4. Field 18.004: Source agency/SRC 5. Field 18.005: DNA Record Header Information (DRI) ... Field 18.005: DNA Record Header Information (DRI) ...

2010-08-03T23:59:59.000Z

34

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

35

DNA Extraction  

NLE Websites -- All DOE Office Websites (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

36

DNA Biometrics  

Science Conference Proceedings (OSTI)

... presentation at Advances in Forensic DNA Analysis workshop held at the American Academy of Forensic Sciences meeting (Seattle, WA), February ...

2013-03-15T23:59:59.000Z

37

Forensic DNA:  

Science Conference Proceedings (OSTI)

... January 17, 2008 Press Release From Mayor Bloomberg's STATE OF THE CITY ADDRESS Efforts towards Portable/Mobile DNA Devices ...

2008-09-29T23:59:59.000Z

38

Controlling DNA Methylation  

NLE Websites -- All DOE Office Websites (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).

39

Cellular responses to environmental DNA damage  

Science Conference Proceedings (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

40

Involvement of DNA polymerase beta in repairing oxidative damages induced by antitumor drug adriamycin  

SciTech Connect

Adriamycin (ADM) is a widely used antineoplastic drug. However, the increasing cellular resistance has become a serious limitation to ADM clinical application. The most important mechanism related to ADM-induced cell death is oxidative DNA damage mediated by reactive oxygen species (ROS). Base excision repair (BER) is a major pathway in the repair of DNA single strand break (SSB) and oxidized base. In this study, we firstly applied the murine embryo fibroblasts wild-type (pol {beta} +/+) and homozygous pol {beta} null cell (pol {beta} -/-) as a model to investigate ADM DNA-damaging effects and the molecular basis underlying these effects. Here, cellular sensitivity to ADM was examined using colorimetric assay and colony forming assay. ADM-induced cellular ROS level and the alteration of superoxide dismutase (SOD) activity were measured by commercial kits. Further, DNA strand break, chromosomal damage and gene mutation were assessed by comet assay, micronucleus test and hprt gene mutation assay, respectively. The results showed that pol {beta} -/- cells were more sensitive to ADM compared with pol {beta} +/+ cells and more severe SSB and chromosomal damage as well as higher hprt gene mutation frequency were observed in pol {beta} -/- cells. ROS level in pol {beta} -/- cells increased along with decreased activity of SOD. These results demonstrated that pol {beta} deficiency could enable ROS accumulation with SOD activity decrease, further elevate oxidative DNA damage, and subsequently result in SSB, chromosome cleavage as well as gene mutation, which may be partly responsible for the cytotoxicity of ADM and the hypersensitivity of pol {beta} -/- cells to ADM. These findings suggested that pol {beta} is vital for repairing oxidative damage induced by ADM.

Liu Shukun; Wu Mei [Department of Environmental Health, Sichuan University, West China School of Public Health, Chengdu (China); Zhang Zunzhen, E-mail: zhangzunzhen@163.co [Department of Environmental Health, Sichuan University, West China School of Public Health, Chengdu (China)

2010-08-01T23:59:59.000Z

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


41

Protocols for the selective cleavage of carbon-sulfur bonds in coal  

SciTech Connect

Removal of the organic sulfur in coal constitutes one of the major challenges facing fossil fuel scientists today. A cost--effective of desulfurizing Illinois coal is non-existent at the present time. Research in our group aims to develop a simple protocol for sulfur removal by gaining understanding of how various additives can enhance the rates of C-S bond cleavage in Illinois coal and coal model compounds, relative to fragmentation of the coal macromolecule via C-C, C-O, and C-N bond cleavage. During this funding period, we plan to carry out examinations of: (a) the effects of various reaction conditions on radical-initiated and Lewis acid-catalyzed C-S bond cleavages; (b) the effects of caustic impregnation and subsequent alcoholic reflux on C-S bond cleavage strategies; (c) the reactions of coal model compounds with electron-deficient substrates; (d) examinations of photooxidative C-S bond cleavage reactions; (e) the effects of moderate (300--400{degrees}C) temperatures and pressures as well as ultrasonic radiation on (a) - (c). Also planned are differential scanning calorimetric (DSC) examinations of selected C-S bond cleavage protocols, including those on Illinois coals that possess varying amounts of organic and inorganic sulfur.

Bausch, M.

1991-01-01T23:59:59.000Z

42

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

E-Print Network (OSTI)

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

Nguyen, Suzanne Pham

2007-01-01T23:59:59.000Z

43

Carotenoids & Retinoids; Molecular Aspects and Health IssuesChapter 9 Formation of -Carotene Cleavage Products  

Science Conference Proceedings (OSTI)

Carotenoids & Retinoids; Molecular Aspects and Health Issues Chapter 9 Formation of -Carotene Cleavage Products Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry Press Downloadable

44

pH dependence of the mechanism of hydrolysis of benzo(a)pyrene-cis-7,8-diol 9,10-epoxide catalyzed by DNA, Poly(G), and Poly(A)  

SciTech Connect

The rates of reaction of (+/-)-7..beta..,8..cap alpha..-dihydroxy-9..beta..,10..beta..-epoxy-7,8,9,10-tetrahydrobenzo(..cap alpha..) pyrene (DE-1, in which the 7-hydroxyl group and epoxide oxygen are cis) in solutions of varied DNA, Poly(A), and Poly(G) concentrations were determined as a function of pH. The rate data were consistent with a mechanism in which DE-1 forms a physical complex with the polynucleotide, and this physical complex than reacts both by a pathway whose rate is first-order in respect to hydronium ion concentration (k/sub cat//sup H/ route) and by a second pathway whose rate is independent of hydronium ion concentration (k/sub cat//sup H/ route) and by a second pathway whose rate is independent of hydronium ion concentration (k/sub cat//sup 0/ route). Product studies showed that > 95% of the products formed from both the k/sub cat//sup H/ and k/sub cat//sup 0/ reactions were tetraols resulting from cis and trans hydration of the epoxide, and < 5% of covalent binding of the diol epoxide to the polynucleotides occurred. The DNA- and Poly(A)-catalyzed hydrolyses of DE-1 are similar to those of DE-2 in that the physically bound diol epoxide reacts significantly faster (> 50 fold) than free diol epoxide by the acid-catalyzed routes (k/sub cat//sup H/ >> k/sub H+/) and moderately faster (< 5) by the spontaneous pathway (k/sub cat//sup 0/ > k/sub 0/). Poly(G) is a significantly better catalyst than either DNA or Poly(A) for both k/sub cat//sup H/ and k/sub cat//sup 0/ reactions. At pH ca. 7, however, the physical DE-1-DNA complex reacts mainly by the k/sub cat//sup 0/ reaction, whereas the physical DE-2-DNA complex reacts mostly by the k/sub cat//sup 0/ reaction.

Islam, N.B.; Whalen, D.L.; Yagi, H.; Jerina, D.M.

1987-04-01T23:59:59.000Z

45

Structural and Functional Elucidation of the Mechanism Promoting Error-prone Synthesis by Human DNA Polymerase [kappa] Opposite the 7,8-Dihydro-8-oxo-2'-deoxyguanosine Adduct  

Science Conference Proceedings (OSTI)

Human polymerase kappa (hPol {kappa}) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol {kappa} bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2{prime}-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol {kappa} bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished 'bursts' for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol {kappa} complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol {kappa} by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol {kappa} to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol {kappa} compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase {eta}.

Irimia, Adriana; Eoff, Robert L.; Guengerich, F.Peter; Egli, Martin; (Vanderbilt)

2009-09-25T23:59:59.000Z

46

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

Science Conference Proceedings (OSTI)

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

John J. Kilbane II

2005-10-01T23:59:59.000Z

47

DNA Activity  

NLE Websites -- All DOE Office Websites (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.

48

Structural Basis of Cell Wall Cleavage by a Staphylococcal  

E-Print Network (OSTI)

The major autolysins (Atl) of Staphylococcus epidermidis and S. aureus play an important role in cell separation, and their mutants are also attenuated in virulence. Therefore, autolysins represent a promising target for the development of new types of antibiotics. Here, we report the high-resolution structure of the catalytically active amidase domain AmiE (amidase S. epidermidis) from the major autolysin of S. epidermidis. This is the first protein structure with an amidase-like fold from a bacterium with a gram-positive cell wall architecture. AmiE adopts a globular fold, with several a-helices surrounding a central b-sheet. Sequence comparison reveals a cluster of conserved amino acids that define a putative binding site with a buried zinc ion. Mutations of key residues in the putative active site result in loss of activity, enabling us to propose a catalytic mechanism. We also identified and synthesized muramyltripeptide, the minimal peptidoglycan fragment that can be used as a substrate by the enzyme. Molecular docking and digestion assays with muramyltripeptide derivatives allow us to identify key determinants of ligand binding. This results in a plausible model of interaction of this ligand not only for AmiE, but also for other PGN-hydrolases that share the same fold. As AmiE active-site mutations also show a severe growth defect, our findings provide an excellent platform for the design of specific inhibitors that target staphylococcal cell

Sebastian Zoll; Bernhard Ptzold; Martin Schlag; Friedrich Gtz; Hubert Kalbacher

2010-01-01T23:59:59.000Z

49

Cleavage of the Nb=O bond of oxoniobium(V) porphyrins. Synthesis and characterization of novel niobium(V) porphyrins with two distinct catechols  

Science Conference Proceedings (OSTI)

A novel catecholato complex, Nb{sup v}(tpp)(cat)(Hcat), where cat and Hcat are two distinct catechol ligands (a bidentate catecholate dianion and a monodentate catecholate monoanion, respectively) and tpp is 5, 10, 15, 20-tetaphenylporphyrin dianion, has been isolated in the reaction of Nb{sup v} (tpp)(O)(AcO) with catechol, where AcO is an acetatoligand. Its molecular structure has been determined by X-ray crystallography. Crystal data: monoclinic, space group P2{sub 1}/c, Z = 4, a = 14.592(3) {Angstrom}, b = 23.46(1) {Angstrom}, c = 14.415(4) {Angstrom}, {beta} = 100.95(2){degrees}, R = 0.079. The heptacoordinate niobium atom is displaced by 1.02 {Angstrom} from the mean plane of the four nitrogen atoms. The structure of the complex in solution and the mechanism of the Nb=O cleavage were investigated by means of {sup 1}H-NMR spectroscopy. The bidentate catechol is oriented in C{sub s} symmetry with respect to the porphyrin plane, and the monodentate catechol is located perpendicularly to both the bidentate catechol and the porphyrin plane. Two intermediates with the bidentate catechol were observed after addition of 2 equiv of catechol to Nb(tmp)(O)(AcO) at -30 {degrees}C, where tmp denotes the 5,10,15,20-tetramesitylporphyrin dianion. These intermediates were determined to be Nb(tmp)(cat)(OH) and Nb(tmp)(cat)(AcO). Thus, the Nb=O bond of Nb(tmp)(O)(AcO) was easily cleaved to create the two intermediates. The authors propose a unique route to the Nb=O cleavage that involves an intramolecular electron transfer from the catechol ligand coordinated at the first stage through a ligand exchange with AcO. Both protonation and electron transfer to the Nb=O moiety play important roles in the Nb=O cleavage.

Kurihara, Masato; Kotoh, Noriyuki; Kojima, Takahiko [Kyushu Univ., Fukuoka (Japan)] [and others

1995-09-13T23:59:59.000Z

50

Degradation of Fluorobenzene by Rhizobiales Strain F11 via ortho Cleavage of 4-Fluorocatechol and Catechol ?  

E-Print Network (OSTI)

The aerobic metabolism of fluorobenzene by Rhizobiales sp. strain F11 was investigated. Liquid chromatography-mass spectrometry analysis showed that 4-fluorocatechol and catechol were formed as intermediates during fluorobenzene degradation by cell suspensions. Both these compounds, unlike 3-fluorocatechol, supported growth and oxygen uptake. Cells grown on fluorobenzene contained enzymes for the ortho pathway but not for meta ring cleavage of catechols. The results suggest that fluorobenzene is predominantly degraded via 4-fluorocatechol with subsequent ortho cleavage and also partially via catechol. During the last decades, environmental contamination by fluorinated organic compounds has received increasing attention because of their use as herbicides, fungicides, surfactants, refrigerants, intermediates in organic synthesis, solvents, and pharmaceuticals (11). Whereas the biodegradation of chlorinated compounds has been studied quite extensively (19), little is known about the bacterial metabolism of fluoroaromatic compounds, even though there have been several reports on the degradation of fluorobenzoic acids (5, 6, 7, 16). With chloroaromatics,

Maria F. Carvalho; Maria Isabel M. Ferreira; Irina S. Moreira; Paula M. L. Castro; Dick B. Janssen

2006-01-01T23:59:59.000Z

51

Physical Interactions between Mcm10, DNA, and DNA Polymerase [alpha  

SciTech Connect

Mcm10 is an essential eukaryotic protein required for the initiation and elongation phases of chromosomal replication. Specifically, Mcm10 is required for the association of several replication proteins, including DNA polymerase {alpha} (pol {alpha}), with chromatin. We showed previously that the internal (ID) and C-terminal (CTD) domains of Mcm10 physically interact with both single-stranded (ss) DNA and the catalytic p180 subunit of pol {alpha}. However, the mechanism by which Mcm10 interacts with pol {alpha} on and off DNA is unclear. As a first step toward understanding the structural details for these critical intermolecular interactions, x-ray crystallography and NMR spectroscopy were used to map the binary interfaces between Mcm10-ID, ssDNA, and p180. The crystal structure of an Mcm10-ID {center_dot} ssDNA complex confirmed and extended our previous evidence that ssDNA binds within the oligonucleotide/oligosaccharide binding-fold cleft of Mcm10-ID. We show using NMR chemical shift perturbation and fluorescence spectroscopy that p180 also binds to the OB-fold and that ssDNA and p180 compete for binding to this motif. In addition, we map a minimal Mcm10 binding site on p180 to a small region within the p180 N-terminal domain (residues 286-310). These findings, together with data for DNA and p180 binding to an Mcm10 construct that contains both the ID and CTD, provide the first mechanistic insight into how Mcm10 might use a handoff mechanism to load and stabilize pol {alpha} within the replication fork.

Warren, Eric M.; Huang, Hao; Fanning, Ellen; Chazin, Walter J.; Eichman, Brandt F.; (Vanderbilt)

2009-10-21T23:59:59.000Z

52

Carotenoids & Retinoids; Molecular Aspects and Health IssuesChapter 8 -Carotene Cleavage Products Impair Cellular and Mitochondrial Functions  

Science Conference Proceedings (OSTI)

Carotenoids & Retinoids; Molecular Aspects and Health Issues Chapter 8 -Carotene Cleavage Products Impair Cellular and Mitochondrial Functions Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry Press 

53

Protocols for the selective cleavage of carbon-sulfur bonds in coal. Quarterly report, September 1, 1991--November 30, 1991  

SciTech Connect

Removal of the organic sulfur in coal constitutes one of the major challenges facing fossil fuel scientists today. A cost--effective of desulfurizing Illinois coal is non-existent at the present time. Research in our group aims to develop a simple protocol for sulfur removal by gaining understanding of how various additives can enhance the rates of C-S bond cleavage in Illinois coal and coal model compounds, relative to fragmentation of the coal macromolecule via C-C, C-O, and C-N bond cleavage. During this funding period, we plan to carry out examinations of: (a) the effects of various reaction conditions on radical-initiated and Lewis acid-catalyzed C-S bond cleavages; (b) the effects of caustic impregnation and subsequent alcoholic reflux on C-S bond cleavage strategies; (c) the reactions of coal model compounds with electron-deficient substrates; (d) examinations of photooxidative C-S bond cleavage reactions; (e) the effects of moderate (300--400{degrees}C) temperatures and pressures as well as ultrasonic radiation on (a) - (c). Also planned are differential scanning calorimetric (DSC) examinations of selected C-S bond cleavage protocols, including those on Illinois coals that possess varying amounts of organic and inorganic sulfur.

Bausch, M.

1991-12-31T23:59:59.000Z

54

The DNA project - CECM  

E-Print Network (OSTI)

Software-package files: dna6.zip (for Maple 6), dna7.zip (for Maple 7). Contents: DNA routines, Release 1.04 ( last updated Nov/06/2001 ). Changes over...

55

Competition between Covalent and Noncovalent Bond Cleavages in Dissociation of Phosphopeptide-Amine Complexes  

DOE Green Energy (OSTI)

Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A3pXA3-NH2 (X=S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. We demonstrate that covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel

Laskin, Julia; Yang, Zhibo; Woods, Amina S.

2011-04-21T23:59:59.000Z

56

Protocols for the selective cleavage of carbon-sulfur bonds in coal. Technical report, December 1, 1992--February 28, 1993  

SciTech Connect

Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. Planned in the second year of our project Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal are investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures and radiation. Other investigations that will result in analyses of the likelihood of C-S bond cleavages resulting from various oxidative processes will also be undertaken. Summarized in this quarterly report are results of our investigations of the following topics: (a) desulfurization of coal model sulfones; (b) desulfurization of coal model sulfides; (c) photooxidation of organic sulfides; and (d) photolytic desulfurization of coal.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States); Ho, K.K. [Illinois Clean Coal Inst., Carterville, IL (United States)

1993-05-01T23:59:59.000Z

57

JGI - Why Sequence Sea Squirt cDNA?  

NLE Websites -- All DOE Office Websites (Extended Search)

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

58

Clinical DNA Online  

Science Conference Proceedings (OSTI)

Welcome to the NIST Clinical DNA Information Resource. ... Future materials have progress updates. General Information. ...

2013-04-26T23:59:59.000Z

59

Quantitative DNA fiber mapping  

DOE Patents (OSTI)

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

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

1998-01-01T23:59:59.000Z

60

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

E-Print Network (OSTI)

a) RAW cells expressing an NF-kB luciferase reporter wereTRIF to induce production of NF-kB elicited transcripts andand a plasmid encoding an NF-kB luciferase reporter (with 5

Ewald, Sarah Elisabeth

2010-01-01T23:59:59.000Z

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


61

Observation of differences between low-energy electron- and positron-diffraction structural determinations of the cleavage faces of CdSe  

Science Conference Proceedings (OSTI)

Low-energy positron diffraction (LEPD) is used in conjunction with low-energy electron diffraction (LEED) to determine the relaxed atomic geometries of the CdSe cleavage surfaces. The LEPD analyses yield optimal fits at smaller top-layer perpendicular relaxations than LEED for both cleavage faces, and significantly better agreement between theoretical and experimental intensity profiles.

Horsky, T.N.; Brandes, G.R.; Canter, K.F.; Duke, C.B.; Horng, S.F.; Kahn, A.; Lessor, D.L.; Mills A.P. Jr.; Paton, A.; Stevens, K.; and others

1989-04-17T23:59:59.000Z

62

How scientists use DNA  

NLE Websites -- All DOE Office Websites (Extended Search)

How scientists use DNA Name: Peter and Edmund Age: NA Location: NA Country: NA Date: NA Question: Dear Scientists, We would like to know some ways that scientists use DNA. For...

63

DNA and Biometrics  

Science Conference Proceedings (OSTI)

... January 17, 2008 Press Release From Mayor Bloomberg's STATE OF THE CITY ADDRESS Efforts towards Portable/Mobile DNA Devices ...

2008-06-25T23:59:59.000Z

64

An unusual carbon?carbon bond cleavage reaction during phosphinothricin biosynthesis  

SciTech Connect

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

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

2010-01-12T23:59:59.000Z

65

The Structural Basis of [beta]-Peptide-Specific Cleavage by the Serine Protease Cyanophycinase  

Science Conference Proceedings (OSTI)

Cyanophycin, or poly-L-Asp-multi-L-Arg, is a non-ribosomally synthesized peptidic polymer that is used for nitrogen storage by cyanobacteria and other select eubacteria. Upon synthesis, it self-associates to form insoluble granules, the degradation of which is uniquely catalyzed by a carboxy-terminal-specific protease, cyanophycinase. We have determined the structure of cyanophycinase from the freshwater cyanobacterium Synechocystis sp. PCC6803 at 1.5-{angstrom} resolution, showing that the structure is dimeric, with individual protomers resembling aspartyl dipeptidase. Kinetic characterization of the enzyme demonstrates that the enzyme displays Michaelis-Menten kinetics with a k{sub cat} of 16.5 s{sup -1} and a k{sub cat}/K{sub M} of 7.5 x 10{sup -6} M{sup -1} s{sup -1}. Site-directed mutagenesis experiments confirm that cyanophycinase is a serine protease and that Gln101, Asp172, Gln173, Arg178, Arg180 and Arg183, which form a conserved pocket adjacent to the catalytic Ser132, are functionally critical residues. Modeling indicates that cyanophycinase binds the {beta}-Asp-Arg dipeptide residue immediately N-terminal to the scissile bond in an extended conformation in this pocket, primarily recognizing this penultimate {beta}-Asp-Arg residue of the polymeric chain. Because binding and catalysis depend on substrate features unique to {beta}-linked aspartyl peptides, cyanophycinase is able to act within the cytosol without non-specific cleavage events disrupting essential cellular processes.

Law, Adrienne M.; Lai, Sandy W.S.; Tavares, John; Kimber, Matthew S.; (Guelph)

2010-10-01T23:59:59.000Z

66

Capstan friction model for DNA ejection from bacteriophages  

E-Print Network (OSTI)

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

Ghosal, Sandip

2013-01-01T23:59:59.000Z

67

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

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

68

Patterning nanocrystals using DNA  

E-Print Network (OSTI)

nanocrystals. Angewandte Chemie-International Edition, [2]linked by DNA. Angewandte Chemie-International Edition, 39(with proteins. Angewandte Chemie-International Edition, 40(

Williams, Shara Carol

2003-01-01T23:59:59.000Z

69

DNA's Role with Proteins  

NLE Websites -- All DOE Office Websites (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!

70

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data  

Science Conference Proceedings (OSTI)

DNA methylation, a well-studied mechanism of epigenetic regulation, plays important roles in cancer. Increased levels of global DNA methylation is observed in primary solid tumors including endometrial carcinomas and is generally associated with silencing ... Keywords: DNA methylation, Steiner tree, cancer recurrence, classification, protein-protein interaction network, random walk

Jianhua Ruan; Md. Jamiul Jahid; Fei Gu; Chengwei Lei; Yi-Wen Huang; Ya-Ting Hsu; David G. Mutch; Chun-Liang Chen; Nameer B. Kirma; Tim H. Huang

2012-10-01T23:59:59.000Z

71

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

72

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

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

73

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

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

74

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways  

NLE Websites -- All DOE Office Websites (Extended Search)

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

75

{beta}-carboline derivatives: Novel photosensitizers that intercalate into DNA to cause direct DNA damage in photodynamic therapy  

SciTech Connect

Novel 1,3,9-trisubstituted {beta}-carboline derivatives were found to exhibit DNA photocleavage properties under visible light irradiation in a cell-free system, which could be reduced by antioxidant vitamin E. Their photo-cytotoxicity to human tumor cell line HeLa was confirmed, in which apoptosis only contributed a small part to the cell death, and necrosis was the dominating outcome of HeLa cells in photodynamic therapy (PDT) using {beta}-carboline derivatives. Different from other clinical PDT drugs, {beta}-carboline derivatives were demonstrated to be able to distribute in the nucleus and intercalate into DNA, and consequently cause direct DNA damage by photochemical reaction products in PDT, which was proved by the distinct DNA tails in the comet assay and the considerable amount of DNA damaged cells quantified by flow cytometry. This mechanism could be the explanation for the delay of cell proliferation at DNA synthesis and mitosis.

Guan Huaji [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Liu Xiaodong [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Peng Wenlie [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Cao Rihui [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Ma Yan [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Chen Hongsheng [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China); Xu Anlong [State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Therapeutic Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen (Zhongshan) University, 135 Xin Gang Xi Road, Guangzhou 510275 (China)]. E-mail: ls36@zsu.edu.cn

2006-04-14T23:59:59.000Z

76

Quantitive DNA Fiber Mapping  

SciTech Connect

Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

2008-01-28T23:59:59.000Z

77

Bohmian Mechanics  

E-Print Network (OSTI)

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

Detlef Duerr; Sheldon Goldstein; Roderich Tumulka; Nino Zanghi

2009-03-15T23:59:59.000Z

78

Protocols for the selective cleavage of carbon-sulfur bonds in coal. [Quarterly] technical report, March 1, 1993--May 31, 1993  

SciTech Connect

Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. Planned in the second year of our project ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` are investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures and radiation. other investigations that will result in analyses of the likelihood of C-S bond cleavages resulting from various oxidative processes will also be undertaken. Summarized in this quarterly report are results of our investigations of the following topics: (a) desulfurization of coal model sulfones and sulfides; (b) photolytic desulfurization of coal; (c) differential scanning calorimetric experiments on photooxidized coal; and (d) discussions on C-S bond strengths in radical cations.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)

1993-09-01T23:59:59.000Z

79

Universal mechanism of aging uncovered?  

Science Conference Proceedings (OSTI)

Researchers at Harvard Medical School (HMS: Boston, USA) have discovered that DNA damage decreases a cells ability to regulate which genes are turned on and off in particular settings. This mechanism, which applies both to fungi and to humans, might repre

80

Mechanical down jar mechanism  

SciTech Connect

This paper describes a mechanical down jar mechanism for freeing stuck objects within a well bore and for conducting other down hole activities. It comprises: an elongate tubular housing having anvil means; mandrel means adapted for connection to an object to be moved downwardly within the well bore and being disposed in telescoping relation with the anvil means and the elongate tubular housing, the mandrel means adapted to be struck by the anvil means to impart a downwardly directed jarring force to the object; the elongate tubular housing having internal firing and recocking detent groove means located in axially spaced relation and forming a firing lug support land therebetween; a radially expandable and retractable firing lug assembly being disposed within the elongate tubular housing and in absence of force being applied axially thereto being radially restrained by the firing lug support land; load spring means being disposed within the elongate tubular housing and being in downward force transmitting relation with the firing lug assembly; recocking spring means being disposed within the elongate tubular housing and having upward axial force transmitting relation with the firing lug assembly.

Taylor, W.T.

1991-12-03T23:59:59.000Z

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81

Generalized Poland-Scheraga model for supercoiled DNA  

E-Print Network (OSTI)

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is applied to the extremities of DNA: We propose a simple model for the energy of twisted DNA and compute the entropy of a loop, subject to angular constraints (supercoiling). The denaturation curves are shifted towards lower or higher temperatures depending on the sign of the torque, and the UV absorption peaks are softened. The properties of supercoiled DNA can be deduced through the use of a numerical Legendre transform. In the homogeneous case, we find that for weak supercoiling, the phenomenological quadratic law relating the torsional energy to the number of unpaired bases is recovered.

Thomas Garel; Henri Orland; Edouard Yeramian

2004-07-28T23:59:59.000Z

82

A thermodynamic model for agglomeration of DNA-looping proteins  

E-Print Network (OSTI)

In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding free energy and the entropy loss due to DNA looping is argued to result in an effective attraction between loops. A mean-field approximation can be described analytically via a mapping to a restricted random-graph ensemble having local degree constraints and global constraints on the number of connected components. It shows the emergence of protein clusters containing a finite fraction of all looping proteins. If the entropy loss due to a single DNA loop is high enough, this transition is found to be of first order.

Sumedha; Martin Weigt

2008-01-09T23:59:59.000Z

83

DNA polymerase having modified nucleotide binding site for DNA sequencing  

DOE Patents (OSTI)

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

Tabor, S.; Richardson, C.

1997-03-25T23:59:59.000Z

84

Protocols for the selective cleavage of carbon-sulfur bonds in coal. Interim final technical report, September 1, 1992--August 31, 1993  

SciTech Connect

This report presents results of research pertaining to chemical reactions that aim to selectively cleave C-S bonds in model compounds as well as Illinois coal. Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. In the second year of the project {open_quotes}Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal, the author has completed investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures, reagents, and radiation. He has also undertaken a series of reactions in which physically cleaned Illinois coal has been subjected to many of the same reaction conditions that were shown, via the use of model sulfides, to result in substantial C-S bond cleavage and or sulfur oxidation. Therefore, summarized in this interim final report are results of the investigations of the photooxidation reactions of coal model sulfones and sulfides; the photolytic desulfurization of coal; and various other topics, including a summary of the endeavors aimed at initiating C-S bond cleavage reactions using oxidation/chlorination/desulfurization protocols, and various tellurium reagents. Important experiments remain to be completed on this project; therefore, efforts in these areas will continue through the end of calendar year 1993.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)

1993-12-31T23:59:59.000Z

85

Protocols for the selective cleavage of carbon-sulfur bonds in coal. Final technical report, September 1, 1992--December 31, 1993  

SciTech Connect

Results of research pertaining to chemical reactions that aim to selectively cleave C-S bonds in model compounds as well as Illinois coal are summarized. Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. In the second year of the project ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures, reagents, and radiation have been completed. A series of reactions have been undertaken in which physically cleaned Illinois coal has been subjected to many of the same reaction conditions that were shown, via the use of model sulfides, to result in substantial C-S bond cleavage and or sulfur oxidation. Therefore, summarized in this final report are results of the investigations of the photooxidation reactions of coal model sulfones and sulfides; the photolytic desulfurization of coal; and various other topics, including a summary of endeavors aimed at initiating C-S bond cleavage reactions using oxidation/chlorination/desulfurization protocols, and various tellurium reagents.

Bausch, M.

1993-12-31T23:59:59.000Z

86

Bohmian mechanics contradicts quantum mechanics  

E-Print Network (OSTI)

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

Neumaier, Arnold

87

Generating DNA code word for DNA computing with realtime PCR  

Science Conference Proceedings (OSTI)

A number of DNA computing models to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP) have been proposed and demonstrated. Normally, the DNA sequences used ... Keywords: DNA computing, TaqMan probes, real-time PCR

Muhammad Faiz Mohamed Saaid; Zuwairie Ibrahim; Nor Haniza Sarmin

2008-03-01T23:59:59.000Z

88

Natural DNA sequencing by synthesis  

E-Print Network (OSTI)

high throughput genome sequencing by natural DNA synthesis.E.E. , et al. , Genome sequencing by natural DNA synthesis.p. 1304-51. Human Genome Sequencing, C.I. , Finishing the

Roller, Eric E.

2011-01-01T23:59:59.000Z

89

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

E-Print Network (OSTI)

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

Drennan, Catherine L.

90

DNA Profiling Standard Reference Materials  

Science Conference Proceedings (OSTI)

... agreement with the NIST Office of Law Enforcement Standards. ... Related Programs and Projects: SRM 2372 - Human DNA Quantitation Standard. ...

2013-03-15T23:59:59.000Z

91

A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication  

Science Conference Proceedings (OSTI)

During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load the 6-subunit mini chromosome maintenance (MCM2-7) complex onto DNA. Loading of MCM2-7 is a prerequisite for DNA licensing that restricts DNA replication to once per cell cycle. During S phase MCM2-7 functions as part of the replicative helicase but within the pre-RC MCM2-7 is inactive. The organization of replicative DNA helicases before and after loading onto DNA has been studied in bacteria and viruses but not eukaryotes and is of major importance for understanding the MCM2-7 loading mechanism and replisome assembly. Lack of an efficient reconstituted pre-RC system has hindered the detailed mechanistic and structural analysis of MCM2-7 loading for a long time. We have reconstituted Saccharomyces cerevisiae pre-RC formation with purified proteins and showed efficient loading of MCM2-7 onto origin DNA in vitro. MCM2-7 loading was found to be dependent on the presence of all pre-RC proteins, origin DNA, and ATP hydrolysis. The quaternary structure of MCM2-7 changes during pre-RC formation: MCM2-7 before loading is a single hexamer in solution but is transformed into a double-hexamer during pre-RC formation. Using electron microscopy (EM), we observed that loaded MCM2-7 encircles DNA. The loaded MCM2-7 complex can slide on DNA, and sliding is not directional. Our results provide key insights into mechanisms of pre-RC formation and have important implications for understanding the role of the MCM2-7 in establishment of bidirectional replication forks.

Evrin, C.; Li, H.; Clarke, P.; Zech, J.; Lurz, R.; Sun, J.; Uhle, S.; Stillman, B.; Speck, C.

2009-12-01T23:59:59.000Z

92

DNA waves and water  

E-Print Network (OSTI)

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

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

2010-12-23T23:59:59.000Z

93

Radiation and viral DNA  

NLE Websites -- All DOE Office Websites (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

94

Charge transport-mediated recruitment of DNA repair enzymes  

E-Print Network (OSTI)

Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains unclear. One hypothesis involves charge transport (CT) along DNA [Yavin, {\\it et al.}, PNAS, {\\bf 102}, 3546, (2005)]. In this CT mechanism, electrons are released by recently adsorbed BER enzymes and travel along the DNA. The electrons can scatter (by heterogeneities along the DNA) back to the enzyme, destabilizing and knocking it off the DNA, or, they can be absorbed by nearby lesions and guanine radicals. We develop a stochastic model to describe the electron dynamics, and compute probabilities of electron capture by guanine radicals and repair enzymes. We also calculate first passage times of electron return, and ensemble-average these results over guanine radical distributions. Our statistical results provide the rules that enable us to perform implicit-electron Monte-Carlo simulations of repair enzyme binding and redistribution near lesions. When lesions are electron absorbing, we show that the CT mechanism suppresses wasteful buildup of enzymes along intact portions of the DNA, maximizing enzyme concentration near lesions.

Pak-Wing Fok; Chin-Lin Guo; Tom Chou

2008-11-18T23:59:59.000Z

95

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

E-Print Network (OSTI)

16, Moser, M.J. et al. WRN helicase expression in WernerCoordinate action of the helicase and 3' to 5' exonucleasestructure of the E.coli RecQ helicase catalytic core. EMBO

2006-01-01T23:59:59.000Z

96

Mechanisms of initiation of DNA mismatch repair in Saccharomyces cerevisiae  

E-Print Network (OSTI)

increased mutation rates increase the rate of accumulationresult in mutation rate increases of up to several thousand-10 -5 (93) Mutation rate (fold increase) a Thr 4.2 [3.6-5.3

Shell, Scarlet Sara

2008-01-01T23:59:59.000Z

97

DNA migration mechanism analyses for applications in capillary and microchip  

E-Print Network (OSTI)

of paper, particle board, and plywood, as well as timber for construc- tion. Approximately two million

Barron, Annelise E.

98

Properties of DnaB helicase in [lambda] DNA replication  

Science Conference Proceedings (OSTI)

A tailed nicked-circle DNA substrate was used to measure the rapid replication fork (RF) movement catalyzed by E. Coli DnaB helicase and DNA polymerase III holoenzyme (pol III HE) (DnaB-RFs) (30 DnaB hexamers/substrate). The DnaB RFs can efficiently utilize the DNA substrate (60% in 5 min at 30C), and the forks move at a rapid rate (550-780 bp/sec at 30C). The DnaB-RFs have an average maximal processivity of 40,000 nt, and addition of either SSB or primase increase the processivity (150,000 nt + SSB, 70,000-140,000 nt + primase). However, SSB and primase do not affect the rate of fork movement or the amount of substrate utilized in the assay. The [lambda] SS proteins are effective at transferring DnaB onto the DNA substrate (8 DnaB hexamers/substrate). The [lambda] SS proteins do not change the rate of RF movement or the amount of substrate utilized. However, the amount of synthesis measured in the assay is [approximately]2-fold higher in the presence of the [lambda] SS proteins. Therefore, the [lambda] SS proteins increase the processivity of DnaB at the RF (100,000 nt). The [lambda] SS proteins do not appear to play a role in elongation because the processivity of the RF in the presence of SSB and primase is equivalent to the processivity of the [lambda] SS-RFs. [lambda] P protein blocks DnaB helicase activity if added to the RF assay prior to initiation or during elongation. DnaB helicase is more resistant to P inhibition, if the helicase is allowed to bind to the substrate prior to addition of [lambda] P or if primase and rNTPs are included in the assay. These results suggest that the conformation of the RF complex (DNA or nucleoprotein structure) blocks the attack of P on DnaB helicase. The heat shock proteins may play an auxiliary role in mediating the effects of [lambda] P if the concentration of P protein in the cells are high.

Stephens, K.M.

1991-01-01T23:59:59.000Z

99

Automating DNA processing  

E-Print Network (OSTI)

Technology is currently available to identify the genetic codes responsible for physical traits and genetic diseases in both plants and animals. Regardless of whether the final goal is medical diagnosis or breeder selection, extensive time and resources must be spent in laboratory research to determine the genetic structure of the relevant organisms. DNA processing is riddled with time intensive laboratory techniques that must be improved or replaced if genotyping large numbers of samples is to be accomplished. This thesis identifies and explains modules in DNA processing and how they can be improved by automation. modules associated with genome mapping are the focus of most of the discussion. A functional biochemistry background is provided so that researchers in automation can be efficiently assimilated to future biochen-fistry/automation projects. The needs of biochemistry researchers at Texas A&M University are specifically addressed. Herein, DNA processing has been defined as a series of discrete sub-processes or process modules in order to aid scheduling of future automation projects. Target process modules (sub-processes with a high probability of automation success) have been identified. In addition, possible automation solutions have been proposed for each target module along with a characterization of fundamental design parameters. Concluding this text is a discussion of procedures in genome mapping that have not been sufficiently automated. The initial focus of this thesis is on short term solutions. However, attention is given to more conceptual solutions accompanied by the biochemistry background necessary to begin developing them. Though systems are proposed to improve the efficiency of many processes, no implementation has been attempted. Design specifications are based on observation of current laboratory techniques and the variance that is typically allowed in relevant process parameters in TAMU laboratories.

Wienen, Michael Jan

1994-01-01T23:59:59.000Z

100

DNA-based asymmetric catalysis.  

E-Print Network (OSTI)

??The goal of the research described in this thesis was to develop the general concept and methodology of DNA-based asymmetric catalysis, with the aim of (more)

Boersma, Arnold Jacob

2009-01-01T23:59:59.000Z

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


101

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

Science Conference Proceedings (OSTI)

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

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

2010-02-01T23:59:59.000Z

102

Compliant mechanisms  

E-Print Network (OSTI)

The motivation for this work has been a variety of motions like navigation of pipelines, insertion operations in assembly, and gripping actions, which require the adaptation of the mechanism to the external constraints, rather than avoid them. To this effect, efforts have been made in building mechanisms that obtain the required degrees of freedom through deformations rather than explicit joints in them. Although the use of many joints provides the required number of degrees of freedom, it does so at the cost of making the system very bulky and complex. With the advent of new polymers, the possibility of building joint-free mechanisms that fulfil the requirements of adaptation has increased. Based on this approach, a Magneto Active Polymer (MAP) material has been developed here at the Texas A\\&M University, in which the actuation is performed by the conversion of electromagnetic energy into mechanical energy. The initial experimentation has proved the vast potential of the use of such a material and a few mechanisms like a magneto active peristaltic pump, have been designed and tested for the first time using this material. In this mechanism, the pumping action is obtained when a moving magnetic field produces peristaltic waves in the magneto active material shaped as a tube. Also for the first time, experiments have been conducted to analyze the response of the MAP material to a pulsating magnetic field with the intent of using the experimental results to develop a model of the MAP. In developing the design for the peristaltic pump and other conceptual models described in this thesis, ideas have been drawn from the different modes of locomotion and actuators present in lower organisms. These have been good sources of inspiration for the work done in this thesis and they have been documented in detail.

Venkataraghavan, Janarthanan T

2001-01-01T23:59:59.000Z

103

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

SciTech Connect

DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn{sup 2+} complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C{sub 2}HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).

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

2012-09-17T23:59:59.000Z

104

Acceleration Mechanisms  

E-Print Network (OSTI)

Glossary I. Background and context of the subject II. Stochastic acceleration III. Resonant scattering IV. Diffusive shock acceleration V. DSA at multiple shocks VI. Applications of DSA VII. Acceleration by parallel electric fields VIII. Other acceleration mechanisms IX. Future directions X. Appendix: Quasilinear equations XI. Bibliography

Melrose, D B

2009-01-01T23:59:59.000Z

105

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

106

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

107

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex  

SciTech Connect

Here we report on a 3.0 {angstrom} crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.

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

2009-01-08T23:59:59.000Z

108

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

SciTech Connect

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

Peng, Jamy C.

2007-05-05T23:59:59.000Z

109

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

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...

110

The Crystal Structure of the Thermus Aquaticus DnaB Helicase Monomer  

Science Conference Proceedings (OSTI)

The ring-shaped hexameric DnaB helicase unwinds duplex DNA at the replication fork of eubacteria. We have solved the crystal structure of the full-length Thermus aquaticus DnaB monomer, or possibly dimer, at 2.9 {angstrom} resolution. DnaB is a highly flexible two domain protein. The C-terminal domain exhibits a RecA-like core fold and contains all the conserved sequence motifs that are characteristic of the DnaB helicase family. The N-terminal domain contains an additional helical hairpin that makes it larger than previously appreciated. Several DnaB mutations that modulate its interaction with primase are found in this hairpin. The similarity in the fold of the DnaB N-terminal domain with that of the C-terminal helicase-binding domain (HBD) of the DnaG primase also includes this hairpin. Comparison of hexameric homology models of DnaB with the structure of the papillomavirus E1 helicase suggests the two helicases may function through different mechanisms despite their sharing a common ancestor.

Bailey,S.; Eliason, W.; Steitz, T.

2007-01-01T23:59:59.000Z

111

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

NLE Websites -- All DOE Office Websites (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

112

Intercalation and buckling instability of DNA linker within locked chromatin fiber  

E-Print Network (OSTI)

The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the nucleosomes are strongly end constrained. Longitudinal thermal fluctuations in these linkers allow intercalative mode of protein binding. We show that mechanical constraints generated in the first stage of the binding process induce linker DNA buckling; buckling in turn modifies the binding energies and activation barriers and creates a force of decondensation at the chromatin fiber level. The unique structure and properties of DNA thus yield a novel physical mechanism of buckling instability that might play a key role in the regulation of gene expression.

Jean-Marc Victor; Eli Ben-Ham; Annick Lesne

2002-11-09T23:59:59.000Z

113

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

E-Print Network (OSTI)

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

Woodruff, Rachel Van Etten

2008-01-01T23:59:59.000Z

114

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

E-Print Network (OSTI)

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

Park, Sunho, 1976-

2009-01-01T23:59:59.000Z

115

Repair of UV damaged DNA, genes and proteins of yeast and human  

Science Conference Proceedings (OSTI)

Our objectives are to determine the molecular mechanism of the incision step of excision repair of ultraviolet (UV) light damaged DNA in eukaryotic organisms, using the yeast Saccharomyces cerevisiae as a model system, as well as studying the human homologs of yeast excision repair and postreplication repair proteins. In addition to its single-stranded DNA-dependent A TPase and DNA helicase activities, we have found that RAD3 protein also possesses DNA-RNA helicase activity, and that like RAD3, the Schizosaccharomyces pombe RAD3 homolog, rhp3{sup +}, is an essential gene. We have overexpressed the human RAD3 homolog, ERCC2, in yeast to facilitate its purification. The RAD10 protein was purified to homogeneity and shown to bind DNA. ERCC3y, the yeast homolog of the human ERCC-3/XP-B gene, has been sequenced and shown to be essential for viability. The Drosophila and human homologs of RAD6, required for postreplication repair and UV induced mutagenesis, were shown to complement the rad6 {Delta} mutation of yeast. Since defective DNA repair and enhanced neoplasia characterize several human genetic diseases, and repair proteins are highly conserved between yeast and man, a thorough understanding of the molecular mechanisms of DNA repir in yeast should provide a better understanding of the causes of carcinogenesis.

Prakash, L.

1991-04-01T23:59:59.000Z

116

INDEXING MECHANISM  

DOE Patents (OSTI)

A device is presented for loading and unloading fuel elements containing material fissionable by neutrons of thermal energy. The device comprises a combination of mechanical features Including a base, a lever pivotally attached to the base, an Indexing plate on the base parallel to the plane of lever rotation and having a plurality of apertures, the apertures being disposed In rows, each aperture having a keyway, an Index pin movably disposed to the plane of lever rotation and having a plurality of apertures, the apertures being disposed in rows, each aperture having a keyway, an index pin movably disposed on the lever normal to the plane rotation, a key on the pin, a sleeve on the lever spaced from and parallel to the index pin, a pair of pulleys and a cable disposed between them, an open collar rotatably attached to the sleeve and linked to one of the pulleys, a pin extending from the collar, and a bearing movably mounted in the sleeve and having at least two longitudinal grooves in the outside surface.

Kock, L.J.

1959-09-22T23:59:59.000Z

117

Preparation Of Dna-Containing Extract For Pcr Amplification  

NLE Websites -- All DOE Office Websites (Extended Search)

Preparation Of Dna-Containing Extract For Pcr Amplification Preparation Of Dna-Containing Extract For Pcr Amplification The method may provide a DNA-containing extract sufficiently...

118

Mechanical Design  

SciTech Connect

The particle beam of the SXR (soft x-ray) beam line in the LCLS (Linac Coherent Light Source) has a high intensity in order to penetrate through samples at the atomic level. However, the intensity is so high that many experiments fail because of severe damage. To correct this issue, attenuators are put into the beam line to reduce this intensity to a level suitable for experimentation. Attenuation is defined as 'the gradual loss in intensity of any flux through a medium' by [1]. It is found that Beryllium and Boron Carbide can survive the intensity of the beam. At very thin films, both of these materials work very well as filters for reducing the beam intensity. Using a total of 12 filters, the first 9 being made of Beryllium and the rest made of Boron Carbide, the beam's energy range of photons can be attenuated between 800 eV and 9000 eV. The design of the filters allows attenuation for different beam intensities so that experiments can obtain different intensities from the beam if desired. The step of attenuation varies, but is relative to the thickness of the filter as a power function of 2. A relationship for this is f(n) = x{sub 0}2{sup n} where n is the step of attenuation desired and x{sub 0} is the initial thickness of the material. To allow for this desired variation, a mechanism must be designed within the test chamber. This is visualized using a 3D computer aided design modeling tool known as Solid Edge.

2010-08-25T23:59:59.000Z

119

Silencing and recombination in yeast ribosomal DNA  

E-Print Network (OSTI)

A bioinformatic and laboratory investigation into S. cerevisiae's system for the maintenance and homogenization of rDNA. Eliminating mutations and heterogeneity in rDNA repeats is necessary evolutionarily, but harmful to ...

O'Kelly, Michael J. T

2008-01-01T23:59:59.000Z

120

Generalized Poland-Scheraga model for DNA hybridization  

E-Print Network (OSTI)

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the same index along the strands are allowed to bind. In this paper, we extend this model by relaxing these constraints: We propose a generalization of the PS model which allows for the binding of two strands of unequal lengths $N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the effect of mismatches on the hybridization of complementary strands (ii) the hybridization of non complementary strands (as resulting from point mutations) of unequal lengths $N_{1}$ and $N_{2}$. The use of a Fixman-Freire scheme scales down the computational complexity of our algorithm from $O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary strands of a few kbps yields results almost identical to the PS model. For short strands of equal or unequal lengths, the binding displays a strong sensitivity to mutations. This model may be relevant to the experimental protocol in DNA microarrays, and more generally to the molecular recognition of DNA fragments. It also provides a physical implementation of sequence alignments.

Thomas Garel; Henri Orland

2004-02-18T23:59:59.000Z

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


121

Low-cost, Rapid DNA Sequencing Technique  

Sequencing DNA is crucial for future breakthroughs in biological and biomedical research. Until now, ... The nucleic acid strand transport

122

Topics and Techniques in Forensic DNA Analysis  

Science Conference Proceedings (OSTI)

... Topics and Techniques for Forensic DNA Analysis NYC OCME Dept of Forensic Biology ... NIST Human Identity Project Leader (1999-present) ...

2012-04-17T23:59:59.000Z

123

Quantum Dot Fluorescence Lifetime Engineering with DNA ...  

Science Conference Proceedings (OSTI)

Quantum Dot Fluorescence Lifetime Engineering with DNA Origami ... such as metal nanoparticles and semiconductor quantum dots is challenging ...

124

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

125

Magnetic tweezers to study DNA motors  

E-Print Network (OSTI)

Magnetic tweezers to study DNA motors Maria Mañosas Ritort lab UB Barcelona Croquette-Bensimon lab ENS France #12;· Introduction to MT (magnetic tweezers) · Applications: 1. Tracking DNA motors: (i) Helicases (ii) Annealing motor 2. Studying a multiprotein system: DNA replication Outline #12;· Atomic force

Ritort, Felix

126

Data hiding methods based upon DNA sequences  

Science Conference Proceedings (OSTI)

In this paper, three data hiding methods are proposed, based upon properties of DNA sequences. It is highlighted that DNA sequences possess some interesting properties which can be utilized to hide data. These three methods are: the Insertion Method, ... Keywords: Complementary pair, DNA, Data hiding, Data recovery

H. J. Shiu; K. L. Ng; J. F. Fang; R. C. T. Lee; C. H. Huang

2010-06-01T23:59:59.000Z

127

Probe and method for DNA detection  

SciTech Connect

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

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

2013-07-02T23:59:59.000Z

128

DNA repair in cells sensitive and resistant to cis-diamminedichloroplatinum(II): Host cell reactivation of damaged plasmid DNA  

SciTech Connect

cis-Diamminedichloroplatinum(II) (cis-DDP) has a broad clinical application as an effective anticancer drug. However, development of resistance to the cytotoxic effects is a limiting factor. In an attempt to understand the mechanism of resistance, the authors have employed a host cell reactivation assay of DNA repair using a cis-DDP-damaged plasmid vector. The efficiency of DNA repair was assayed by measuring the activity of an enzyme coded for by the plasmid vector. The plasmid expression vector pRSV cat contains the bacterial gene coding for chloramphenicol acetyltransferase (CAT) in a configuration which permits expression in mammalian cells. The plasmid was transfected into repair-proficient and -deficient Chinese hamster ovary cells, and CAT activity was subsequently measured in cell lysates. In the repair-deficient cells, one cis-DDP adduct per cat gene was sufficient to eliminate expression. An equivalent inhibition of CAT expression in the repair-proficient cells did not occur until about 8 times the amount of damage was introduced into the plasmid. These results implicate DNA intrastrand cross-links as the lesions responsible for the inhibition of CAT expression. This assay was used to investigate the potential role of DNA repair in mediating cis-DDP resistance in murine leukemia L1210 cells. The assay readily detects the presence or absence of repair and confirms that these resistant L1210 cells have an enhanced capacity for repair of cis-DDP-induced intrastrand cross-links.

Sheibani, N.; Jennerwein, M.M.; Eastman, A. (Univ. of Nebraska Medical Center, Omaha (USA))

1989-04-04T23:59:59.000Z

129

Physicalism versus quantum mechanics  

E-Print Network (OSTI)

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

Stapp, Henry P; Theoretical Physics Group; Physics Division

2009-01-01T23:59:59.000Z

130

Binary electrokinetic separation of target DNA from background DNA primers.  

Science Conference Proceedings (OSTI)

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

James, Conrad D.; Derzon, Mark Steven

2005-10-01T23:59:59.000Z

131

Fleet DNA Project (Fact Sheet)  

SciTech Connect

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

Not Available

2012-10-01T23:59:59.000Z

132

Human Genome Research: Decoding DNA  

NLE Websites -- All DOE Office Websites (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.

133

Translationally Controlled Tumor Protein Protects against DNA Damage in Low  

NLE Websites -- All DOE Office Websites (Extended Search)

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

134

Calculation of complex DNA damage induced by ions  

SciTech Connect

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

Surdutovich, Eugene [Department of Physics, Oakland University, Rochester, Michigan 48309 (United States); Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main (Germany); Gallagher, David C. [Department of Physics, Oakland University, Rochester, Michigan 48309 (United States); Solov'yov, Andrey V. [Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main (Germany)

2011-11-15T23:59:59.000Z

135

Channel plate for DNA sequencing  

DOE Patents (OSTI)

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

Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

1998-01-01T23:59:59.000Z

136

Channel plate for DNA sequencing  

DOE Patents (OSTI)

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

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

1998-01-13T23:59:59.000Z

137

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

138

Single Cell Mechanics BIOMATERIALS  

E-Print Network (OSTI)

Single Cell Mechanics BIOMATERIALS Our goal is to develop fundamental tools to measure the response of live cells to mechanical stimulation. The mechanisms by which cells convert mechanical forces evaluate the underlying mechanisms of cell mechanics. Objective Impact and Customers · Cancer, heart

139

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation  

SciTech Connect

DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.

Song, Jikui; Teplova, Marianna; Ishibe-Murakami, Satoko; Patel, Dinshaw J. (MSKCC)

2012-03-26T23:59:59.000Z

140

The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways  

Science Conference Proceedings (OSTI)

Reactivation of repaired DNA replication forks is essential for complete duplication of bacterial genomes. However, not all bacteria encode homologs of the well-studied Escherichia coli DNA replication restart primosome proteins, suggesting that there might be distinct mechanistic differences among DNA replication restart pathways in diverse bacteria. Since reactivation of repaired DNA replication forks requires coordinated DNA and protein binding by DNA replication restart primosome proteins, we determined the crystal structure of Neisseria gonorrhoeae PriB at 2.7 {angstrom} resolution and investigated its ability to physically interact with DNA and PriA helicase. Comparison of the crystal structures of PriB from N. gonorrhoeae and E. coli reveals a well-conserved homodimeric structure consisting of two oligosaccharide/oligonucleotide-binding (OB) folds. In spite of their overall structural similarity, there is significant species variation in the type and distribution of surface amino acid residues. This correlates with striking differences in the affinity with which each PriB homolog binds single-stranded DNA and PriA helicase. These results provide evidence that mechanisms of DNA replication restart are not identical across diverse species and that these pathways have likely become specialized to meet the needs of individual organisms.

Dong, Jinlan; George, Nicholas P.; Duckett, Katrina L.; DeBeer, Madeleine A.P.; Lopper, Matthew E. (UDRI); (UW-MED)

2010-05-25T23:59:59.000Z

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


141

Searching fast for a target on a DNA without falling to traps  

E-Print Network (OSTI)

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other non-specific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox by allowing the target sites to be located by proteins within short time scales even in the presence of traps. Our theoretical analysis shows that the mechanism is robust in the presence of generic disorder in the DNA sequence and does not require a specially designed target site.

O. Bnichou; Y. Kafri; M. Sheinman; R. Voituriez

2009-01-27T23:59:59.000Z

142

DNA Sequencing Using capillary Electrophoresis  

Science Conference Proceedings (OSTI)

The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other application papers of sequencing up to this level were also published in the mid 1990's. A major interest of the sequencing community has always been read length. The longer the sequence read per run the more efficient the process as well as the ability to read repeat sequences. We therefore devoted a great deal of time to studying the factors influencing read length in capillary electrophoresis, including polymer type and molecule weight, capillary column temperature, applied electric field, etc. In our initial optimization, we were able to demonstrate, for the first time, the sequencing of over 1000 bases with 90% accuracy. The run required 80 minutes for separation. Sequencing of 1000 bases per column was next demonstrated on a multiple capillary instrument. Our studies revealed that linear polyacrylamide produced the longest read lengths because the hydrophilic single strand DNA had minimal interaction with the very hydrophilic linear polyacrylamide. Any interaction of the DNA with the polymer would lead to broader peaks and lower read length. Another important parameter was the molecular weight of the linear chains. High molecular weight (> 1 MDA) was important to allow the long single strand DNA to reptate through the entangled polymer matrix. In an important paper, we showed an inverse emulsion method to prepare reproducibility linear polyacrylamide polymer with an average MWT of 9MDa. This approach was used in the polymer for sequencing the human genome. Another critical factor in the successful use of capillary electrophoresis for sequencing was the sample preparation method. In the Sanger sequencing reaction, high concentration of salts and dideoxynucleotide remained. Since the sample was introduced to the capillary column by electrokinetic injection, these salt ions would be favorably injected into the column over the sequencing fragments, thus reducing the signal for longer fragments and hence reading read length. In two papers, we examined the role of individual components from the sequencing reaction and then developed a protocol to reduce the deleterio

Dr. Barry Karger

2011-05-09T23:59:59.000Z

143

Enhancing the DNA Patent Database  

Science Conference Proceedings (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

144

DNA-guided nanoparticle assemblies  

DOE Patents (OSTI)

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

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

2013-07-16T23:59:59.000Z

145

Immunoglobulin motif DNA recognition and  

E-Print Network (OSTI)

binding domains of NF-kB, NFAT1, p53 and the STAT proteins. NMR spectroscopy of a 43.6 kD RD­b­DNA ternary for NF-kB3-4, the nuclear factor of acti- vated T-cells NFAT1 (refs 5,6), STAT1 (ref. 7) and STAT3b8 72 and Ser 73. In con- trast, the N-terminus of NF-kB3-4 and NFAT1 (refs 5, 6) loops around

Sali, Andrej

146

DNA sequencing using fluorescence background electroblotting membrane  

DOE Patents (OSTI)

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

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

1992-01-01T23:59:59.000Z

147

DNA sequencing using fluorescence background electroblotting membrane  

DOE Patents (OSTI)

A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

1992-05-12T23:59:59.000Z

148

Precision Biochemistry Tracks DNA Damage in Fish  

Science Conference Proceedings (OSTI)

... Like coal-mine canaries, fish DNA can serve as a measure of the biological impact of water and sediment pollutionor pollution clean-up. ...

2012-10-17T23:59:59.000Z

149

Topics in Forensic DNA Analysis & Interpretation  

Science Conference Proceedings (OSTI)

... Experience University of Virginia/FBI Laboratory (1992-1995) Work ... Most forensic DNA laboratories follow PCR ... for the polymer) If a lab is not ...

2011-03-24T23:59:59.000Z

150

Available Technologies: Highly Selective, Highly Efficient DNA ...  

... applications where extraction of minute amounts of DNA plays a critical role, such as in basic and applied molecular biology research, bioforensics, ...

151

Overview of DNA Programs at NIST  

Science Conference Proceedings (OSTI)

... during the PCR amplification process This is highly affected by DNA quantity and quality ... PCR inhibitors present in the sample may reduce PCR ...

2013-04-10T23:59:59.000Z

152

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

E-Print Network (OSTI)

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

Ng, Jin Kiat

153

MECHANICAL TESTING OF CARBON STEEL IN HIGH PRESSURE HYDROGEN  

DOE Green Energy (OSTI)

The methods and interim results from a testing program to quantify hydrogen effects on mechanical properties of carbon steel pipeline and pipeline weld materials are provided. The scope is carbon steels commonly used for natural gas pipelines in the United States that are candidates for hydrogen service in the hydrogen economy. The mechanical test results will be applied in future analyses to evaluate service life of the pipelines. The results are also envisioned to be part of the bases for construction codes and structural integrity demonstrations for hydrogen service pipeline and vessels. Tensile properties of one type of steel (A106 Grade B) in base metal, welded and heat affected zone conditions were tested at room temperature in air and high pressure (1500 psig) hydrogen. A general reduction in the materials ability to plastically deform was noted in this material when specimens were tested in 1500 psig hydrogen. Furthermore, the primary mode of fracture was changed from ductile rupture in air to cleavage with secondary tearing in hydrogen. The mechanical test program will continue with tests to quantify the fracture behavior in terms of J-R curves for these materials at air and hydrogen pressure conditions.

Duncan, A

2006-05-11T23:59:59.000Z

154

MechanicalTesting  

NLE Websites -- All DOE Office Websites (Extended Search)

structures, validation of encapsulant cure stress models, development of frac- ture mechanics tests for use in adhesion studies and understanding the failure mechanism of...

155

1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report  

SciTech Connect

This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair.

1999-02-12T23:59:59.000Z

156

Synthesis, Characterization and Reactivity of Fe Complexes Containing Cyclic Diazadiphosphine Ligands: The Role of the Pendant Base in Heterolytic Cleavage of H2  

Science Conference Proceedings (OSTI)

The iron complexes CpFe(PPh2NBn2)Cl (1-Cl), CpFe(PPh2NPh2)Cl (2-Cl), CpFe(PPh2C5)Cl (3-Cl) (where PPh2NBn2 is 1,5-dibenzyl-1,5-diaza-3,7-diphenyl-3,7-diphosphacyclooctane, PPh2NPh2 is 1,3,5,7-tetraphenyl-1,5-diaza-3,7-diphosphacyclooctane, and PPh2C5 is 1,4-diphenyl-1,4-diphosphacycloheptane) have been synthesized and characterized by NMR spectroscopy, electrochemical studies, and X-ray diffraction studies. These chloride derivatives are readily converted to the corresponding hydride complexes CpFe(PPh2NBn2)H (1-H), CpFe(PPh2NPh2)H (2-H), CpFe(PPh2C5)H (3-H)] and H2 complexes [CpFe(PPh2NBn2)(H2)]BArF4, [1-H2]BArF4, (where BArF4 is B[(3,5-(CF3)2C6H3)4]?), [CpFe(PPh2NPh2)(H2)]BArF4, [2-H2]BArF4, and [CpFe(PPh2C5)(H2)]BArF4, [3-H2]BArF4 as well as [CpFe(PPh2NBn2)(CO)]BArF4, [1-CO]BArF4. Structural studies are reported for [1-H2]BArF4, 1-H, 2-H, and [1-CO]BArF4. The conformations adopted by the chelate rings of the PPh2NBn2 ligand in the different complexes are determined by attractive or repulsive interactions between the sixth ligand of these pseudo-octahedral complexes and the pendant N atom of the ring adjacent to the sixth ligand. An example of an attractive interaction is the observation that the distance between the N atom of the pendant amine and the C atom of the coordinated CO ligand for [1-CO]BArF4 is 2.848 , considerably shorter than the sum of the van der Waals radii of N and C atoms. Experimental and theoretical studies of H/D exchange by the complexes [1-H2]+, [2-H2]+, and [3-H2]+ indicate that the relatively rapid exchange observed for [1-H2]+ and [2-H2]+ compared to [3-H2]+ is consistent with intramolecular heterolytic cleavage of H2 mediated by the pendant amine. These mononuclear FeII dihydrogen complexes containing pendant amines in the ligands mimic crucial features of the distal Fe site of the active site of the [FeFe] hydrogenase required for H-H bond formation and cleavage. We thank the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences and Geosciences, for support of this research. S.C. (DFT computations) and M. J. O. (NMR experiments) were supported by the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under FWP 56073. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Liu, Tianbiao L.; Chen, Shentan; O'Hagan, Molly J.; Rakowski DuBois, Mary; Bullock, R. Morris; DuBois, Daniel L.

2012-04-11T23:59:59.000Z

157

Recombinant DNA encoding a desulfurization biocatalyst  

DOE Patents (OSTI)

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

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

1994-01-01T23:59:59.000Z

158

Recombinant DNA encoding a desulfurization biocatalyst  

DOE Patents (OSTI)

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

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

1994-10-18T23:59:59.000Z

159

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (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.

160

Slow closure of denaturation bubbles in DNA: twist matters  

E-Print Network (OSTI)

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

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

2013-02-07T23:59:59.000Z

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


161

Allosteric Modulation of DNA by Small Molecules  

NLE Websites -- All DOE Office Websites (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.

162

Storing data encoded DNA in living organisms  

DOE Patents (OSTI)

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

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

2006-06-06T23:59:59.000Z

163

Method for sequencing DNA base pairs  

DOE Patents (OSTI)

The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

Sessler, A.M.; Dawson, J.

1993-12-14T23:59:59.000Z

164

Improved method for sequencing DNA base pairs  

DOE Patents (OSTI)

The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 1 ref.

Sessler, A.M.; Dawson, J.

1990-12-31T23:59:59.000Z

165

Improved method for sequencing DNA base pairs  

DOE Patents (OSTI)

The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 1 ref.

Sessler, A.M.; Dawson, J.

1990-01-01T23:59:59.000Z

166

Flow cytometric detection method for DNA samples  

Science Conference Proceedings (OSTI)

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

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

2011-07-05T23:59:59.000Z

167

Flow cytometric detection method for DNA samples  

DOE Patents (OSTI)

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

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

2006-08-01T23:59:59.000Z

168

Flow cytometric detection method for DNA samples  

DOE Patents (OSTI)

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

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

2011-07-05T23:59:59.000Z

169

CARTESIAN MECHANICS* Sophie Roux  

E-Print Network (OSTI)

1 CARTESIAN MECHANICS* Sophie Roux (Centre Alexandre Koyré, EHESS, Paris) Introduction For many the search for a mathematical treatment of phenomena, on the other hand the demand for mechanical as the typical mechanical philosopher, and contrasted as such to the founder of mechanics as a science, namely

Paris-Sud XI, Université de

170

INTRODUCTION TO THE MECHANICS  

E-Print Network (OSTI)

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

Kaminski, Edouard

171

Mechanism of pressure welding  

SciTech Connect

Thesis. The mechanism in polycrystalline aluminum, copper, silver, and gold was investigated. (19 figures) (DLC)

Mohamed, H.A.E.F.

1973-12-01T23:59:59.000Z

172

Graduate quantum mechanics reform  

Science Conference Proceedings (OSTI)

We address four main areas in which graduatequantum mechanics education can be improved: course content

L. D. Carr; S. B. McKagan

2009-01-01T23:59:59.000Z

173

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 +

174

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (Extended Search)

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...

175

DNA damage responses in the context of the cell division cycle  

E-Print Network (OSTI)

and binds to human Chk1 235 61. Strategy for the design of Rad9-h/ggMCPH1 hybrid constructs 237 LIST OF DIAGRAMS 1. Possible mechanisms of action of the CMG helicase complex during DNA unwinding Pg... helicase. Indeed, the MCM complex remains associated with the fork during S-phase and plays a role ahead of the fork as an helicase to unwind the DNA duplex, with a 3 to 5 polarity shown for the archaeal MCM (Kelman et al., 1999; Chong et al., 2000...

Giunta, Simona

2010-11-16T23:59:59.000Z

176

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

Science Conference Proceedings (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

177

The Molecular Mechanism of Stretch Activation in Insect Muscle | Advanced  

NLE Websites -- All DOE Office Websites (Extended Search)

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

178

Electronic transport and localization in short and long DNA  

E-Print Network (OSTI)

The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations. Here, we review recent theoretical progress by concentrating on quantum-chemical, molecular dynamics-based approaches to short DNA strands and physics-motivated tight-binding transport studies of long or even complete DNA sequences. In both cases, we observe small, but significant differences between specific DNA sequences such as periodic repetitions and aperiodic sequences of AT bases, lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.

H. Wang; R. Marsh; J. P. Lewis; R. A. Roemer

2005-11-04T23:59:59.000Z

179

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

Description Sequencing DNA is crucial for future breakthroughs in biological and biomedical research. ... DNA sequencing for medical applications has been restricted ...

180

NREL: Fleet Test and Evaluation - Fleet DNA: Vehicle Drive Cycle...  

NLE Websites -- All DOE Office Websites (Extended Search)

Fleet DNA Project graphic depicting a trail of data emerging from trucks. Fleet DNA helps vehicle manufacturers and fleet managers understand the broad operational range for many...

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


181

Computational Challenges in Simulating Large DNA over Long Times  

Science Conference Proceedings (OSTI)

Simulating DNAs dynamics requires a sophisticated array of algorithms appropriate for DNAs impressive spectrum of spatial and temporal levels. The authors describe computational challenges

Tamar Schlick; Daniel A. Beard; Jing Huang; Daniel A. Strahs; Xiaoliang Qian

2000-01-01T23:59:59.000Z

182

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (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.

183

The Initiation of Bacterial DNA Replication  

NLE Websites -- All DOE Office Websites (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.

184

NSLS Mechanical Tech  

NLE Websites -- All DOE Office Websites (Extended Search)

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

185

Method of quantitating dsDNA  

DOE Patents (OSTI)

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

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

2002-01-01T23:59:59.000Z

186

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

Science Conference Proceedings (OSTI)

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

GRAHAM, DAVID A.

2013-10-10T23:59:59.000Z

187

Internal pipe attachment mechanism  

DOE Patents (OSTI)

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

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

1994-12-13T23:59:59.000Z

188

Torque determination on DNA with magnetic tweezers  

E-Print Network (OSTI)

We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces (F>1 pN) this method, which is simple and does not require a sophisticated set-up, allows for lower force estimates. We used this approach to deduce the effective torsional modulus of DNA, which decreases with force and to estimate the buckling torque of DNA as a function of force in various salt conditions.

Francesco Mosconi; Jean-Franois Allemand; David Bensimon; Vincent Croquette

2008-09-03T23:59:59.000Z

189

Structural basis for DNA bending  

Science Conference Proceedings (OSTI)

The authors report proton NMR studies on DNA oligonucleotides that contain A tracts of lengths known to produce various degrees of bending. Spectra of duplexes in the series 5{prime}-(GGCA{sub n}CGG){center dot}(CCGT{sub n}GCC) (n = 3,4,5,7,9) reveal substantial structural changes within the A{sub n}{center dot}T{sub n} tract as its length is increased. Chemical-shift comparisons show that A tracts with fewer than about seven members do not contain regions of uniform structure. Throughout the series, there is a striking monotonic relationship between the location of an A{center dot}T pair in the A tract and the relative position of its ThyH3 resonance. The direction of this chemical-shift dispersion is opposite to that expected from consideration of ring-current effects alone. This model features a substantial negative base-pair tilt, which has been suggested previously as the source of A-tract bending. In contrast, the nuclear Overhauser effect distances are inconsistent with at least one known crystallographic A-tract structure which lacks appreciable base-pair tilt.

Nadeau, J.G.; Crothers, D.M. (Yale Univ., New Haven, CT (USA))

1989-04-01T23:59:59.000Z

190

The Department of Mechanical Engineering --Engineering Mechanics  

E-Print Network (OSTI)

, Missile, Research, Development and Engineering Directorate's Propulsion Iaborato'. Ills primaly areas of research are in numerical combustion, and the thermal and mechanical aging ofnitrate esterpropellants decomposition and combustion. Stabilizers are added to the propellants to neutralize the decomposition products

Endres. William J.

191

Compliant mechanism learning toolkit  

E-Print Network (OSTI)

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

Allard, Nicholas (Nicholas A.)

2006-01-01T23:59:59.000Z

192

The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation  

Science Conference Proceedings (OSTI)

Helicases move on DNA via an ATP binding and hydrolysis mechanism coordinated by well-characterized helicase motifs. However, the translocation along single-stranded DNA (ssDNA) and the strand separation of double-stranded (dsDNA) may be loosely or tightly coupled. Dda is a phage T4 SF1B helicase with sequence homology to the Pif1 family of helicases that tightly couples translocation to strand separation. The crystal structure of the Dda-ssDNA binary complex reveals a domain referred to as the pin that was previously thought to remain static during strand separation. The pin contains a conserved phenylalanine that mediates a transient base-stacking interaction that is absolutely required for separation of dsDNA. The pin is secured at its tip by protein-protein interactions through an extended SH3 domain thereby creating a rigid strut. The conserved interface between the pin and the SH3 domain provides the mechanism for tight coupling of translocation to strand separation.

He, Xiaoping; Byrd, Alicia K.; Yun, Mi-Kyung; Pemble IV, Charles W.; Harrison, David; Yeruva, Laxmi; Dahl, Christopher; Kreuzer, Kenneth N.; Raney, Kevin D.; White, Stephen W. (Duke); (SJCH); (Arkansas)

2012-10-16T23:59:59.000Z

193

Why DNA is a double helix  

NLE Websites -- All DOE Office Websites (Extended Search)

Guest14 Location: NA Country: NA Date: NA Question: Why is DNA in a double-helix shape? Replies: The why questions are always the worst. Why is anything the way it is? The...

194

Deoxyribose oxidation chemistry and endogenous DNA adducts  

E-Print Network (OSTI)

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

Zhou, Xinfeng

2006-01-01T23:59:59.000Z

195

Linear Thermodynamics of Rodlike DNA Filtration  

E-Print Network (OSTI)

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

Li, Zirui

196

Everything a Trial Judge Needs to Know about DNA (in a ...  

Science Conference Proceedings (OSTI)

... evidence Paternity testing -- identifying father Missing persons investigations Military DNA dog tag Convicted felon DNA databases ...

2013-06-25T23:59:59.000Z

197

QUICK QUANTUM MECHANICS ---Introduction ---  

E-Print Network (OSTI)

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

Jackson, Andrew D.

198

Multiple tag labeling method for DNA sequencing  

DOE Patents (OSTI)

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

Mathies, Richard A. (Contra Costa County, CA); Huang, Xiaohua C. (Mt. View, CA); Quesada, Mark A. (San Francisco, CA)

1995-01-01T23:59:59.000Z

199

Oligonucleotide and Long Polymeric DNA Encoding  

Science Conference Proceedings (OSTI)

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

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

2003-11-24T23:59:59.000Z

200

HYDRAULIC SERVO CONTROL MECHANISM  

DOE Patents (OSTI)

A hydraulic servo control mechanism of compact construction and low fluid requirements is described. The mechanism consists of a main hydraulic piston, comprising the drive output, which is connected mechanically for feedback purposes to a servo control piston. A control sleeve having control slots for the system encloses the servo piston, which acts to cover or uncover the slots as a means of controlling the operation of the system. This operation permits only a small amount of fluid to regulate the operation of the mechanism, which, as a result, is compact and relatively light. This mechanism is particuiarly adaptable to the drive and control of control rods in nuclear reactors. (auth)

Hussey, R.B.; Gottsche, M.J. Jr.

1963-09-17T23:59:59.000Z

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


201

Mechanical Seal Assembly  

DOE Patents (OSTI)

An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transferring it to the mechanical diode.

Kotlyar, Oleg M.

1999-06-18T23:59:59.000Z

202

Mechanical seal assembly  

DOE Patents (OSTI)

An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transferring it to the mechanical diode.

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

2001-01-01T23:59:59.000Z

203

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (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.

204

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (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.

205

Pyrolysis mechanisms of lignin model compounds  

DOE Green Energy (OSTI)

The flash vacuum pyrolysis of lignin model compounds was studied under conditions optimized for the production of liquid products to provide mechanistic insight into the reaction pathways that lead to product formation. The major reaction products can be explained by cleavage of the C-O either linkage by a free radial or concerted 1,2-elimination.

Britt, P.F.; Buchanan, A.C. III; Cooney, M.J.

1997-06-01T23:59:59.000Z

206

Classifying aging genes into DNA repair or non-DNA repair-related categories  

Science Conference Proceedings (OSTI)

The elderly population in almost every country is growing faster than ever before. However, our knowledge about the aging process is still limited despite decades of studies on this topic. In this report, we focus on the gradual accumulation of DNA damage ... Keywords: DNA-repair, aging, classification, feature selection, random forest

Yaping Fang, Xinkun Wang, Elias K. Michaelis, Jianwen Fang

2013-07-01T23:59:59.000Z

207

Mechanics of Funding matrix  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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

208

Structures and Mechanical Properties  

Science Conference Proceedings (OSTI)

Mar 7, 2013... Refractory High-entropy Alloy: Chien-Chang Juan1; Jien-Wei Yeh1; ... The main wear mechanism was adhesive wear in deionized water,...

209

Mechanical Behavior II  

Science Conference Proceedings (OSTI)

Mar 5, 2013 ... Impact of Cooling Rate on Low Silver Sn-Ag-Cu Solder Interconnect Board Level Mechanical Shock and Thermal Cycling Performance:...

210

Mechanical Behavior I  

Science Conference Proceedings (OSTI)

Mar 5, 2013... (IMC) is essential for understandingthe mechanical behavior of the ... Reliability and by the SHaRE User Facility, Scientific User Facilities...

211

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

212

Mecanica Clasica (Classical Mechanics)  

E-Print Network (OSTI)

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

Rosu, H C

1999-01-01T23:59:59.000Z

213

Quantum Mechanics Measurements, Mutually  

E-Print Network (OSTI)

Quantum Mechanics Measurements, Mutually Unbiased Bases and Finite Geometry Or why six is the first) #12;Quantum Mechanics for Dummies Finite dimensional quantum states are represented by trace one,1 -icS1,1[ ] #12;Quantum systems evolve and are measured. The evolution of a quantum system using

Gruner, Daniel S.

214

Complexation of DNA with Cationic Surfactant  

E-Print Network (OSTI)

Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic acid, allowing the DNA-surfactant complex to approach a negatively charged membrane. The paper develops a theory for solutions composed of polyelectrolyte, salt, and ionic surfactant. The theoretical predictions are compared with the experimental measurements. PACS.05.70.Ce- Thermodynamic functions and equations of state PACS.61.20.Qg- Structure of associated liquids: electrolytes, molten salts, etc. PACS.61.25.Hq- Macromolecular and polymer solutions; polymer melts; swelling Corresponding author;

Paulo S. Kuhn; Marcia C. Barbosa; Yan Levin

1999-01-01T23:59:59.000Z

215

Mechanical code comparator  

DOE Patents (OSTI)

A new class of mechanical code comparators is described which have broad potential for application in safety, surety, and security applications. These devices can be implemented as micro-scale electromechanical systems that isolate a secure or otherwise controlled device until an access code is entered. This access code is converted into a series of mechanical inputs to the mechanical code comparator, which compares the access code to a pre-input combination, entered previously into the mechanical code comparator by an operator at the system security control point. These devices provide extremely high levels of robust security. Being totally mechanical in operation, an access control system properly based on such devices cannot be circumvented by software attack alone.

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

2002-01-01T23:59:59.000Z

216

Structural Mechanics & Solid Mechanics A finite element toolbox to MATLAB  

E-Print Network (OSTI)

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

Ehrhardt, Matthias

217

Conserved XPB Core Structure and Motifs for DNA Unwinding:Implications for Pathway Selection of Transcription or ExcisionRepair  

Science Conference Proceedings (OSTI)

The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with Implications for XPB damage verification in nucleotide excision repair.

Fan, Li; Arval, Andrew S.; Cooper, Priscilla K.; Iwai, Shigenori; Hanaoka, Fumio; Tainer, John A.

2005-04-01T23:59:59.000Z

218

Analysis of Two Widespread Versions of a Bacterial Replicative DNA Polymerase  

E-Print Network (OSTI)

DnaE1-pol subunits and the helicase (DnaB). SSB stands forto each polymerase, a (2) helicase for unwinding DNA into

Guenther, Joel Michael

2010-01-01T23:59:59.000Z

219

Structures of Clamp-Loader Complexes Are Key to DNA Replication  

NLE Websites -- All DOE Office Websites (Extended Search)

of various other cellular pathways, such as DNA repair, cell cycle control, and chromatin structure. Sliding DNA clamps are loaded onto DNA by pentameric clamp-loader...

220

Rotary mechanical latch  

Science Conference Proceedings (OSTI)

A rotary mechanical latch for positive latching and unlatching of a rotary device with a latchable rotating assembly having a latching gear that can be driven to latched and unlatched states by a drive mechanism such as an electric motor. A cam arm affixed to the latching gear interfaces with leading and trailing latch cams affixed to a flange within the drive mechanism. The interaction of the cam arm with leading and trailing latch cams prevents rotation of the rotating assembly by external forces such as those due to vibration or tampering.

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

2012-11-13T23:59:59.000Z

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


221

Quantum Mechanics Without Observers  

E-Print Network (OSTI)

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

W. H. Sulis

2013-02-18T23:59:59.000Z

222

Electronic door locking mechanism  

SciTech Connect

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

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

1997-01-01T23:59:59.000Z

223

Electronic door locking mechanism  

DOE Patents (OSTI)

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

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

1997-10-21T23:59:59.000Z

224

Is quantum mechanics exact?  

SciTech Connect

We formulate physically motivated axioms for a physical theory which for systems with a finite number of degrees of freedom uniquely lead to quantum mechanics as the only nontrivial consistent theory. Complex numbers and the existence of the Planck constant common to all systems arise naturally in this approach. The axioms are divided into two groups covering kinematics and basic measurement theory, respectively. We show that even if the second group of axioms is dropped, there are no deformations of quantum mechanics which preserve the kinematic axioms. Thus, any theory going beyond quantum mechanics must represent a radical departure from the usual a priori assumptions about the laws of nature.

Kapustin, Anton [California Institute of Technology, Pasadena, California 91125 (United States)] [California Institute of Technology, Pasadena, California 91125 (United States)

2013-06-15T23:59:59.000Z

225

STRBase and Information Resources on Forensic DNA  

E-Print Network (OSTI)

Genetics Information Gathering and Sharing · We live in the information age and need to share what we learn a solid foundation for research and future work #12;Applied Genetics Presentation Outline Information of Journals in Our Group Library We now have on-line access to all forensic DNA journals #12;Applied Genetics

226

Physical approaches to DNA sequencing and detection  

E-Print Network (OSTI)

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single nucleotide level. This is in sharp contrast to current techniques and instruments which probe, through chemical elongation, electrophoresis, and optical detection, length differences and terminating bases of strands of DNA. In this Colloquium we review several physical approaches to DNA detection that have the potential to deliver fast and low-cost sequencing. Center-fold to these approaches is the concept of nanochannels or nanopores which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. We emphasize the physics behind these methods and ideas, critically describe their advantages and drawbacks, and discuss future research opportunities in this field.

Michael Zwolak; Massimiliano Di Ventra

2007-08-20T23:59:59.000Z

227

EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA  

E-Print Network (OSTI)

spliced DNA to unspliced genomic DNA. It is written in ANSI C and has been tested under Digital OSF3.2. The spurce code and documentation are available from ftp:// www.sanger.ac.uky ftp/pub / badger/est_genome.2.tar.Z. The prediction of genes in uncharacterized genomic DNA sequence is currently one of the main problems facing sequence annotators. Methods based on de novo prediction, e.g. searching for motifs like the splice-site consensus, or on statistical properties such as biased codon usage, etc. (Solovyev et al., 1994; Hebsgaard et al., 1996) have been only partially successful, and investigators have often found that the surest way of predicting a gene is by alignment with a homologous protein sequence (Birney et al., 1996; Gelfand et al., 1996; Huang and Zhang, 1996), or a spliced gene product [an expressed sequence tag (EST), mRNA or cDNA],

Richard Mott

1997-01-01T23:59:59.000Z

228

RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III  

E-Print Network (OSTI)

Passage Activity of RecQ Helicase and Topo III 28. DiGate,2003 Printed in U.S.A. RecQ Helicase Stimulates Both DNA95616 Together, RecQ helicase and topoisomerase III (Topo

Harmon, Frank G; Brockman, Joel P; Kowalczykowski, Stephen C

2003-01-01T23:59:59.000Z

229

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

E-Print Network (OSTI)

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

Sen, Yi-Heng

2012-01-01T23:59:59.000Z

230

DNA Duplication Revealed in New Beginnings | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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

231

DNA hybridization : fundamental studies and applications in directed assembly  

E-Print Network (OSTI)

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

Bajaj, Manish G. (Manish Gopal)

2005-01-01T23:59:59.000Z

232

Manipulation of cellular DNA repair by early adenovirus proteins  

E-Print Network (OSTI)

of the Bloom's syndrome helicase and its role in recoveryand Ira, G. (2008a). Sgs1 helicase and two nucleases Dna2and Ira, G. (2008b). Sgs1 helicase and two nucleases Dna2

Orazio, Nicole Ise

2010-01-01T23:59:59.000Z

233

International congress on DNA damage and repair: Book of abstracts  

SciTech Connect

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

Not Available

1987-01-01T23:59:59.000Z

234

Mitigating security issues in the evolving DNA synthesis industry  

E-Print Network (OSTI)

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

Turlington, Ralph Donald, III

2013-01-01T23:59:59.000Z

235

Genome scanning : an AFM-based DNA sequencing technique  

E-Print Network (OSTI)

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

Elmouelhi, Ahmed (Ahmed M.), 1979-

2003-01-01T23:59:59.000Z

236

Analysis of the structural changes caused by positive DNA supercoiling  

E-Print Network (OSTI)

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

Barth, Marita Christine

2007-01-01T23:59:59.000Z

237

Building Energy Software Tools Directory: eDNA  

NLE Websites -- All DOE Office Websites (Extended Search)

many small eDNA systems to be deployed in disparate locations and a central eDNA database (at the summary or enterprise level) can provide access to all of the data from the...

238

Lectin cDNA and transgenic plants derived therefrom  

DOE Patents (OSTI)

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

Raikhel, Natasha V. (Okemos, MI)

2000-10-03T23:59:59.000Z

239

Counter Current Multiplier Mechanism  

NLE Websites -- All DOE Office Websites (Extended Search)

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

240

Conservative-Bayesian Mechanisms  

E-Print Network (OSTI)

We put forward a new class of mechanisms. In this extended abstract, we exemplify our approach only for single-good auctions in what we call a conservative-Bayesian setting. (Essentially, no common-knowledge about the ...

Azar, Pablo

2010-09-08T23:59:59.000Z

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


241

Mechanical Testing of Plastics  

Science Conference Proceedings (OSTI)

Table 7   ASTM and ISO mechanical test standards for plastics...by pendulum method D 1938 6383-1 Tear propagation resistance of plastic film and thin

242

Nbs1-dependent binding of Mre11 to adenovirus E4 mutant viral DNA is important for inhibiting DNA replication  

Science Conference Proceedings (OSTI)

Adenovirus (Ad) infections stimulate the activation of cellular DNA damage response and repair pathways. Ad early regulatory proteins prevent activation of DNA damage responses by targeting the MRN complex, composed of the Mre11, Rad50 and Nbs1 proteins, for relocalization and degradation. In the absence of these viral proteins, Mre11 colocalizes with viral DNA replication foci. Mre11 foci formation at DNA damage induced by ionizing radiation depends on the Nbs1 component of the MRN complex and is stabilized by the mediator of DNA damage checkpoint protein 1 (Mdc1). We find that Nbs1 is required for Mre11 localization at DNA replication foci in Ad E4 mutant infections. Mre11 is important for Mdc1 foci formation in infected cells, consistent with its role as a sensor of DNA damage. Chromatin immunoprecipitation assays indicate that both Mre11 and Mdc1 are physically bound to viral DNA, which could account for their localization in viral DNA containing foci. Efficient binding of Mre11 to E4 mutant DNA depends on the presence of Nbs1, and is correlated with a significant E4 mutant DNA replication defect. Our results are consistent with a model in which physical interaction of Mre11 with viral DNA is mediated by Nbs1, and interferes with viral DNA replication.

Mathew, Shomita S. [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States); Bridge, Eileen [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States)], E-mail: BridgeE@muohio.edu

2008-04-25T23:59:59.000Z

243

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

E-Print Network (OSTI)

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

Dmitry B. Uskov; Alexander L. Burin

2008-03-15T23:59:59.000Z

244

REACTOR CONTROL MECHANISM  

DOE Patents (OSTI)

A quick-releasing mechanism is described which may be used to rapidiy drop a device supported from beneath during normal use, such as a safety rod in a nuclear reactor. In accordance with this invention an electrical control signal, such as may be provided by radiation detection or other alarm condition sensing devices, is delivered to an electromagnetic solenoid, the armature of which is coupled to an actuating mechanism. The solenoid is energized when the mechanism is in its upper or cocked position. In such position, the mechanism engages a plurality of retaining balls, forcing them outward into engagement with a shoulder or recess in a corresponding section of a tubular extension on the upheld device. When the control signal to the solenoid suddenly ceases, the armature drops out, allowing the actuating mechanism to move slightly but rapidly under the force of a compressed spring. The weight of the device will urge the balls inward against a beveled portion of the actuating mechanism and away from the engaging section on the tubular extension, thus allowing the upheld device to fall freely under the influence of gravity.

Lane, J.A.; Engberg, R.E.; Welch, J.M.

1959-05-12T23:59:59.000Z

245

Studying DNA translocation in nanocapillaries using single molecule fluorescence  

E-Print Network (OSTI)

We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the accompanying characteristic ionic current blockage. By tracking the motion of individual DNA molecules in the nanocapillary perpendicular to the optical axis and using a model, we can extract an effective mobility constant for DNA in our geometry under high electric fields.

Thacker, Vivek V; Hernndez-Ainsa, Silvia; Bell, Nicholas A W; Keyser, Ulrich F; 10.1063/1.4768929

2013-01-01T23:59:59.000Z

246

Low-cost, Rapid DNA Sequencing Technique - Oak Ridge ...  

Sequencing DNA is crucial for future breakthroughs in biological and biomedical ... Transportation Sciences UT-Battelle, LLC Oak Ridge National ...

247

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

E-Print Network (OSTI)

Magnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to study DNA motorsDNA motorsDNA motorsDNA motors MariaMariaMariaMaria MañosasMañosasMañosasMañosas RitortCroquetteCroquetteCroquette----BensimonBensimonBensimonBensimon lablablablab ENS FranceENS FranceENS FranceENS France #12;· Introduction to MT (magnetic tweezers

Ritort, Felix

248

Transport and Confinement of DNA within Polymer nano ...  

Science Conference Proceedings (OSTI)

Transport and Confinement of DNA within Polymer nano-tubes. Ana Jofre, Rani Kishore, Kris Helmerson. We have recently ...

249

DNA fragment sizing and sorting by laser-induced fluorescence  

DOE Patents (OSTI)

A method is provided for obtaining DNA fingerprints using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a selected sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is directly proportional to the fragment length. Additional dyes can be bound to the DNA piece and DNA fragments to provide information additional to length information. Oligonucleotide specific dyes and/or hybridization probes can be bound to the DNA fragments to provide information on oligonucleotide distribution or probe hybridization to DNA fragments of different sizes.

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

1992-12-31T23:59:59.000Z

250

Fuzzy C-Means Based DNA Motif Discovery  

Science Conference Proceedings (OSTI)

In this paper, we examined the problem of identifying motifs in DNA sequences. Transcription-binding sites, which are functionally significant subsequences, are considered as motifs. In order to reveal such DNA motifs, our method makes use of Fuzzy clustering ... Keywords: DNA Sequences, Fuzzy Clustering, Motif Finding

Mustafa Karabulut; Turgay Ibrikci

2008-09-01T23:59:59.000Z

251

Role of retinoic acid in the modulation of benzo(a)pyrene-DNA adducts in human hepatoma cells: Implications for cancer prevention  

SciTech Connect

Carcinogen-DNA adducts could lead to mutations in critical genes, eventually resulting in cancer. Many studies have shown that retinoic acid (RA) plays an important role in inducing cell apoptosis. Here we have tested the hypothesis that levels of carcinogen-DNA adducts can be diminished by DNA repair and/or by eliminating damaged cells through apoptosis. Our results showed that the levels of total DNA adducts in HepG2 cells treated with benzo(a)pyrene (BP, 2 {mu}M) + RA (1 {mu}M) were significantly reduced compared to those treated with BP only (P = 0.038). In order to understand the mechanism of attenuation of DNA adducts, further experiments were performed. Cells were treated with BP (4 {mu}M) for 24 h to initiate DNA adduct formation, following which the medium containing BP was removed, and fresh medium containing 1 {mu}M RA was added. The cells were harvested 24 h after RA treatment. Interestingly, the levels of total DNA adducts were lower in the BP/RA group (390 {+-} 34) than those in the BP/DMSO group (544 {+-} 33), P = 0.032. Analysis of cell apoptosis showed an increase in BP + RA group, compared to BP or RA only groups. Our results also indicated that attenuation of BP-DNA adducts by RA was not primarily due to its effects on CYP1A1 expression. In conclusion, our results suggest a mechanistic link between cellular apoptosis and DNA adduct formation, phenomena that play important roles in BP-mediated carcinogenesis. Furthermore, these results help understand the mechanisms of carcinogenesis, especially in relation to the chemopreventive properties of nutritional apoptosis inducers.

Zhou Guodong, E-mail: gzhou@ibt.tamhsc.edu [Department of Environmental and Occupational Health, School of Rural Public Health, Texas A and M University System, College Station, Texas (United States); Institute of Biosciences and Technology, Texas A and M University System, Houston, Texas (United States); Richardson, Molly [Department of Environmental and Occupational Health, School of Rural Public Health, Texas A and M University System, College Station, Texas (United States); Fazili, Inayat S. [Department of Pediatrics, Baylor College of Medicine, Houston, Texas (United States); Wang, Jianbo [Institute of Biosciences and Technology, Texas A and M University System, Houston, Texas (United States); Donnelly, Kirby C. [Department of Environmental and Occupational Health, School of Rural Public Health, Texas A and M University System, College Station, Texas (United States); Wang Fen; Amendt, Brad [Institute of Biosciences and Technology, Texas A and M University System, Houston, Texas (United States); Moorthy, Bhagavatula [Department of Pediatrics, Baylor College of Medicine, Houston, Texas (United States)

2010-12-15T23:59:59.000Z

252

Structure of DNA-Bound FEN1 Reveals Mechanism of Action  

NLE Websites -- All DOE Office Websites (Extended Search)

it's also overproduced in many cancers and associated with aggressive tumors. Designing drugs that induce changes in specific structures is the first step in creating more...

253

NMR structure of the N-terminal domain of the replication initiator protein DnaA  

E-Print Network (OSTI)

recruitment of the DnaBC helicase, and the assembly of theDnaA then recruits the DnaB helicase with help from DnaC to

Lowery, Thomas J.

2008-01-01T23:59:59.000Z

254

Jar mechanism energizer  

Science Conference Proceedings (OSTI)

An energizer for use with a jar mechanism incorporated on inner and outer bodies in a well string to assist the jar mechanism in delivering an upward jar to the well string includes longitudinally spaced seal means between the inner and outer bodies forming a chamber for receiving a compressible medium therein. A differential area formed on one of the bodies within the compressible medium chamber compresses a compressible medium in the chamber as the well string is lowered to position the inner and outer bodies so that the jar mechanism is actuated to restrain relative longitudinal movement between the inner and outer bodies to an extended position whereby a pull force may be developed in the well string in one of the bodies. The differential area is responsive to the compressed gas in the chamber to assist the jar mechanism in applying an upward jarring force when the jar mechanism, in response to a predetermined pull force in the well string, releases the bodies for contact to apply an upward force to the well string.

Webb, D. D.; Anderson, E. A.

1985-10-08T23:59:59.000Z

255

Jar mechanism accelerator  

SciTech Connect

This patent describes an accelerator for use with a jar mechanism in a well pipe string to enhance the jarring impact delivered to a stuck object wherein the jar mechanism includes inner and outer members for connection, respectively, between the well pipe string the stuck object. The jar mechanism members are constructed to (1) restrict relative longitudinal movement therebetween to build up energy in the well pipe string and accelerator and then (2) to release the jar mechanism members for unrestrained, free relative longitudinal movement therebetween to engage jarring surfaces on the jar mechanism members for delivering a jarring impact to the stuck object. The accelerator includes: inner and outer telescopically connected members relatively movable longitudinally to accumulate energy in the accelerator; the inner and outer accelerator members each having means for connecting the accelerator in the well pipe string; means associated with the inner and outer members for initially accomodating a predetermined minimum length of unrestrained, free relative longitudinal movement between the inner and outer accelerator members.

Anderson, E.A.; Webb, D.D.

1989-07-11T23:59:59.000Z

256

Mutations Altering the Interplay between GkDnaC Helicase and DNA Reveal an Insight into Helicase Unwinding  

E-Print Network (OSTI)

Replicative helicases are essential molecular machines that utilize energy derived from NTP hydrolysis to move along nucleic acids and to unwind double-stranded DNA (dsDNA). Our earlier crystal structure of the hexameric helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in complex with single-stranded DNA (ssDNA) suggested several key residues responsible for DNA binding that likely play a role in DNA translocation during the unwinding process. Here, we demonstrated that the unwinding activities of mutants with substitutions at these key residues in GkDnaC are 24-fold higher than that of wildtype protein. We also observed the faster unwinding velocities in these mutants using single-molecule experiments. A partial loss in the interaction of helicase with ssDNA leads to an enhancement in helicase efficiency, while their ATPase activities remain unchanged. In strong contrast, adding accessory proteins (DnaG or DnaI) to GkDnaC helicase alters the ATPase, unwinding efficiency and the unwinding velocity of the helicase. It suggests that the unwinding velocity of helicase

Yu-hua Lo; Shih-wei Liu; Yuh-ju Sun; Hung-wen Lizz; Chwan-deng Hsiao

2011-01-01T23:59:59.000Z

257

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

E-Print Network (OSTI)

and complexity. We discuss the design and demonstration of molecular-scale devices that make use of DNA, error-free methods for self-assembly of complex devices out of large number of molecular componentsSelf-assembled DNA Nanostructures and DNA Devices John Reif Harish Chandran Nikhil Gopalkrishnan

Reif, John H.

258

Sequencing Intractable DNA to Close Microbial Genomes  

Science Conference Proceedings (OSTI)

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01T23:59:59.000Z

259

Fast DNA Sequencing via Transverse Electronic Transport  

E-Print Network (OSTI)

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

Johan Lagerqvist; Michael Zwolak; Massimiliano Di Ventra

2006-01-18T23:59:59.000Z

260

Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing  

Science Conference Proceedings (OSTI)

Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 {angstrom} crystal structure of the core domain of Rtt106p, which adopts an unusual 'double pleckstrin homology' domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

Liu, Y.; Huang, H; Zhou, B; Wang, S; Hu, Y; Li, X; Liu, J; Niu, L; Wu, J; et. al.

2010-01-01T23:59:59.000Z

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


261

Breakthrough in fracture mechanics  

SciTech Connect

Fracture mechanics, the science of calculating material characteristics, stress, and flaws in plant equipment to evaluate structural integrity, usually spares the owners of nuclear power plants unnecessary expense. Instead of replacing equipment prematurely or waiting for costly, unscheduled materials failures that can take months to repair and cost thousands of dollars a day for replacement power, utilities use fracture mechanics techniques to carefully consider their options. If analyses show repair is unnecessary, plant operation can confidently be resumed. If repair is required, it can either be done immediately or, if deferrable, be scheduled for a later, more convenient outage.

Lihach, N.

1981-05-01T23:59:59.000Z

262

Experimental unsaturated soil mechanics  

E-Print Network (OSTI)

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

Delage, Pierre

2008-01-01T23:59:59.000Z

263

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

NLE Websites -- All DOE Office Websites (Extended Search)

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

264

When DNA Needs to Stand Up and Be Counted  

NLE Websites -- All DOE Office Websites (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.

265

Organic Data Memory using the DNA Approach  

Science Conference Proceedings (OSTI)

A data preservation problem looms large behind today's information superhighway. During the prehistoric age, humans preserved their knowledge by engraving bones and rocks. About two millenniums ago, people invented paper and started writing and publishing. In today?s electronic age, we use magnetic media and silicon chips to store our data. But bones and rocks erode, paper disintegrates, and electronic memory simply loses its contents into thin air. All these storage media require constant attention to maintain their information content. All of them can easily be destroyed intentionally or accidentally by people or natural disasters. With the large amount of information generated by our society every day, it is time to think of a new generation of data memory. In an effort to search for an inexpensive and lasting data memory, scientists at the Pacific Northwest National Laboratory (PNNL) have investigated the use of deoxyribonucleic acid--commonly known as DNA--as an information storage medium since 1998. The ambitious goal is to develop a data memory technology that has a life expectancy much longer than any of the existing ones. The creation of our initial DNA memory prototype consists of four major steps: encoding meaningful information as artificial DNA sequences, transforming the sequences to living organisms, allowing the organisms to grow and multiply, and eventually extracting the information back from the organisms. This article describes the objective of our investigation, followed by a brief description of our recent experiments and several potential applications being considered at PNNL.

Wong, Pak C.; Wong, Kwong K.; Foote, Harlan P.

2003-01-01T23:59:59.000Z

266

Low Dose Radiation Research Program: Assessing Biological Function of DNA  

NLE Websites -- All DOE Office Websites (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

267

STATISTICAL MECHANICS AND FIELD THEORY  

E-Print Network (OSTI)

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

Samuel, S.A.

2010-01-01T23:59:59.000Z

268

Low Dose Radiation Research Program: Genetic Mechanisms of Induced  

NLE Websites -- All DOE Office Websites (Extended Search)

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

269

DEPARTMENT OF MECHANICAL ENGINEERING  

E-Print Network (OSTI)

the Chair Advanced Power Systems Research Group Engineering Education Innovation Research Group Mechanics of MultiScale Materials Research Group MultiScale Systems and Sensors Research Group Space Systems Research Group Sustainable Manufacturing and Design Research Group Faculty Profiles Michigan

Endres. William J.

270

MECHANICAL TEST LAB CAPABILITIES  

E-Print Network (OSTI)

MECHANICAL TEST LAB CAPABILITIES · Static and cyclic testing (ASTM and non-standard) · Impact drop testing · Slow-cycle fatigue testing · High temperature testing to 2500°F · ASTM/ Boeing/ SACMA standard testing · Ability to design and fabricate non-standard test fixtures and perform non-standard tests

271

Higgs Mechanism for Gravitons  

E-Print Network (OSTI)

Just like the vector gauge bosons in the gauge theories, it is now known that gravitons acquire mass in the process of spontaneous symmetry breaking of diffeomorphisms through the condensation of scalar fields. The point is that we should find the gravitational Higgs mechanism such that it results in massive gravity in a flat Minkowski space-time without non-unitary propagating modes. This is usually achieved by including higher-derivative terms in scalars and tuning the cosmological constant to be a negative value in a proper way. Recently, a similar but different gravitational Higgs mechanism has been advocated by Chamseddine and Mukhanov where one can relax the negative cosmological constant to zero or positive one. In this work, we investigate why the non-unitary ghost mode decouples from physical Hilbert space in a general space-time dimension. Moreover, we generalize the model to possess an arbitrary potential and clarify under what conditions the general model exhibits the gravitational Higgs mechanism. By searching for solutions to the conditions, we arrive at two classes of potentials exhibiting gravitational Higgs mechanism. One class includes the model by Chamseddine and Mukhanov in a specific case while the other is completely a new model.

Ichiro Oda

2010-03-07T23:59:59.000Z

272

SAFETY-MECHANICAL STANDARDS  

SciTech Connect

Hanford Atomic Production Operation specification guides and standards for plumbing, chemical ngineering, mechanical engineering, sanitary engineering, exhaust systems, steam engineering, stainless steel, dry boxes, thermal insulation, filtration, and materials testing are presented. Details of this manual are given in TID-4100 (Suppl.). (N.W.R.)

1964-10-31T23:59:59.000Z

273

Fractals and quantum mechanics  

Science Conference Proceedings (OSTI)

A new application of a fractal concept to quantum physics has been developed. The fractional path integrals over the paths of the Lvy flights are defined. It is shown that if fractality of the Brownian trajectories leads to standard quantum mechanics

Nick Laskin

2000-01-01T23:59:59.000Z

274

Quantum Mechanics and Black Holes  

E-Print Network (OSTI)

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

Jose N. Pecina-Cruz

2005-11-11T23:59:59.000Z

275

On the distribution of DNA translocation times in solid-state nanopores: an analysis using Schrodinger's first-passage-time theory  

E-Print Network (OSTI)

In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this 1D linear translocation model is equivalent to the one that was considered by Schrodinger [3] for the Enrenhaft-Millikan measurements [4,5] on electron charge. Here we apply Schrodinger's first-passage-time distribution formula to the data set in [1]. It is found that Schrodinger's formula can be used to describe the time distribution of DNA translocation in solid-state nanopores. These fittings yield two useful parameters: drift velocity of DNA translocation and diffusion constant of DNA inside the nanopore. The results suggest two regimes of DNA translocation: (I) at low voltages, there are clear deviations from Smoluchowski's linear law of electrophoresis [6] which we attribute to the entropic barrier effects; (II) at high voltages, the translocation velocity is a linear function of the applied electric field. In regime II, the apparent diffusion constant exhibits a quadratic dependence on applied electric field, suggesting a mechanism of Taylor dispersion effect likely due the electro-osmotic flow field in the nanopore channel. This analysis yields a dispersion-free diffusion constant value for the segment of DNA inside the nanopore which is in agreement with Stokes-Einstein theory quantitatively. The implication of Schrodinger's formula for DNA sequencing is discussed.

Daniel Y. Ling; X. S. Ling

2013-06-11T23:59:59.000Z

276

Lithium chloride protects retinal neurocytes from nutrient deprivation by promoting DNA non-homologous end-joining  

SciTech Connect

Lithium chloride is a therapeutic agent for treatment of bipolar affective disorders. Increasing numbers of studies have indicated that lithium has neuroprotective effects. However, the molecular mechanisms underlying the actions of lithium have not been fully elucidated. This study aimed to investigate whether lithium chloride produces neuroprotective function by improving DNA repair pathway in retinal neurocyte. In vitro, the primary cultured retinal neurocytes (85.7% are MAP-2 positive cells) were treated with lithium chloride, then cultured with serum-free media to simulate the nutrient deprived state resulting from ischemic insult. The neurite outgrowth of the cultured cells increased significantly in a dose-dependent manner when exposed to different levels of lithium chloride. Genomic DNA electrophoresis demonstrated greater DNA integrity of retinal neurocytes when treated with lithium chloride as compared to the control. Moreover, mRNA and protein levels of Ligase IV (involved in DNA non-homologous end-joining (NHEJ) pathway) in retinal neurocytes increased with lithium chloride. The end joining activity assay was performed to determine the role of lithium on NHEJ in the presence of extract from retinal neurocytes. The rejoining levels in retinal neurocytes treated with lithium were significantly increased as compared to the control. Furthermore, XRCC4, the Ligase IV partner, and the transcriptional factor, CREB and CTCF, were up-regulated in retinal cells after treating with 1.0 mM lithium chloride. Therefore, our data suggest that lithium chloride protects the retinal neural cells from nutrient deprivation in vitro, which may be similar to the mechanism of cell death in glaucoma. The improvement in DNA repair pathway involving in Ligase IV might have an important role in lithium neuroprotection. This study provides new insights into the neural protective mechanisms of lithium chloride.

Zhuang Jing; Li Fan; Liu Xuan; Liu Zhiping; Lin Jianxian [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 S Xianlie Road, Guangzhou, Guangdong 510060 (China); Ge Yihong [Department of Stomatology, the Southern Medical University (China); Kaminski, Joseph M. [National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology, and Transplantation, University of South Alabama (United States); Summers, James Bradley [Department of Radiology, University of South Alabama (United States); Wang Zhichong [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 S Xianlie Road, Guangzhou, Guangdong 510060 (China); Ge Jian [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 S Xianlie Road, Guangzhou, Guangdong 510060 (China)], E-mail: gejian@mail.sysu.edu.cn; Yu Keming [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 S Xianlie Road, Guangzhou, Guangdong 510060 (China)], E-mail: yukeming@mail.sysu.edu.cn

2009-03-13T23:59:59.000Z

277

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

SciTech Connect

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

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

2010-05-17T23:59:59.000Z

278

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

Science Conference Proceedings (OSTI)

The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7- 1 dbf). Analysis of chromosomalaberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

Marchetti, Francesco; Marchetti, Francesco; Wryobek, Andrew J

2008-02-21T23:59:59.000Z

279

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

Science Conference Proceedings (OSTI)

The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7-1 dbf). Analysis of chromosomal aberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

Marchetti, Francesco; Marchetti, Francesco; Wyrobek, Andrew J.

2007-12-01T23:59:59.000Z

280

Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation  

SciTech Connect

The understanding of interactions between double stranded (ds) DNA and charged nanoparticles will have a broad bearing on many important applications from drug delivery [ 1 4 ] to DNAtemplated metallization. [ 5 , 6 ] Cationic nanoparticles (NPs) can bind to DNA, a negatively charged molecule, through a combination of electrostatic attraction, groove binding, and intercalation. Such binding events induce changes in the conformation of a DNA strand. In nature, DNA wraps around a cylindrical protein assembly (diameter and height of 6 nm) [ 7 ] with an 220 positive charge, [ 8 ] creating the complex known as chromatin. Wrapping and bending of DNA has also been achieved in the laboratory through the binding of highly charged species such as molecular assemblies, [ 9 , 10 ] cationic dendrimers, [ 11 , 12 ] and nanoparticles. [ 13 15 ] The charge of a nanoparticle plays a crucial role in its ability to induce DNA structural changes. If a nanoparticle has a highly positive surface charge density, the DNA is likely to wrap and bend upon binding to the nanoparticle [ 13 ] (as in the case of chromatin). On the other hand, if a nanoparticle is weakly charged it will not induce dsDNA compaction. [ 9 , 10 , 15 ] Consequently, there is a transition zone from extended to compact DNA conformations which depends on the chemical nature of the nanoparticle and occurs for polycations with charges between 5 and 10. [ 9 ] While the interactions between highly charged NPs and DNA have been extensively studied, the processes that occur within the transition zone are less explored.

Railsback, Justin [North Carolina State University; Singh, Abhishek [North Carolina State University; Pearce, Ryan [North Carolina State University; McKnight, Timothy E [ORNL; Collazo, Ramon [North Carolina State University; Sitar, Zlatko [ORNL; Yingling, Yaroslava [North Carolina State University; Melechko, Anatoli Vasilievich [ORNL

2012-01-01T23:59:59.000Z

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


281

Unraveling the Fanconi anaemia-DNA repair connection through DNA helicase and translocase activities  

Science Conference Proceedings (OSTI)

How the Fanconi anaemia (FA) chromosome stability pathway functions to cope with interstrand crosslinks and other DNA lesions has been elusive, even after FANCD1 proved to be BRCA2, a partner of Rad51 in homologous recombination. The identification and characterization of two new Fanconi proteins having helicase motifs, FANCM and FANCJ/BRIP1/BACH1, implicates the FANC nuclear core complex as a participant in recognizing or processing damaged DNA, and the BRIP1 helicase as acting independently of this complex.

Thompson, L H

2005-08-16T23:59:59.000Z

282

Intragenic and extragenic suppressors of temperature sensitive mutations replication initiation genes dnaD and dnaB of Bacillus subtilis  

E-Print Network (OSTI)

Background: The Bacillus subtilis genes dnaD and dnaB are essential for the initiation of DNA replication and are required for loading of the replicative helicase at the chromosomal origin of replication oriC. Wild type ...

Grossman, Alan D.

283

Mechanical Operations and Maintenance  

NLE Websites -- All DOE Office Websites (Extended Search)

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

284

NUT SCREW MECHANISMS  

DOE Patents (OSTI)

A reactor control mechanism is described wherein the control is achieved by the partial or total withdrawal of the fissile material which is in the form of a fuel rod. The fuel rod is designed to be raised and lowered from the reactor core area by means of two concentric ball nut and screw assemblies that may telescope one within the other. These screw mechanisms are connected through a magnetic clutch to a speed reduction gear and an accurately controllable prime motive source. With the clutch energized, the fuel rod may be moved into the reactor core area, and fine adjustments may be made through the reduction gearing. However, in the event of a power failure or an emergency signal, the magnetic clutch will become deenergized, and the fuel rod will drop out of the core area by the force of gravity, thus shutting down the operation of the reactor.

Glass, J.A.F.

1958-07-01T23:59:59.000Z

285

Testing quantum mechanics  

E-Print Network (OSTI)

As experiments continue to push the quantum-classical boundary to include increasingly complex dynamical systems, the interpretation of experimental data becomes more and more challenging: when the observations are noisy, indirect, and limited, how can we be sure that we are observing quantum behavior? This tutorial highlights some of the difficulties in such experimental tests of quantum mechanics, using optomechanics as the central example, and discusses how the issues can be resolved using techniques from statistics and insights from quantum information theory.

Mankei Tsang

2013-06-12T23:59:59.000Z

286

Mechanical Compression Heat Pumps  

E-Print Network (OSTI)

Mechanical compression heat pumping is not new in industrial applications. In fact, industry history suggests that the theoretical concept was developed before 1825. Heat pump manufacturers gained the support of consultants and end-users when the energy crisis hit this country in 1973. That interest, today, has been dampened because there is a current abundance of the basic sources of industrial energy (namely oil and natural gas). Meanwhile, Mycom used the window of the current opportunities to develop, design and test compressors built to meet the needs of the mechanically demanding industrial heat pump applications which often require high compression ratios and temperatures in excess of 200 degrees F. This paper will review the theoretical foundation for heat pumps and present the mechanical and thermal requirements of the compressors which constitute the heart and soul of the system. It will also provide a quick survey of the available types of compressors for heat pumping and some of the industrial processes where simultaneous heating and cooling proceed along parallel demand paths. The case history will examine the system flexibility and the economic advantages realized in a barley malting process.

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

1986-06-01T23:59:59.000Z

287

TRANSIENT QUANTUM MECHANICAL PROCESSES  

SciTech Connect

Our principal objective has centered on the development of sophisticated computational techniques to solve the time-dependent Schroedinger equation that governs the evolution of quantum mechanical systems. We have perfected two complementary methods, discrete variable representation and real space product formula, that show great promise in solving these complicated temporal problems. We have applied these methods to the interaction of laser light with molecules with the intent of not only investigating the basic mechanisms but also devising schemes for actually controlling the outcome of microscopic processes. Lasers now exist that produce pulses of such short duration as to probe a molecular process many times within its characteristic period--allowing the actual observation of an evolving quantum mechanical system. We have studied the potassium dimer as an example and found agreement with experimental changes in the intermediate state populations as a function of laser frequency--a simple control prescription. We have also employed elaborate quantum chemistry programs to improve the accuracy of basic input such as bound-bound and bound-free coupling moments. These techniques have far-ranging applicability; for example, to trapped quantum systems at very low temperatures such as Bose-Einstein condensates.

L. COLLINS; J. KRESS; R. WALKER

1999-07-01T23:59:59.000Z

288

Understanding Bohmian mechanics: A dialogue  

E-Print Network (OSTI)

This paper is an introduction to the ideas of Bohmian mechanics, an interpretation of quantum mechanics in which the observer plays no fundamental role. Bohmian mechanics describes, instead of probabilities of measurement results, objective microscopic events. In recent years, Bohmian mechanics has attracted increasing attention by researchers. The form of a dialogue allows me to address questions about the Bohmian view that often arise.

Roderich Tumulka

2004-08-18T23:59:59.000Z

289

Bohmian Mechanics Detlef Durr1  

E-Print Network (OSTI)

Bohmian Mechanics Detlef D¨urr1 , Sheldon Goldstein2 , Roderich Tumulka3 , and Nino Zangh`i4, Via Dodecaneso 33, 16146 Genova, Italy. E-mail: zanghi@ge.infn.it #12;Bohmian mechanics is a theory mechanics, observers see the same statistics for experimental results as predicted by quantum mechanics

Goldstein, Sheldon

290

Measurement of Mechanical and Electrical  

Science Conference Proceedings (OSTI)

Measurement of Mechanical and Electrical Properties of Ultra-thin Insulating Films. NIST Nanomechanical Properties Group ...

2012-10-01T23:59:59.000Z

291

On the possibility of electronic DNA nanobiochips  

E-Print Network (OSTI)

We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the majority of cases the conductance of double-stranded nucleotides considerably exceeds that of single-stranded ones. The results obtained are in agreement with recent experiments on measuring the oligonucleotide conductance. It has been shown that an electronic biochip containing 11 nucleotide pairs will recognize approximately 97% sequences. It has also been demonstrated that the percentage of identifiable sequences will grow with the sequence length.

Lakhno, V D; 10.1021/ct6003438

2013-01-01T23:59:59.000Z

292

Persistent DNA damage foci, cellular senescence and low dose radiation  

NLE Websites -- All DOE Office Websites (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

293

Electrophoretic Capture of a DNA Chain into a Nanopore  

E-Print Network (OSTI)

Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption to a sink placed on top of an energy barrier. Reproducing the previously observed diffusion-limited and barrier-limited regimes as two different limits of the particle absorption process and matching the data, our model suggests a slower growth of the capture rate with the DNA length for very large DNA molecules than the previous model, motivating more experiments beyond the current range of electric field and DNA length. At moderately weak electric fields, our model predicts a different effect, stating that the DNA length dependence of the capture rate first disappears as the field is reduced and eventually reverses to a decreasing trend with $N$.

Payam Rowghanian; Alexander Y. Grosberg

2013-06-19T23:59:59.000Z

294

Electrophoretic Capture of a DNA Chain into a Nanopore  

E-Print Network (OSTI)

Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption to a sink placed on top of an energy barrier. Reproducing the previously observed diffusion-limited and barrier-limited regimes as two different limits of the particle absorption process and matching the data, our model suggests a slower growth of the capture rate with the DNA length for very large DNA molecules than the previous model, motivating more experiments beyond the current range of electric field and DNA length. At moderately weak electric fields, our model predicts a different effect, stating that the DNA length dependence of the capture rate first disappears as the field is reduced and eventually reverses to a decreasing trend with $N$.

Rowghanian, Payam

2013-01-01T23:59:59.000Z

295

Connecting Chromatin Modifying Factors to DNA Damage Response  

E-Print Network (OSTI)

Abstract: Cells are constantly damaged by factors that can induce DNA damage. Eukaryotic cells must rapidly load DNA repair proteins onto damaged chromatin during the DNA damage response (DDR). Chromatin-remodeling complexes use the energy from ATP hydrolysis to remodel nucleosomes and have well-established functions in transcription. Emerging lines of evidence indicate that chromatin-remodeling complexes are important and may remodel nucleosomes during DNA damage repair. New studies also reveal that ATP-dependent chromatin remodeling is involved in cell cycle progression, signal transduction pathways, and interaction and modification of DDR-related proteins that are specifically and intimately connected with the process of DNA damage. This article summarizes the recent advances in our understanding of the interplay between chromatin remodeling and DNA damage response.

Weiwei Lai; Hongde Li; Shuang Liu; Yongguang Tao

2013-01-01T23:59:59.000Z

296

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

Science Conference Proceedings (OSTI)

Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

2008-12-16T23:59:59.000Z

297

Chloroplast DNA insertions into the nuclear genome of rice: the ...  

Science Conference Proceedings (OSTI)

Shahmuradov IA, Akbarova YY, Solovyev VV, Aliye JA (2003). Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol Biol...

298

Binding Parameters of Alkaloids Berberine and Sanguinarine with DNA  

E-Print Network (OSTI)

We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the concentration ratio N/c between the DNA base pairs and alkaloid molecules in the solutions are considered, and the manifestations of the alkaloid-DNA binding are revealed. The character of binding is found to depend on N/c. The parameters of the binding of berberine and sanguinarine with DNA are determined, by using the modified Scatchard and McGhee-von Hippel equations

Gumenyuk, V G; Kutovyy, S Yu; Yashchuk, V M; Zaika, L A

2012-01-01T23:59:59.000Z

299

Clustered DNA Damage Spectrum in Primary Human Hematopoietic...  

NLE Websites -- All DOE Office Websites (Extended Search)

94805 Villejuif Cedex France Clustered DNA Damages Induced by Low Radiation Doses Irradiation of cells with low doses of X- or -rays induces clustered damages in mammalian...

300

Technology Commercialization and Partnerships | BSA 01-02: DNA ...  

Research laboratories and diagnositcs developers may have use for assays designed to assess the levels of DNA-PK activity of various cell types. ... c ...

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


301

Gel Electrophoresis of Gold-DNA Nano-Conjugates  

E-Print Network (OSTI)

electrophoresis of Gold-DNA nano-conjugates Abstract SingleEuropean Union (STREP program NANO-SA) and the Center for

Pellegrino, T.; Sperling, R.A.; Alivisatos, A.P.; Parak, W.J.

2008-01-01T23:59:59.000Z

302

A Golden Ruler Used to Measure DNA Structure in Solution  

NLE Websites -- All DOE Office Websites (Extended Search)

In this work, we have developed a molecular ruler that utilizes 14- gold nanocrystal probes attached site-specifically to DNA duplexes. The experiments were carried out...

303

Modular Systems Biology applied to TGFbeta and DNA Damage Response...  

NLE Websites -- All DOE Office Websites (Extended Search)

Modular Systems Biology applied to TGFbeta and DNA Damage Response Signaling following Low Dose Radiation Francis Cucinotta NASA Johnson Space Center Abstract Modular systems...

304

Available Technologies: j5: Automated DNA Assembly Design Software  

... PCR/SOE, or oligo-embedding), designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 ...

305

Method for priming and DNA sequencing  

DOE Patents (OSTI)

A method is presented for improving the priming specificity of an oligonucleotide primer that is non-unique in a nucleic acid template which includes selecting a continuous stretch of several nucleotides in the template DNA where one of the four bases does not occur in the stretch. This also includes bringing the template DNA in contract with a non-unique primer partially or fully complimentary to the sequence immediately upstream of the selected sequence stretch. This results in polymerase-mediated differential extension of the primer in the presence of a subset of deoxyribonucleotide triphosphates that does not contain the base complementary to the base absent in the selected sequence stretch. These reactions occur at a temperature sufficiently low for allowing the extension of the non-unique primer. The method causes polymerase-mediated extension reactions in the presence of all four natural deoxyribonucleotide triphosphates or modifications. At this high temperature discrimination occurs against priming sites of the non-unique primer where the differential extension has not made the primer sufficiently stable to prime. However, the primer extended at the selected stretch is sufficiently stable to prime.

Mugasimangalam, R.C.; Ulanovsky, L.E.

1997-12-01T23:59:59.000Z

306

Drill drive mechanism  

DOE Patents (OSTI)

A drill drive mechanism is especially adapted to provide both rotational drive and axial feed for a drill of substantial diameter such as may be used for drilling holes for roof bolts in mine shafts. The drill shaft is made with a helical pattern of scroll-like projections on its surface for removal of cuttings. The drill drive mechanism includes a plurality of sprockets carrying two chains of drive links which are arranged to interlock around the drill shaft with each drive link having depressions which mate with the scroll-like projections. As the chain links move upwardly or downwardly the surfaces of the depressions in the links mate with the scroll projections to move the shaft axially. Tangs on the drive links mate with notch surfaces between scroll projections to provide a means for rotating the shaft. Projections on the drive links mate together at the center to hold the drive links tightly around the drill shaft. The entire chain drive mechanism is rotated around the drill shaft axis by means of a hydraulic motor and gear drive to cause rotation of the drill shaft. This gear drive also connects with a differential gearset which is interconnected with a second gear. A second motor is connected to the spider shaft of the differential gearset to produce differential movement (speeds) at the output gears of the differential gearset. This differential in speed is utilized to drive said second gear at a speed different from the speed of said gear drive, this speed differential being utilized to drive said sprockets for axial movement of said drill shaft.

Dressel, Michael O. (Englewood, CO)

1979-01-01T23:59:59.000Z

307

Mechanical Systems Qualification Standard  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

61-2008 61-2008 June 2008 DOE STANDARD MECHANICAL SYSTEMS QUALIFICATION STANDARD DOE Defense Nuclear Facilities Technical Personnel U.S. Department of Energy AREA TRNG Washington, D.C. 20585 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. DOE-STD-1161-2008 ii This document is available on the Department of Energy Technical Standards Program Web Site at http://www.hss.energy.gov/nuclearsafety/techstds/ DOE-STD-1161-2008 iv INTENTIONALLY BLANK DOE-STD-1161-2008 v TABLE OF CONTENTS ACKNOWLEDGMENT................................................................................................................ vii PURPOSE ....................................................................................................................................1

308

Bee algorithms for solving DNA fragment assembly problem with noisy and noiseless data  

Science Conference Proceedings (OSTI)

DNA fragment assembly problem is one of the crucial challenges faced by computational biologists where, given a set of DNA fragments, we have to construct a complete DNA sequence from them. As it is an NP-hard problem, accurate DNA sequence is hard to ... Keywords: bioinformatics, combinatorial optimization, dna computing, genetic algorithms, meta-heuristics

Jesun Sahariar Firoz; M. Sohel Rahman; Tanay Kumar Saha

2012-07-01T23:59:59.000Z

309

A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota  

Science Conference Proceedings (OSTI)

Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol{iota}) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol{iota} through use of the fixed-conformation nucleotide North-methanocarba-2{prime}-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol{iota} in complex with DNA containing a template 2{prime}-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol{iota} inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol{iota}. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol{iota} by preventing the Hoogsteen base-pairing mode normally observed for hpol{iota}-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L. (Cornell); (Vanderbilt); (NCI); (Arkansas)

2012-10-25T23:59:59.000Z

310

Tensor analysis of spatial mechanisms  

Science Conference Proceedings (OSTI)

The position analysis of a general four-bar spatial mechanism is developed using tensor notation and operations. To exemplify the convenience of tensors in kinematic analysis the solution is obtained for a mechanism containing two revolute pairs of links ...

C. Y. Ho

1966-05-01T23:59:59.000Z

311

On Randomness in Quantum Mechanics  

E-Print Network (OSTI)

The quantum mechanical probability densities are compared with the probability densities treated by the theory of random variables. The relevance of their difference for the interpretation of quantum mechanics is commented.

Alberto C. de la Torre

2007-07-19T23:59:59.000Z

312

Essays on dynamic sales mechanisms  

E-Print Network (OSTI)

This thesis is a collection of three essays on dynamic sales mechanisms. The first chapter analyzes the Name Your Own Price (NYOP) mechanism adopted by Priceline.com. Priceline.com, a website helping travelers obtain ...

Chen, Chia-Hui, Ph. D. Massachusetts Institute of Technology

2009-01-01T23:59:59.000Z

313

Mechanics of Peridynamic Membranes  

National Nuclear Security Administration (NNSA)

JBAidun AdvMatSci090831 JBAidun AdvMatSci090831 1 Accurate Prediction of Dynamic Fracture with Peridynamics John B. Aidun & Stewart A. Silling Multiscale Dynamic Material Modeling Sandia National Laboratories Prague, Czech Republic August 30 - September 3, 2009 Joint U.S.-Russian Conference on Advances in Materials Science SAND2009-5095C Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. JBAidun AdvMatSci090831 2 Fracture Mechanics Theory and Dynamic Fracture * Onset of crack growth can be accurately predicted * Crack growth speed and direction cannot! Wanted: A successful method for simulating Dynamic Fracture * Such a method must be able to reproduce the

314

Rotary drive mechanism  

Science Conference Proceedings (OSTI)

This patent describes a rotary drive mechanism which includes a rotary solenoid having a stator and multi-poled rotor. A moving member rotates with the rotor and is biased by a biasing device. The biasing device causes a further rotational movement after rotation by the rotary solenoid. Thus, energization of the rotary solenoid moves the member in one direction to one position and biases the biasing device against the member. Subsequently, de- energization of the rotary solenoid causes the biasing device to move the member in the same direction to another position from where the moving member is again movable by energization and de-energization of the rotary solenoid. Preferably, the moving member is a multi-lobed cam having the same number of lobes as the rotor has poles. An anti- overdrive device is also preferably provided for preventing overdrive in the forward direction or a reverse rotation of the moving member and for precisely aligning the moving member.

Kenderdine, E.W.

1991-10-08T23:59:59.000Z

315

Rotary drive mechanism  

Science Conference Proceedings (OSTI)

A rotary drive mechanism includes a rotary solenoid having a stator and multi-poled rotor. A moving member rotates with the rotor and is biased by a biasing device. The biasing device causes a further rotational movement after rotation by the rotary solenoid. Thus, energization of the rotary solenoid moves the member in one direction to one position and biases the biasing device against the member. Subsequently, de-energization of the rotary solenoid causes the biasing device to move the member in the same direction to another position from where the moving member is again movable by energization and de-energization of the rotary solenoid. Preferably, the moving member is a multi-lobed cam having the same number of lobes as the rotor has poles. An anti-overdrive device is also preferably provided for preventing overdrive in the forward direction or a reverse rotation of the moving member and for precisely aligning the moving member.

Kenderdine, Eugene W. (Albuquerque, NM)

1991-01-01T23:59:59.000Z

316

Mechanically expandable annular seal  

DOE Patents (OSTI)

A mechanically expandable annular reusable seal assembly to form an annular hermetic barrier between two stationary, parallel, and planar containment surfaces. A rotatable ring, attached to the first surface, has ring wedges resembling the saw-tooth array of a hole saw. Matching seal wedges are slidably attached to the ring wedges and have their motion restricted to be perpendicular to the second surface. Each seal wedge has a face parallel to the second surface. An annular elastomer seal has a central annular region attached to the seal wedges' parallel faces and has its inner and outer circumferences attached to the first surface. A rotation of the ring extends the elastomer seal's central region perpendicularly towards the second surface to create the fluidtight barrier. A counterrotation removes the barrier.

Gilmore, Richard F. (Kennewick, WA)

1983-01-01T23:59:59.000Z

317

Mechanically expandable annular seal  

DOE Patents (OSTI)

A mechanically expandable annular reusable seal assembly to form an annular hermetic barrier between two stationary, parallel, and planar containment surfaces is described. A rotatable ring, attached to the first surface, has ring wedges resembling the saw-tooth array of a hole saw. Matching seal wedges are slidably attached to the ring wedges and have their motion restricted to be perpendicular to the second surface. Each seal wedge has a face parallel to the second surface. An annular elastomer seal has a central annular region attached to the seal wedges' parallel faces and has its inner and outer circumferences attached to the first surface. A rotation of the ring extends the elastomer seal's central region perpendicularly towards the second surface to create the fluid tight barrier. A counter rotation removes the barrier. 6 figs.

Gilmore, R.F.

1983-07-19T23:59:59.000Z

318

Mechanical well jar  

Science Conference Proceedings (OSTI)

This patent describes a mechanical well jar having inner and outer tubular members movable longitudinally relative to each other a limited distance. Means for connecting one of the members to a pipe string extends above the jar. Means connect the other member to the pipe string below the jar. Annular shoulders on the members engage to limit the relative longitudinal movement of the members. The improvement comprises: laterally spaced, arcuate cam plates each attached to the inner surface of the outer member by threaded members that extend through the wall of the outer member and that can be removed from outside the outer member to allow the cam plates to be removed and repaired or replaced.

Burton, C.A.

1987-05-19T23:59:59.000Z

319

Security Components and Mechanisms Group  

Science Conference Proceedings (OSTI)

Security Components and Mechanisms Group. Welcome. ... A security checklist is a document that contains instructions for securely configuring ...

2013-01-17T23:59:59.000Z

320

Mechanical Behavior at Nanoscale I  

Science Conference Proceedings (OSTI)

Jul 31, 2011 ... -Deformation mechanisms of nano structures including nanocrystalline, nano- twinned, nanowires, nano-laminates, and nano-pillars.

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


321

Mechanical Behavior of Materials Committee  

Science Conference Proceedings (OSTI)

The Mechanical Behavior of Materials Committee is part of the Structural Materials Division. Our Mission: Covers relationships between microstructure and

322

Chloroplast DNA Variation Confirms a Single Origin of Domesticated  

E-Print Network (OSTI)

diversity. This result led them to conclude that these lines do, in fact, trace back to a single origin of single vs. multiple origins of sunflower domestication based on patterns of cpDNA variation in wild loci per lane on an automated DNA sequencer, PCR products were labeled by including a fluorescently

Burke, John M.

323

Energy and Technology Review: Unlocking the mysteries of DNA repair  

SciTech Connect

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

Quirk, W.A.

1993-04-01T23:59:59.000Z

324

Google matrix analysis of DNA sequences Vivek Kandiah1  

E-Print Network (OSTI)

1 Google matrix analysis of DNA sequences Vivek Kandiah1 , Dima L. Shepelyansky1, 1 Laboratoire de.quantware.ups-tlse.fr/dima Abstract For DNA sequences of various species we construct the Google matrix G of Markov tran- sitions their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google

Shepelyansky, Dima

325

cDNA encoding a polypeptide including a hevein sequence  

DOE Patents (OSTI)

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

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

1993-02-16T23:59:59.000Z

326

Studies of the chemical mechanisms of flavoenzymes  

E-Print Network (OSTI)

Flavocytochrome b2 catalyzes the oxidation of lactate to pyruvate. Primary deuterium and solvent kinetic isotope effects have been used to determine the relative timing of cleavage of the lactate OH and CH bonds by the wild type enzyme, a mutant protein lacking the heme domain, and the D282N enzyme. The DVmax and D(V/Klactate) values are both 3.0, 3.6 and 4.5 for the wild type enzyme, flavin domain and D282N enzymes, respectively. The D20Vmax values are 1.38, 1.18, and 0.98 for the wild type enzyme, the flavin domain, and the D282N enzyme; the respective D20(V/Klactate) values are 0.9, 0.44, and 1.0. The Dkred value is 5.4 for the wild type enzyme and 3.5 for the flavin domain, whereas the D2Okred is 1.0 for both enzymes. The V/Klactate value for the flavin domain increases 2-fold at moderate concentrations of glycerol. The data are consistent with the lactate hydroxyl proton not being in flight in the transition state for CH bond cleavage and there being an internal equilibrium prior to CH bond cleavage which is sensitive to solution conditions. Removal of the hydroxyl proton may occur in this pre-equilibrium. Tryptophan 2-monooxygenase catalyzes the oxidative decarboxylation of tryptophan to indoleacetamide, carbon dioxide and water. Sequence alignments identified this enzyme as a member of the L-amino acid oxidase family. The tyrosine and arginine residues in L-amino acid oxidase that bind the carboxylate of o-aminobenzoate are conserved and correspond to Tyr413 and Arg98 in tryptophan 2-monooxygenase. Mutation and characterization of the Y413A, Y413F, R98K and R98A enzymes indicate that these residues are in the active site and interact with the substrate. Deletion of the OH group of Tyr413 increases the Kd for the substrate and makes CH bond cleavage totally rate limiting. The pH V/Ktrp rate profile for the Tyr413 mutant enzymes shows that this residue must be protonated for activity. For both the R98A and R98K enzymes flavin reduction is rate limiting. The Vmax and V/Ktrp pH profiles indicate that the unprotonated form of the substrate is the active form for activity.

Sobrado, Pablo

2003-08-01T23:59:59.000Z

327

Hybridization and Selective Release of DNA Microarrays  

SciTech Connect

DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.

Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K

2011-11-29T23:59:59.000Z

328

SOLID MECHANICS James R. Rice  

E-Print Network (OSTI)

1 SOLID MECHANICS James R. Rice School of Engineering and Applied Sciences, and Department of Earth: February 2010 Downloadable at: http://esag.harvard.edu/rice/e0_Solid_Mechanics_94_10.pdf TABLE OF CONTENTS provided on last three pages, pp. 87-89 INTRODUCTION The application of the principles of mechanics to bulk

329

Ideas By Statistical Mechanics (ISM)  

Science Conference Proceedings (OSTI)

Ideas by Statistical Mechanics (ISM) is a generic program to model evolution and propagation of ideas/patterns throughout populations subjected to endogenous and exogenous interactions. The program is based on the author's work in Statistical Mechanics ... Keywords: neocortical interactions, risk management, simulated annealing, statistical mechanics

Lester Ingber

2007-08-01T23:59:59.000Z

330

NV-020-08-DNA-52 | Open Energy Information  

Open Energy Info (EERE)

DNA-52 DNA-52 Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home NEPA Document Collection for: NV-020-08-DNA-52 DNA at {{{GeothermalArea}}} for Geothermal/Exploration, {{{NEPA_Name}}} General NEPA Document Info Energy Sector Geothermal energy Environmental Analysis Type DNA Applicant Gerlach Geothermal LLC Geothermal Area {{{GeothermalArea}}}"{{{GeothermalArea}}}" cannot be used as a page name in this wiki. Project Location Project Phase Geothermal/Exploration Techniques Thermal Gradient Holes Comments NOI for TGH at Gavvs Valley Time Frame (days) Application Time 14 Participating Agencies Lead Agency BLM Funding Agency none provided Managing District Office Winnemucca Managing Field Office BLM Black Rock Field Office Funding Agencies none provided

331

Development of new tools for the production of plasmid DNA biopharmaceuticals  

E-Print Network (OSTI)

DNA vaccines and gene therapies that use plasmid DNA (pDNA) as a vector have gained attention in recent years for their good safety profile, ease of manufacturing, and potential to treat a host of diseases. With this ...

Bower, Diana M. (Diana Morgan)

2012-01-01T23:59:59.000Z

332

Entanglement Exchange and Bohmian Mechanics  

E-Print Network (OSTI)

This paper analyses the phenomenon of entanglement exchange in Bohm's pilot wave interpretation of quantum mechanics. The interesting feature of the phenomenon is that systems become entangled without causal interaction; hence it is a useful situation for investigating the unique nature of interaction in Bohmian mechanics. The first two sections introduce, respectively, entanglement exchange in the standard interpretation of quantum mechanics, and the basic principles of Bohmian mechanics. The next section shows that the Bohmian interpretation makes the same experimental predictions about entanglement exchange as the standard one. The final section draws some conclusions about interactions and entanglement in Bohmian mechanics.

Nick Huggett; Tiziana Vistarini

2009-05-25T23:59:59.000Z

333

A Novel Fold in the Tral Relaxase-Helicase C-Terminal Domain Is Essential for Conjugative DNA Transfer  

Science Conference Proceedings (OSTI)

TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-{angstrom} resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal {alpha}-domain connected by a proline-rich loop to a compact {alpha}/{beta}-domain. Both the globular nature of the {alpha}/{beta}-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.

Guogas, Laura M.; Kennedy, Sarah A.; Lee, Jin-Hyup; Redinbo, Matthew R.; (UNC)

2009-06-04T23:59:59.000Z

334

Relativistic mechanism of superconductivity  

E-Print Network (OSTI)

According to the theory of relativity, the relativistic Coulomb's force between an electron pair is composed of two parts, the main part is repulsive, while the rest part can be attractive in certain situations. Thus the relativistic attraction of an electron pair provides an insight into the mechanism of superconductivity. In superconductor, there are, probably at least, two kinds of collective motions which can eliminate the repulsion between two electrons and let the attraction being dominant, the first is the combination of lattice and electron gas, accounting for traditional superconductivity; the second is the electron gas themselves, accounting for high $T_c$ superconductivity. In usual materials, there is a good balance between the repulsion and attraction of an electron pair, the electrons are regarded as free electrons so that Fermi gas theory plays very well. But in some materials, when the repulsion dominates electron pairs, the electron gas will has a behavior opposite to superconductivity. In the present paper the superconducting states are discussed in terms of relativistic quantum theory in details, some significant results are obtained including quantized magnetic flux, London equation, Meissner effect and Josephson effect.

H. Y. Cui

2002-12-17T23:59:59.000Z

335

N=8 superconformal mechanics  

E-Print Network (OSTI)

We construct new models of N=8 superconformal mechanics associated with the off-shell N=8, d=1 supermultiplets (3,8,5) and (5,8,3). These two multiplets are derived as N=8 Goldstone superfields and correspond to nonlinear realizations of the N=8, d=1 superconformal group OSp(4^*|4) in its supercosets OSp(4^*|4)/U(1)_R x SO(5) and OSp(4^*|4)/SU(2)_R x SO(4), respectively. The irreducibility constraints for these superfields automatically follow from appropriate superconformal covariant conditions on the Cartan superforms. The N=8 superconformal transformations of the superspace coordinates and the Goldstone superfields are explicitly given. Interestingly, each N=8 supermultiplet admits two different off-shell N=4 decompositions, with different N=4 superconformal subgroups SU(1,1|2) and OSp(4^*|2) of OSp(4^*|4) being manifest as superconformal symmetries of the corresponding N=4, d=1 superspaces. We present the actions for all such N=4 splittings of the N=8 multiplets considered.

S. Bellucci; E. Ivanov; S. Krivonos; O. Lechtenfeld

2003-12-31T23:59:59.000Z

336

Bayesian models for DNA microarray data analysis  

E-Print Network (OSTI)

Selection of signi?cant genes via expression patterns is important in a microarray problem. Owing to small sample size and large number of variables (genes), the selection process can be unstable. This research proposes a hierarchical Bayesian model for gene (variable) selection. We employ latent variables in a regression setting and use a Bayesian mixture prior to perform the variable selection. Due to the binary nature of the data, the posterior distributions of the parameters are not in explicit form, and we need to use a combination of truncated sampling and Markov Chain Monte Carlo (MCMC) based computation techniques to simulate the posterior distributions. The Bayesian model is ?exible enough to identify the signi?cant genes as well as to perform future predictions. The method is applied to cancer classi?cation via cDNA microarrays. In particular, the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify the set of signi?cant genes to classify BRCA1 and others. Microarray data can also be applied to survival models. We address the issue of how to reduce the dimension in building model by selecting signi?cant genes as well as assessing the estimated survival curves. Additionally, we consider the wellknown Weibull regression and semiparametric proportional hazards (PH) models for survival analysis. With microarray data, we need to consider the case where the number of covariates p exceeds the number of samples n. Speci?cally, for a given vector of response values, which are times to event (death or censored times) and p gene expressions (covariates), we address the issue of how to reduce the dimension by selecting the responsible genes, which are controlling the survival time. This approach enables us to estimate the survival curve when n << p. In our approach, rather than ?xing the number of selected genes, we will assign a prior distribution to this number. The approach creates additional ?exibility by allowing the imposition of constraints, such as bounding the dimension via a prior, which in e?ect works as a penalty. To implement our methodology, we use a Markov Chain Monte Carlo (MCMC) method. We demonstrate the use of the methodology with (a) di?use large B??cell lymphoma (DLBCL) complementary DNA (cDNA) data and (b) Breast Carcinoma data. Lastly, we propose a mixture of Dirichlet process models using discrete wavelet transform for a curve clustering. In order to characterize these time??course gene expresssions, we consider them as trajectory functions of time and gene??speci?c parameters and obtain their wavelet coe?cients by a discrete wavelet transform. We then build cluster curves using a mixture of Dirichlet process priors.

Lee, Kyeong Eun

2006-05-01T23:59:59.000Z

337

Sensitive method for measurement of telomeric DNA content in human tissues  

DOE Patents (OSTI)

A sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue.

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

1999-02-16T23:59:59.000Z

338

Polymorphism of DNA-anionic Liposome Complexes Reveals Hierarchy of  

NLE Websites -- All DOE Office Websites (Extended Search)

Polymorphism of DNA-anionic Polymorphism of DNA-anionic Liposome Complexes Reveals Hierarchy of Ion-mediated Interactions Hongjun Liang,* Daniel Harries,+ and Gerard C. L. Wong* *Department of Materials Science & Engineering, Department of Physics, Department of Bioengineering, University of Illinois at Urbana-Champaign, IL 61801, USA +Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA Gene therapy using either viral or synthetic vectors is currently one of the most promising strategies for developing cures for many hereditary and acquired diseases. Protocols have been approved for cancer, hemophilia, cystic fibrosis, neuromuscular disorders, and others. Although synthetic nonviral systems such as cationic liposomes generally transfect less efficiently than viruses, they have a number of advantages such as high DNA packaging capacity and low immunogenicity. Since their introduction in 1987, cationic lipid-DNA complexes (CL-DNA) have emerged as one of the major non-viral DNA delivery platforms. CL-DNA complexes have been used in gene therapy for a broad range of cell types as well as delivery systems for cancer vaccines.

339

Specificity, flexibility and valence of DNA bonds guide emulsion architecture  

E-Print Network (OSTI)

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

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

2013-02-28T23:59:59.000Z

340

Nanomaterials: Mechanics and Mechanisms (2008), by K.T. Ramesh  

Science Conference Proceedings (OSTI)

Mar 10, 2010 ... At nanoscale, matters show distinctly different behaviors from their bulk materials, from mechanical properties to physical and chemical...

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


341

Wave Mechanics without Probability  

E-Print Network (OSTI)

The behavior of monochromatic electromagnetic waves in stationary media is shown to be ruled by a frequency dependent function, which we call Wave Potential, encoded in the structure of the Helmholtz equation. Contrary to the common belief that the very concept of "ray trajectory" is reserved to the eikonal approximation, a general and exact ray-based Hamiltonian treatment, reducing to the eikonal approximation in the absence of Wave Potential, shows that its presence induces a mutual, perpendicular ray-coupling, which is the one and only cause of any typically wave-like phenomenon, such as diffraction and interference. Recalling, then, that the time-independent Schroedinger and Klein-Gordon equations (associating stationary "matter waves" to mono-energetic particles) are themselves Helmholtz-like equations, the exact, ray-based treatment developed for classical electromagnetic waves is extended - without resorting to statistical concepts - to the exact, trajectory-based Hamiltonian dynamics of mono-energetic point-like particles, both in the non-relativistic and in the relativistic case. The trajectories turn out to be perpendicularly coupled, once more, by an exact, stationary, energy-dependent Wave Potential, coinciding in the form, but not in the physical meaning, with the statistical, time-varying, energy-independent "Quantum Potential" of Bohm's theory, which views particles, just like the standard Copenhagen interpretation, as traveling wave-packets. These results, together with the connection which is shown to exist between Wave Potential and Uncertainty Principle, suggest a novel, non-probabilistic interpretation of Wave Mechanics.

Adriano Orefice; Raffaele Giovanelli; Domenico Ditto

2013-02-18T23:59:59.000Z

342

A statistical mechanical curiosity  

E-Print Network (OSTI)

Unlike most other laws of nature, the second law of thermodynamics is according to Boltzmann statistical in nature, meaning that its reliability arises from the vast number of particles present in macroscopic systems. This means that such systems will lead towards their most likely state, that is, the one with the most homogeneous probability distribution. But Boltzmann states that entropy decreasing processes can occur (without doing any work), it is just very improbable. It is therefore not impossible, in principle, for all 6 x 10^23 atoms in a mole of a gas to spontaneously move to one half of a container; it is only fantastically unlikely. A similar idea has been applied on a human cell. All somatic cells seem to age and deteriorate in unfavorable conditions. If the aging process is defined as the accumulation of dysfunctional polymers resulting from among other things chemical bond breakage, where polymers aggregate into harmful arrangements, spreading randomly out in the cell, leading to an altered function, then it also applies that there will be a difference in entropy between an individual of, say, 20 years, and the same individual 80 years old. The goal of this article is to demonstrate that the second law does not tell us that the cell necessarily must go toward a high entropy state and stay that way, but that it is possible according to statistical mechanics for an old cell to experience a return to a younger state. We find the probability of this spontaneous return to a more ordered state to be expressed by P = 10^(-202)^(-889). In spite of this number, it does show that a reversal of the aging process is not prohibited by nature. There is a theoretical possibility of rejuvenation. Whether this will ever become a practical reality is another matter.

Ian von Hegner

2012-12-05T23:59:59.000Z

343

Mechanical drill string jar  

SciTech Connect

An improved mechanical drill string jar is described that allows uninhibited telescoping movement to the normal drilling condition. The drill string jar consists of: (a) an elongated, generally cylindrical, body usable as a drill string element; (b) axial motion resistance means situated in the annular opening; (c) bias means operatively associated with at least one element of the splined pair to rotate the pair out of alignment when the splined pair is rotationally disengaged; (d) opposed cooperating surfaces on at least two of the spline teeth situated such that forced axial relative motion of the splined pair will produce opposed radial forces on the teeth; (e) means intrinsic to at least one element of the splined pair to permit resisted radial displacement of the spline teeth when forced axial relative motion occurs, to permit one element to move axially through the other; (f) cam surfaces on at least one of the teeth situated to force rotational alignment of the splined pair when telescoping movement is from a jarring condition toward the normal drilling condition; (g) relative rotation resistance means situated in the annular opening, structurally engaged with the pair of telescoping members such that relative rotation therebetween will be resisted; (h) striker and anvil means situated in the annular opening, operatively associated with the telescoping pair of elements, such that axial relative movement therebetween will be solidly stopped at the axial extreme condition; (i) a flow-through fluid channel means extending between the means to attach to the continuing drill string; and (j) seal means situated in the annular opening, operatively associated with the telescoping pair of members, to provide fluid tightness therebetween.

Buck, D.A.

1987-08-25T23:59:59.000Z

344

Apoptosis as a Mechanism for Low Dose Radiation-and Amifostine-Mediated  

NLE Websites -- All DOE Office Websites (Extended Search)

Apoptosis as a Mechanism for Low Dose Radiation- and Amifostine-Mediated Apoptosis as a Mechanism for Low Dose Radiation- and Amifostine-Mediated Chromosomal Inversion Responses Pam Sykes Flinders University and Medical Centre Abstract Low dose radiation and the chemical radioprotector amifostine have both been shown to protect cells from the immediate and delayed effects of radiation exposure. They display a number of distinct similarities including their ability to protect cells against radiation-induced DNA damage, radiation-induced cell death and metastases formation. Amifostine, which protects cells from the toxic effects of ionizing radiation, has a broad range of activities including free radical scavenging, polyamine-like DNA binding, and induction of hypoxia and redox-regulated genes. Amifostine’s ability to protect cells is often

345

Helicase activity on DNA as a propagating front  

E-Print Network (OSTI)

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.

Somendra M. Bhattacharjee

2003-07-16T23:59:59.000Z

346

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

Soares, M.B.; Efstratiadis, A.

1996-01-09T23:59:59.000Z

347

THERMODYNAMICS AND MECHANISMS OF SINTERING  

E-Print Network (OSTI)

E. Hoge and Joseph A. Pask, "Thermodynamics of So:!.id StateJoseph A. Pask, "Thermodynamics and Geometric Considerations8419 r- ,y / ( /)~; - - I THERMODYNAMICS AND MECHANISMS OF

Pask, J.A.

2011-01-01T23:59:59.000Z

348

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

Science Conference Proceedings (OSTI)

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

Suh, Myungkoo

1995-12-06T23:59:59.000Z

349

PNNL: Doing Business - Contracting Mechanisms  

NLE Websites -- All DOE Office Websites (Extended Search)

Contracting Mechanisms for Work with PNNL Does your small business need expert advice on a technical problem? Does your university research project require state-of-the-art...

350

Mechanical Properties of Thermoelectric Materials  

Science Conference Proceedings (OSTI)

Room Temperature Mechanical Properties of Natural Mineral Based Thermoelectrics: Xiaofeng Fan1; Eldon Case1; Xu Lu1; Donald Morelli1; 1 Michigan State...

351

Mechanical Behavior - Programmaster.org  

Science Conference Proceedings (OSTI)

Oct 20, 2011 ... Ceramic Matrix Composites: Mechanical Behavior ... such as leading edges and combustor liners, are subjected to simultaneous thermal and...

352

Creative cleavages : distributive politics and electoral alignment  

E-Print Network (OSTI)

Distributive politics plays an important role for political elites for their electoral goal. Since the resources that politicians can distribute are limited, they have to decide how to distribute them in order to maximize ...

Kim, Jiyoon, Ph. D. Massachusetts Institute of Technology

2005-01-01T23:59:59.000Z

353

Quantum chaos in elementary quantum mechanics  

E-Print Network (OSTI)

chaos in elementary quantum mechanics so-called integrableIntroduction to Quantum Mechanics (Englewoods Cliff, NJ:Lifshitz E M 1977 Quantum Mechanics (New York: Pergamon) [

Dabaghian, Yuri A; Jensen, R

2005-01-01T23:59:59.000Z

354

129 Lecture Notes Relativistic Quantum Mechanics  

E-Print Network (OSTI)

129 Lecture Notes Relativistic Quantum Mechanics 1 Need for Relativistic Quantum Mechanics's equation of motion in mechanics. The initial condtions to solve the Newton's equation of motion

Murayama, Hitoshi

355

Modeling the Mechanics of the Cytoskeleton  

E-Print Network (OSTI)

Mechanics . . . . . . . . . . . . . . . . . . . . . . .t contribute to the networks mechanics have been removed.R.D. Kamm, Cytoskeletal Mechanics, models and measurements,

Bai, Mo

2012-01-01T23:59:59.000Z

356

6.7 Engineered Enzyme Accelerates DNA Sequencing  

NLE Websites -- All DOE Office Websites (Extended Search)

6 6/1/2011 6 6/1/2011 6.7 Engineered Enzyme Accelerates DNA Sequencing The international effort to decode the human genome is ahead of schedule, thanks in part to new tools that have accelerated DNA sequencing and reduced its cost. (The DOE sequencing team can generate more data in 8 days now than it did in all of 1998, its first full year of operation.) One such tool developed in the mid- 1990s is an enzyme, a type of DNA polymerase. Polymerases, which in their natural form help cells replicate genetic material, are used in sequencing to incorporate fluorescent tags into DNA to identify the locations of specific chemical units. Naturally occurring polymerases tend to reject fluorescent labels. But Stanley Tabor and Charles Richardson of Harvard Medical School, with Office of Science support, applied

357

Photoelectromechanical synthesis of low-cost DNA microarrays  

E-Print Network (OSTI)

Recent advances in de novo gene synthesis, library construction, and genomic selection for target sequencing using DNA from custom microarrays have demonstrated that microarrays can effectively be used as the world's ...

Chow, Brian, 1978-

2008-01-01T23:59:59.000Z

358

DNA repair is the target of novel antibiotics  

E-Print Network (OSTI)

Lloyd, (2006) Rep and PriA helicase activities prevent RecAR. G. Lloyd, (2004) RecG helicase promotes DNA double-strandM. A. Petit, (2005) UvrD helicase, unlike Rep helicase,

Gunderson, Carl Wayne

2007-01-01T23:59:59.000Z

359

Bayesian unsupervised learning of DNA regulatory binding regions  

Science Conference Proceedings (OSTI)

Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either ...

Jukka Corander; Magnus Ekdahl; Timo Koski

2009-01-01T23:59:59.000Z

360

Differential Maintenance of DNA Sequences in Telomeric and Centromeric Heterochromatin  

E-Print Network (OSTI)

Repeated DNA in heterochromatin presents enormous difficulties for whole-genome sequencing; hence, sequence organization in a significant portion of the genomes of multicellular organisms is relatively unknown. Two sequenced ...

DeBaryshe, P. G.

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


361

Optical studies of DNA-wrapped carbon nanotubes  

E-Print Network (OSTI)

This thesis presents a series of detailed optical studies of phonon-assisted relaxation processes in DNA-wrapped single walled carbon nanotubes. Using resonance Raman spectroscopy (RRS) and photoluminescence spectroscopy ...

Chou, Shin Grace

2006-01-01T23:59:59.000Z

362

Low Dose Radiation Research Program: Comparison of DNA Damage...  

NLE Websites -- All DOE Office Websites (Extended Search)

Comparison of DNA Damage Risk from Low-Dose Radiation and Folate Deficiency Arnold C. Huang,1,2 Chantal Courtemanche,1,2 Nicole Kerry,1,2 Susan T. Mashiyama,1,2 Michael Fenech,3...

363

Modulating radiation induced TGFB and ATM signaling in the DNA...  

NLE Websites -- All DOE Office Websites (Extended Search)

TGF and ATM signaling in the DNA damage response Jennifer A. Anderson 1 , Francis A. Cucinotta 2 and Peter O'Neill 1 1 Gray Institute for Radiation Oncology and Biology,...

364

An integrated software tool for detecting criminals using DNA databases  

Science Conference Proceedings (OSTI)

The work showed that the integrated suite of software tools for detecting criminals using DNA databases has achieved the overall objective by providing a working platform for sequence analysis. The work also demonstrated that by integrating BLAST and ...

K. S. Kong; E. Y. K. Ng

2008-04-01T23:59:59.000Z

365

Method for rapid base sequencing in DNA and RNA  

DOE Patents (OSTI)

A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

1987-10-07T23:59:59.000Z

366

Damages to DNA that result in neoplastic transformation  

SciTech Connect

Some topics discussed are: correlation between carcinogens and mutagens; defective DNA repair in uv-damaged xeroderma pigmentosum cells; analysis of nucleotide damage to DNA following exposure to chemicals or radiations; photoreactivation in uv-irradiated Escherichia coli; tumor development in fish; excision repair as an aid in identifying damage; detection of excision repair; role of endonucleases in repair of uv damage; and alkylation products and tumors. (HLW)

Setlow, R.B.

1975-01-01T23:59:59.000Z

367

Unzipping DNA by force: thermodynamics and finite size behaviour  

E-Print Network (OSTI)

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.

Rajeev Kapri; Somendra M. Bhattacharjee

2005-11-22T23:59:59.000Z

368

Lectin cDNA and transgenic plants derived therefrom  

DOE Patents (OSTI)

Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

Raikhel, Natasha V. (Okemos, MI)

1994-01-04T23:59:59.000Z

369

Lectin cDNA and transgenic plants derived therefrom  

DOE Patents (OSTI)

Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon. .

Raikhel, N.V.

1994-01-04T23:59:59.000Z

370

Reactivity studies of antitumor active dirhodium compounds with DNA oligonucleotides  

E-Print Network (OSTI)

The study of the mechanism of action of an antitumor active drug is essential for improving the efficacy and reducing the side effects of the drug as well as for developing better alternatives. In this vein, reactions of dirhodium compounds with DNA oligonucleotides were investigated by the techniques of mass spectrometry, HPLC, and NMR spectroscopic analytical methods. The relative reactivities of three dirhodium compounds, namely Rh2(O2CCH3)4, Rh2(O2CCF3)4, and [Rh2(O2CCH3)2(CH3CN)6](BF4)2, with DNA oligonucleotides were studied and compared to the clinically used anticancer drugs cisplatin and carboplatin using both MALDI and ESI mass spectrometric methods. The compound Rh2(O2CCF3)4 exhibits the highest reactivity among the dirhodium compounds, which is comparable to cisplatin, followed by [Rh2(O2CCH3)2(CH3CN)6](BF4)2, and finally Rh2(O2CCH3)4 which is the least reactive. Various dirhodium-oligonucleotide adducts were detected with both MALDI and ESI methods, which involve substitution of different numbers of the original ligands of the given dirhodium compound. ESI MS was found to be a sufficiently soft ionization method for detecting intact metal adducts, and CID MS-MS was useful for detecting weakly bound species such as axial adducts [M+Rh2(O2CCH3)4] and for comparing the relative bond strength between ligands in the metal adduct. A combination of anion exchange HPLC purification and enzymatic digestion studies of the adducts of Rh2(O2CCH3)4 with the 5'-CCTTCAACTCTC oligonucleotide revealed that Rh2(O2CCH3)4 binds to the center or to the ends of the oligonucleotide sequence by displacement of one or two acetate groups. Kinetic products of the type [M+Rh2(O2CCH3)3] obtained from the reaction of Rh2(O2CCH3)4 with 5'-CTCTCAACTTCC were separated by employing both reverse phase and anion exchange HPLC methods. The adduct that involves binding of the dirhodium unit to the exocyclic N4 atom of C5 and the N7 of A6 was found to be most stable whereas other adducts involving binding of C3 or C12 residues are clearly less stable. Reaction of cis-[Rh2(DAP)(O2CCH3)3(CH3OH)](O2CCH3) (DAP = 1,12- diazaperylene) with 5'-CTCTCAACTTCC produced a major adduct in which DAP group intercalates between 6A and 7A in the double stranded adduct with the rhodium atom that is not coordinated to the DAP group forming a covalent bond to the N7 atom of 6A which lends stability to the adduct.

Kang, Mijeong

2005-12-01T23:59:59.000Z

371

Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA Chains  

Science Conference Proceedings (OSTI)

Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century. Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.

Lee, James Weifu [ORNL; Meller, Amit [Harvard University

2007-01-01T23:59:59.000Z

372

Recombinant methods for screening human DNA excision repair proficiency  

SciTech Connect

A method for measuring DNA excision repair in response to ultraviolet radiation (UV)-induced DNA damage has been developed, validated, and field-tested in cultured human lymphocytes. The methodology is amenable to population-based screening and should facilitate future epidemiologic studies seeking to investigate associations between excision repair proficiency and cancer susceptibility. The impetus for such endeavors derives from the belief that the high incidence of skin cancer in the genetic disorder xeroderma pigmentosum (XP) primarily is a result of the reduced capacity of patients cells to repair UV-induced DNA damage. For assay, UV-irradiated non-replicating recombinant plasmid DNA harboring a chloramphenicol acetyltransferase (CAT) indicator gene is introduced into lymphocytes using DEAE-dextran short-term transfection conditions. Exposure to UV induces transcriptionally-inactivating DNA photoproducts in the plasmid DNA which inactivate CAT gene expression. Excision repair of the damaged CAT gene is monitored indirectly as a function of reactivated CAT enzyme activity following a 40 hour repair/expression incubation period.

Athas, W.F.

1988-01-01T23:59:59.000Z

373

Exploring the specificity and mechanisms of siRNA-mediated gene silencing in mammalian cells  

E-Print Network (OSTI)

Complementary short interfering RNAs (siRNAs) are routinely used to knockdown gene expression. siRNAs bind to their target sequence and guide transcript cleavage and subsequent degradation. This type of silencing is ...

Alemn, Lourdes Maria

2008-01-01T23:59:59.000Z

374

The Role of Chromatin Structure and Histone Modifications in Gene Silencing at the Ribosomal DNA Locus in Saccharomyces cerevisiae  

E-Print Network (OSTI)

One of the fundamental questions in science is how chromatin transitions from actively transcribed euchromatin to silent heterochromatin, and what factors affect this transition. One area of my research has focused on understanding the differences in the chromatin structure of active and silent regions in the ribosomal DNA locus (rDNA), a heterochromatin region in S. cerevisiae. Secondly, I have focused on understanding a histone methyltransferase Set1, which is involved in both euchromatin and heterochromatin regions. To distinguish actively transcribed open regions of chromatin from silent and closed regions of chromatin, we have expressed a DNA methyltransferase M.CviPI in vivo to utilize its accessibility to GpC sites. We have used this technique to study changes in nucleosome positioning within the NTS2 region of the rDNA in two cases: as a result of a silencing defect caused by the loss of Sir2, a histone deacetylase involved in silencing at the rDNA, and as an indicator of active transcription by RNA Pol I. Using this technique, we observed differences between open and closed chromatin structure by changes in nucleosome positioning within NTS2. Additionally, we have observed the presence of bound factors within the 35S rRNA gene promoter that are unique to actively transcribed genes. The second area of my research focused on the protein methyltransferase Set1 that mono-, di-, and trimethylates lysine 4 of histone H3 (H3K4) utilizing the methyl group from S-adenosyl methionine (SAM). Set1 is part of a multi protein complex called COMPASS (Complex associated with Set1), and is associated with both actively transcribed and silent regions. Thirty mutants of Set1 were made within the SET domain to learn more about the catalytic mechanism of Set1. The crystal structures of human SET domain proteins, as well as sequence alignments and a random mutagenesis of yeast Set1, were used to identify conserved amino acids in the SET domain of Set1. Mutants were analyzed for their effect on histone methylation in vivo, silencing of RNA Pol II transcription within the rDNA, suppression of ipl1-2, and COMPASS complex formation. Our results show that trimethylated H3K4 is required for silencing of RNA Pol II transcription at the rDNA. Overall, we have shown the importance of tyrosine residues in SET domain proteins. To summarize, my research has strived to understand chromatin structure and the factors that affect the transition between euchromatin and heterochromatin.

Williamson, Kelly M.

2011-05-01T23:59:59.000Z

375

Quantum mechanics as "space-time statistical mechanics"?  

E-Print Network (OSTI)

In this paper we discuss and analyse the idea of trying to see (non-relativistic) quantum mechanics as a ``space-time statistical mechanics'', by using the classical statistical mechanical method on objective microscopic space-time configurations. It is argued that this could perhaps be accomplished by giving up the assumption that the objective ``state'' of a system is independent of a future measurement performed on the system. This idea is then applied in an example of quantum state estimation on a qubit system.

Anders Mnsson

2005-01-24T23:59:59.000Z

376

Nov. 6, 2001. DNA routines for Maple 7 Contents: 1) Instructions for ...  

E-Print Network (OSTI)

... Janeiro - UERJ - Brazil. *********************************************************** ********** 1) Instructions for Windows users 1) unzip dna.zip into any directory !

377

Crystal Structure of pi Initiator Protein-iteron Complex of Plasmid R6K: Implications for Initiation of Plasmid DNA Replication  

Science Conference Proceedings (OSTI)

We have determined the crystal structure of a monomeric biologically active form of the {pi} initiator protein of plasmid R6K as a complex with a single copy of its cognate DNA-binding site (iteron) at 3.1-{angstrom} resolution. The initiator belongs to the family of winged helix type of proteins. The structure reveals that the protein contacts the iteron DNA at two primary recognition helices, namely the C-terminal {alpha}4' and the N-terminal {alpha}4 helices, that recognize the 5' half and the 3' half of the 22-bp iteron, respectively. The base-amino acid contacts are all located in {alpha}4', whereas the {alpha}4 helix and its vicinity mainly contact the phosphate groups of the iteron. Mutational analyses show that the contacts of both recognition helices with DNA are necessary for iteron binding and replication initiation. Considerations of a large number of site-directed mutations reveal that two distinct regions, namely {alpha}2 and {alpha}5 and its vicinity, are required for DNA looping and initiator dimerization, respectively. Further analysis of mutant forms of {pi} revealed the possible domain that interacts with the DnaB helicase. Thus, the structure-function analysis presented illuminates aspects of initiation mechanism of R6K and its control.

Swan,M.; Bastia, D.; Davies, C.

2006-01-01T23:59:59.000Z

378

An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996  

Science Conference Proceedings (OSTI)

The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.

Netzel, T.L.

1997-03-01T23:59:59.000Z

379

Probing 3'-ssDNA Loop Formation in E. coli RecBCD/RecBC-DNA Com-plexes using Non-natural DNA: A Model for "Chi" Recognition Complexes  

E-Print Network (OSTI)

in RecBCD-DNA Complexes Keywords: helicase; fluorescence; motor protein; recombination; thermodynamics with a Cy3-labeled reference DNA which undergoes a Cy3 fluorescence enhancement upon protein binding. We) and two series of non-fluorescent competitor DNA molecules (II and III in Figure 1a) for the reasons

Ju, Tao

380

Geometric Mechanics -Part I January 13, 2009  

E-Print Network (OSTI)

Geometric Mechanics - Part I Bob Rink January 13, 2009 Contents 1 Mechanical systems 4 1.1 Two Lagrangian mechanics 9 2.1 New position variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-Lagrange equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.4 Natural mechanical systems

Hanssmann, Heinz

Note: This page contains sample records for the topic "dna cleavage mechanism" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
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381

Geometric Mechanics -Part I January 23, 2009  

E-Print Network (OSTI)

Geometric Mechanics - Part I Bob Rink January 23, 2009 Contents 1 Mechanical systems 4 1.1 Two Lagrangian mechanics 9 2.1 New position variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-Lagrange equations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.4 Natural mechanical systems

Rink, Bob

382

Quantum Mechanics and Representation Theory Columbia University  

E-Print Network (OSTI)

Quantum Mechanics and Representation Theory Peter Woit Columbia University Texas Tech, November 21 2013 Peter Woit (Columbia University) Quantum Mechanics and Representation Theory November 2013 1 / 30 #12;Does Anyone Understand Quantum Mechanics? "No One Understands Quantum Mechanics" "I think

Woit, Peter

383

Microstructure Components and Mechanical Properties of an ...  

Science Conference Proceedings (OSTI)

Effects of Microstructural and Mechanical Length Scales on Fatigue Crack ... Components and Mechanical Properties of an Acicular Ferrite Pipeline Steel.

384

Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase  

Science Conference Proceedings (OSTI)

Hexameric DnaB helicase unwinds the DNA double helix during replication of genetic material in bacteria. DnaB is an essential bacterial protein; therefore, it is an important potential target for antibacterial drug discovery. We report a crystal structure of the N-terminal region of DnaB from the pathogen Mycobacterium tuberculosis (MtDnaBn), determined at 2.0 {angstrom} resolution. This structure provides atomic resolution details of formation of the hexameric ring of DnaB by two distinct interfaces. An extensive hydrophobic interface stabilizes a dimer of MtDnaBn by forming a four-helix bundle. The other, less extensive, interface is formed between the dimers, connecting three of them into a hexameric ring. On the basis of crystal packing interactions between MtDnaBn rings, we suggest a model of a helicase-primase complex that explains previously observed effects of DnaB mutations on DNA priming.

Biswas, Tapan; Tsodikov, Oleg V. (Michigan)

2009-01-15T23:59:59.000Z

385

Construction and biological activities of the first infectious cDNA clones of the genus Foveavirus  

SciTech Connect

Grapevine rupestris stem pitting-associated virus (GRSPaV, genus Foveavirus, family Betaflexiviridae) is one of the most prevalent viruses in grapevines and is associated with three distinct diseases: rupestris stem pitting, vein necrosis and Syrah decline. Little is known about the biology and pathological properties of GRSPaV. In this work, we engineered a full-length infectious cDNA clone for GRSPaV and a GFP-tagged variant, both under the transcriptional control of Cauliflower mosaic virus 35 S promoter. We demonstrated that these cDNA clones were infectious in grapevines and Nicotiana benthamiana through fluorescence microscopy, RT-PCR, Western blotting and immuno electron microscopy. Interestingly, GRSPaV does not cause systemic infection in four of the most commonly used herbaceous plants, even in the presence of the movement proteins of two other viruses which are known to complement numerous movement-defective viruses. These infectious clones are the first of members of Foveavirus which would allow further investigations into mechanisms governing different aspects of replication for GRSPaV and perhaps related viruses.

Meng, Baozhong, E-mail: bmeng@uoguelph.ca [Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada N1G2W1 (Canada)] [Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada N1G2W1 (Canada); Venkataraman, Srividhya; Li, Caihong; Wang, Weizhou [Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada N1G2W1 (Canada)] [Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada N1G2W1 (Canada); Dayan-Glick, Cathy; Mawassi, Munir [The Plant Pathology Department-The Virology Unit, Plant Protection Institute, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250 (Israel)] [The Plant Pathology Department-The Virology Unit, Plant Protection Institute, Agricultural Research Organization, The Volcani Center, Bet-Dagan 50250 (Israel)

2013-01-20T23:59:59.000Z

386

Endogenous DNA Damage and Risk of Testicular Germ Cell Tumors  

SciTech Connect

Testicular germ cell tumors (TGCT) are comprised of two histologic groups, seminomas and nonseminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable endogenous DNA damage. To assess our hypothesis, we conducted a case-case analysis of seminomas and nonseminomas using the alkaline comet assay to quantify single-strand DNA breaks and alkali-labile sites. The Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort provided 112 TGCT cases (51 seminomas & 61 nonseminomas). A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95%CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modeled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with nonseminoma compared to seminoma (OR{sub 50th percentile} = 3.31, 95%CI: 1.00, 10.98; OR{sub 75th percentile} = 3.71, 95%CI: 1.04, 13.20; p for trend=0.039). OTM exhibited similar, albeit statistically non-significant, risk estimates (OR{sub 50th percentile} = 2.27, 95%CI: 0.75, 6.87; OR{sub 75th percentile} = 2.40, 95%CI: 0.75, 7.71; p for trend=0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that endogenous DNA damage levels are higher in patients who develop nonseminoma compared with seminoma. This may partly explain the more aggressive biology and younger age-of-onset of this histologic subgroup compared with the relatively less aggressive, later-onset seminoma.

Cook, M B; Sigurdson, A J; Jones, I M; Thomas, C B; Graubard, B I; Korde, L; Greene, M H; McGlynn, K A

2008-01-18T23:59:59.000Z

387

Mechanical Behavior of Indium Nanostructures  

NLE Websites -- All DOE Office Websites (Extended Search)

Mechanical Behavior of Indium Nanostructures Print Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of Waterloo, California Institute of Technology, and Los Alamos National Laboratory have collaborated with a team at ALS Beamline 12.3.2 to investigate the small-scale mechanics of indium nanostructures. Scanning x-ray microdiffraction (μSXRD) studies revealed that the indium microstructure is typical of a well-annealed metal, containing very few initial dislocations and showing close-to-theoretical strength.

388

Mechanical properties of nanophase materials  

SciTech Connect

It has become possible in recent years to synthesize new materials under controlled conditions with constituent structures on a nanometer size scale (below 100 nm). These novel nanophase materials have grain-size dependent mechanical properties significantly different than those of their coarser-grained counterparts. For example, nanophase metals are much stronger and apparently less ductile than conventional metals, while nanophase ceramics are more ductile and more easily formed than conventional ceramics. The observed mechanical property changes are related to grain size limitations and/or the large percentage of atoms in grain boundary environments; they can also be affected by such features as flaw populations, strains and impurity levels that can result from differing synthesis and processing methods. An overview of what is presently known about the mechanical properties of nanophase materials, including both metals and ceramics, is presented. Some possible atomic mechanisms responsible for the observed behavior in these materials are considered in light of their unique structures.

Siegel, R.W. [Argonne National Lab., IL (United States); Fougere, G.E. [Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering

1993-11-01T23:59:59.000Z

389

Dislocations and Mechanical Properties - TMS  

Science Conference Proceedings (OSTI)

... 3.11 The Herring-Galt Experiment; 3.12 Multiplication Mechanisms of Dislocations; 3.13 The Frank-Read Double Mill ("Dislocation Source") and the Bulge...

390

The Interpretation of Quantum Mechanics  

E-Print Network (OSTI)

In this paper, we demonstrate how the interpretation of quantum mechanics due to Land\\'e resolves the Schr\\"odinger cat paradox and disposes of the problem of wave function collapse.

H. V. Mweene

2004-11-09T23:59:59.000Z

391

Hyper-Hamiltonian quantum mechanics  

E-Print Network (OSTI)

We present a modification of quantum mechanics with a *possible worlds* semantics. It is shown that `gauge' degrees of freedom along possible worlds can be used to encode gravitational information.

Vladimir Trifonov

2006-03-02T23:59:59.000Z

392

Quantum mechanics needs no interpretation  

E-Print Network (OSTI)

Probabilistic description of results of measurements and its consequences for understanding quantum mechanics are discussed. It is shown that the basic mathematical structure of quantum mechanics like the probability amplitude, Born rule, probability density current, commutation relations, momentum operator, uncertainty relations, rules for including the scalar and vector potentials and existence of antiparticles can be derived from the definition of the mean values of the space coordinates and time. Equations of motion of quantum mechanics, the Klein-Gordon equation, Schroedinger equation and Dirac equation are obtained from requirement of the relativistic invariance of the theory. Limit case of localized probability densities leads to the Hamilton-Jacobi equation of classical mechanics. Many particle systems are also discussed.

L. Skala; V. Kapsa

2004-12-22T23:59:59.000Z

393

Free will and quantum mechanics  

E-Print Network (OSTI)

A simple example is provided showing that violation of free will allows to reproduce the quantum mechanical predictions, and that the Clauser-Horne parameter can take the maximum value 4 for a proper choice.

Antonio Di Lorenzo

2011-05-05T23:59:59.000Z

394

Mechanisms of Banner Cloud Formation  

Science Conference Proceedings (OSTI)

Banner clouds are clouds in the lee of steep mountains or sharp ridges. Their formation has previously been hypothesized as due to three different mechanisms: (i) vertical uplift in a lee vortex (which has a horizontal axis), (ii) adiabatic ...

Matthias Voigt; Volkmar Wirth

2013-11-01T23:59:59.000Z

395

Alloy by Double Mechanical Milling  

Science Conference Proceedings (OSTI)

The results show that the morphology of double mechanical milling powder is regular and the TiAl phase and Ti3Al phase were observed in the powders.

396

Mechanical Behavior of Indium Nanostructures  

NLE Websites -- All DOE Office Websites (Extended Search)

Mechanical Behavior of Indium Nanostructures Print Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of Waterloo, California Institute of Technology, and Los Alamos National Laboratory have collaborated with a team at ALS Beamline 12.3.2 to investigate the small-scale mechanics of indium nanostructures. Scanning x-ray microdiffraction (μSXRD) studies revealed that the indium microstructure is typical of a well-annealed metal, containing very few initial dislocations and showing close-to-theoretical strength.

397

Mechanical Behavior of Indium Nanostructures  

NLE Websites -- All DOE Office Websites (Extended Search)

Mechanical Behavior of Indium Nanostructures Print Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended ductility, and high electrical conductivity. With the size of electronic devices continuing to shrink and the promise of indium-based nanotechnologies, it is important to develop a fundamental understanding of this material's small-scale mechanical properties and reliability. Researchers from the University of Waterloo, California Institute of Technology, and Los Alamos National Laboratory have collaborated with a team at ALS Beamline 12.3.2 to investigate the small-scale mechanics of indium nanostructures. Scanning x-ray microdiffraction (μSXRD) studies revealed that the indium microstructure is typical of a well-annealed metal, containing very few initial dislocations and showing close-to-theoretical strength.

398

Mechanical drive for blood pump  

DOE Patents (OSTI)

This patent relates to a highly efficient blood pump to be used as a replacement for a ventricle of the human heart to restore people disabled by heart disease. The mechanical drive of the present invention is designed to operate in conjunction with a thermoelectric converter power source. The mechanical drive system essentially converts the output of a rotary power into pulsatile motion so that the power demand from the thermoelectric converter remains essentially constant while the blood pump output is pulsed. (auth)

Bifano, N.J.; Pouchot, W.D.

1975-07-29T23:59:59.000Z

399

Functionalized nanopore-embedded electrodes for rapid DNA sequencing  

E-Print Network (OSTI)

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Green's Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.

Haiying He; Ralph H. Scheicher; Ravindra Pandey; Alexandre Reily Rocha; Stefano Sanvito; Anton Grigoriev; Rajeev Ahuja; Shashi P. Karna

2007-08-29T23:59:59.000Z

400

First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G  

Science Conference Proceedings (OSTI)

APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S. (Pitt); (UMASS, MED); (SLUHSC); (UCSF); (UMM)

2012-04-04T23:59:59.000Z

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


401

Links between persistent DNA damage, genome instability, and aging  

NLE Websites -- All DOE Office Websites (Extended Search)

Links between persistent DNA damage, genome instability, and aging Links between persistent DNA damage, genome instability, and aging William Dynan Medical College of Georgia Abstract There is considerable overlap between cellular and molecular changes that occur in response to low doses of ionizing radiation and those that occur during aging. Both processes are characterized by accumulation of persistent DNA damage ("wear and tear" on the genome), accumulation of protein and lipid oxidation products, loss of regenerative capacity at the cellular and tissue level, and increased incidence of cancer. These observations support a hypothesis that exposure to low-dose ionizing radiation accelerates normal, aging-related tissue changes. We have investigated this hypothesis using a genetically tractable model organism, the Japanese medaka fish. The medaka is a whole-animal vertebrate

402

Nonlinear excitations in DNA: Aperiodic models vs actual genome sequences  

E-Print Network (OSTI)

We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Dom\\'\\i nguez-Adame {\\em et al.}, Phys. Rev. E {\\bf 52}, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on the specific sequence. The results of our model are consistent with the stick-slip dynamics of the unzipping process observed in experiments. We also show that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A {\\bf 193}, 263 (1994)] is a useful tool to identify key regions in DNA that control the dynamical behavior of large segments. Additionally, our results lead to further insights in the phenomenology observed in aperiodic systems.

Sara Cuenda; Angel Sanchez

2004-07-02T23:59:59.000Z

403

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. 1 fig.

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

1997-12-30T23:59:59.000Z

404

Privacy issues with DNA databases and retention of individuals' DNA information by law enforcement agencies: the holding of the European Court of Human Rights case S and Marper v. United Kingdom should be adapted to American Fourth Amendment jurisprudence  

Science Conference Proceedings (OSTI)

When law enforcement agencies collect, retain, and use individuals' DNA information in DNA databases for crime prevention purposes the presumption of innocence is reduced for those individuals. Collection and use of DNA information has benefits, greatly ... Keywords: DNA, DNA databases, European Court of Human Rights, comparative law, constitutional law, criminal procedure, fourth amendment, privacy

Michael Lwin

2010-06-01T23:59:59.000Z

405

Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation  

E-Print Network (OSTI)

At the onset of X Chromosomes Inactivation, the vital process whereby female mammal cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-Inactivation Center) regions. The mechanism inducing recognition and pairing of the X's remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called ``pairing sites'') involved, we dissect the mechanical basis of Xic colocalization by using a Statistical Physics model. We show that soluble DNA specific binding molecules, as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes, but only when their concentration, or chemical affinity, rises above a threshold value, as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data.

A. Scialdone; M. Nicodemi

2009-10-13T23:59:59.000Z

406

Evolutionary theory, web-search technology combine for DNA analysis  

NLE Websites -- All DOE Office Websites (Extended Search)

Sequedex: bioinformatics breakthrough Sequedex: bioinformatics breakthrough Evolutionary theory, web-search technology combine for DNA analysis Sequedex: bioinformatics breakthrough with clinical & environmental applications. October 4, 2012 From left, Los Alamos scientists Joel Berendzen, Ben McMahon, Mira Dimitrijevic, Nick Hengartner and Judith Cohn From left, Los Alamos scientists Joel Berendzen, Ben McMahon, Mira Dimitrijevic, Nick Hengartner and Judith Cohn Contact Nancy Ambrosiano Communications Office (505) 667-0471 Email The Sequedex team was originally tasked with investigating DNA analysis on the Laboratory's Roadrunner supercomputer, but quickly realized that improvements in the algorithm made having so much hardware unnecessary. "They asked us to build a rocket ship," Berendzen said, "but instead

407

cDNA encoding a polypeptide including a hevein sequence  

DOE Patents (OSTI)

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

1993-02-16T23:59:59.000Z

408

KTH Mechanics SE-100 44 Stockholm, Sweden  

E-Print Network (OSTI)

KTH Mechanics SE-100 44 Stockholm, Sweden Activity Report 2009 Contents 1. Introduction 2 a short overview of the structure and activities at the depart- ment of Mechanics, KTH during the year courses in mechanics, fluid mechanics and structural mechanics given for students and programmes from

Haviland, David

409

Does the Higgs Mechanism Exist?  

E-Print Network (OSTI)

This paper explores the argument structure of the concept of spontaneous symmetry breaking in the electroweak gauge theory of the Standard Model: the so-called Higgs mechanism. As commonly understood, the Higgs argument is designed to introduce the masses of the gauge bosons by a spontaneous breaking of the gauge symmetry of an additional field, the Higgs field. The technical derivation of the Higgs mechanism, however, consists in a mere re-shuffling of degrees of freedom by transforming the Higgs Lagrangian in a gauge-invariant manner. This already raises serious doubts about the adequacy of the entire manoeuvre. It will be shown that no straightforward ontic interpretation of the Higgs mechanism is tenable since gauge transformations possess no real instantiations. In addition, the explanatory value of the Higgs argument will be critically examined.

Holger Lyre

2008-06-08T23:59:59.000Z

410

Reaction mechanisms of pair transfer  

E-Print Network (OSTI)

The mechanisms of nuclear transfer reactions are described for the transfer of two nucleons from one nucleus to another. Two-nucleon overlap functions are defined in various coordinate systems, and their transformation coefficients given between coordinate systems. Post and prior couplings are defined for sequential transfer mechanisms, and it is demonstrated that the combination of `prior-post' couplings avoids non-orthogonality terms, but does not avoid couplings that do not have good zero-range approximations. The simultaneous and sequential mechanisms are demonstrated for the $^{124}$Sn(p,t)$^{122}$Sn reaction at 25 MeV using shell-model overlap functions. The interference between the various simultaneous and sequential amplitudes is shown.

Ian J. Thompson

2012-04-13T23:59:59.000Z

411

Majorana Electroformed Copper Mechanical Analysis  

SciTech Connect

The MAJORANA DEMONSTRATOR is a large array of ultra-low background high-purity germanium detectors, enriched in 76Ge, designed to search for zero-neutrino double-beta decay. The DEMONSTRATOR will utilize ultra high purity electroformed copper for a variety of detector components and shielding. A preliminary mechanical evaluation was performed on the Majorana prototype electroformed copper material. Several samples were removed from a variety of positions on the mandrel. Tensile testing, optical metallography, scanning electron microscopy, and hardness testing were conducted to evaluate mechanical response. Analyses carried out on the Majorana prototype copper to this point show consistent mechanical response from a variety of test locations. Evaluation shows the copper meets or exceeds the design specifications.

Overman, Nicole R.; Overman, Cory T.; Kafentzis, Tyler A.; Edwards, Danny J.; Hoppe, Eric W.

2012-04-30T23:59:59.000Z

412

The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier?Gorlin syndrome  

Science Conference Proceedings (OSTI)

The recognition of distinctly modified histones by specialized 'effector' proteins constitutes a key mechanism for transducing molecular events at chromatin to biological outcomes. Effector proteins influence DNA-templated processes, including transcription, DNA recombination and DNA repair; however, no effector functions have yet been identified within the mammalian machinery that regulate DNA replication. Here we show that ORC1 - a component of ORC (origin of replication complex), which mediates pre-DNA replication licensing - contains a bromo adjacent homology (BAH) domain that specifically recognizes histone H4 dimethylated at lysine 20 (H4K20me2). Recognition of H4K20me2 is a property common to BAH domains present within diverse metazoan ORC1 proteins. Structural studies reveal that the specificity of the BAH domain for H4K20me2 is mediated by a dynamic aromatic dimethyl-lysine-binding cage and multiple intermolecular contacts involving the bound peptide. H4K20me2 is enriched at replication origins, and abrogating ORC1 recognition of H4K20me2 in cells impairs ORC1 occupancy at replication origins, ORC chromatin loading and cell-cycle progression. Mutation of the ORC1 BAH domain has been implicated in the aetiology of Meier-Gorlin syndrome (MGS), a form of primordial dwarfism, and ORC1 depletion in zebrafish results in an MGS-like phenotype. We find that wild-type human ORC1, but not ORC1-H4K20me2-binding mutants, rescues the growth retardation of orc1 morphants. Moreover, zebrafish depleted of H4K20me2 have diminished body size, mirroring the phenotype of orc1 morphants. Together, our results identify the BAH domain as a novel methyl-lysine-binding module, thereby establishing the first direct link between histone methylation and the metazoan DNA replication machinery, and defining a pivotal aetiological role for the canonical H4K20me2 mark, via ORC1, in primordial dwarfism.

Kuo, Alex J.; Song, Jikui; Cheung, Peggie; Ishibe-Murakami, Satoko; Yamazoe, Sayumi; Chen, James K.; Patel, Dinshaw J.; Gozani, Or (Stanford); (MSKCC); (Stanford-MED)

2012-07-11T23:59:59.000Z

413

Mechanical model for ductility loss  

Science Conference Proceedings (OSTI)

A mechanical model was constructed to probe into the mechanism of ductility loss. Fracture criterion based on critical localized deformation was undertaken. Two microstructure variables were considered in the model. Namely, the strength ratio of grain boundary affected area to the matrix, ..cap omega.., and the linear fraction, x, of grain boundary affected area. A parametrical study was carried out. The study shows that the ductility is very sensitive to those microstructure parameters. The functional dependence of ductility to temperature as well as strain-rate, suggested by the model, is demonstrated to be consistent with the observation.

Hu, W.L.

1980-02-11T23:59:59.000Z

414

Stock Mechanics: a classical approach  

E-Print Network (OSTI)

New theoretical approaches about forecasting stock markets are proposed. A mathematization of the stock market in terms of arithmetical relations is given, where some simple (non-differential, non-fractal) expressions are also suggested as general stock price formuli in closed forms which are able to generate a variety of possible price movements in time. A kind of mechanics is submitted to cover the price movements in terms of classical concepts. Where utilizing stock mechanics to grow the portfolios in real markets is also proven.

Tuncay, C

2005-01-01T23:59:59.000Z

415

DNA damage produced by exposure of supercoiled plasmid DNA to high- and low-LET ionizing radiation: Effects of hydroxyl radical quenchers. DNA breakage, neutrons, OH radicals  

SciTech Connect

A supercoiled plasmid of 7300 base pairs was isolated and exposed in an aqueous environment to {sup 60}Co {gamma} rays and JANUS 0.85 MeV fission-spectrum neutrons. Dose responses for the production of single-strand breaks (SSBs), double-strand breaks (DSBs) and alkali-labile sites (ALSs) were compared with computations made from the conversion of the supercoil to its relaxed and linear forms. The relative biological effectiveness (RBE) for production of SSBs and DSBs was similar to that previously measured in the cellular environment. The RBE for destruction of genetic transforming activity of M13 viral DNA followed that for DNA damage. This is in contrast to the situation for biological effects such as lethality, mutagenesis, and cellular transformation measured in mammalian cells, where the RBE values are reversed. The role of hydroxyl (OH) radical in DNA damage induction by neutrons was investigated by exposure of plasmid in the presence of known quenchers of this species. Of four quenchers tested, all were able to reduce the yields of both SSBs and DSBs. These findings are consistent with a model for SSB and DSB induction by high linear energy transfer that involves OH radical mediation.

Peak, J.G.; Ito, T.; Peak, M.J. [Argonne National Lab., IL (United States); Robb, F.T. [Univ. of Maryland, Baltimore, MD (United States). Center for Marine Biotechnology

1994-08-01T23:59:59.000Z

416

221B Lecture Notes Relativistic Quantum Mechanics  

E-Print Network (OSTI)

221B Lecture Notes Relativistic Quantum Mechanics 1 Need for Relativistic Quantum Mechanics We, similarly to the Newton's equation of motion in mechanics. The initial condtions to solve the Newton

Murayama, Hitoshi

417

Mathematics 658 Nonlinear Dynamics and Mechanics  

E-Print Network (OSTI)

Mathematics 658 Nonlinear Dynamics and Mechanics Instructor: Anthony M. Bloch. Office: 4842 East differential equations and dynamical systems, with applications to various mechanical and physical systems, nonlinear stability theory, Lagrangian and Hamiltonian mechanics, integrable systems, reduction

Bloch, Anthony

418

Statistical mechanics of a cat's cradle  

E-Print Network (OSTI)

cells. In our view, cell mechanics remains at an early stagefor physics Statistical mechanics of a cats cradle Tongyemodel [2, 3] of cell mechanics [7], but here we limit

Shen, Tongye; Wolynes, Peter G

2006-01-01T23:59:59.000Z

419

MECHANICS AND NONLINEAR CONTROL: MAKING UNDERWATER VEHICLES  

E-Print Network (OSTI)

MECHANICS AND NONLINEAR CONTROL: MAKING UNDERWATER VEHICLES RIDE AND GLIDE Naomi Ehrich Leonard \\Lambda \\Lambda Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544 naomi@princeton.edu Abstract: Methods from geometric mechanics and dynamical systems theory make

Leonard, Naomi

420

221B Lecture Notes Relativistic Quantum Mechanics  

E-Print Network (OSTI)

221B Lecture Notes Relativistic Quantum Mechanics 1 Need for Relativistic Quantum Mechanics We's equation of motion in mechanics. The initial condtions to solve the Newton's equation of motion

Murayama, Hitoshi

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


421

High-level open evolvable systems design by process-oriented modeling: application to DNA replication mechanism  

Science Conference Proceedings (OSTI)

Open Evolvable Systems' design requires a methodological [1] and conceptual paradigm different from the conventional software design. Evolvable Systems' research [2, 6, 16, and 17] has established itself as a new research field, but the content is more ... Keywords: abstractions, design, design patterns, evolvable systems, framework, method, methodologies, modeling, process-oriented modeling, requirements analysis, requirements and architecture modeling, software engineering, specification

Behzad Bastani; Hoda Bastani

2007-11-01T23:59:59.000Z

422

Novel genotoxins that target estrogen receptor- and androgen receptor- positive cancers : identification of DNA adducts, pharmacokinetics, and mechanism  

E-Print Network (OSTI)

We have designed and synthesized novel molecules capable of selectively killing tumor cells that aberrantly express steroid hormone receptors. Many human breast cancers express high levels of the estrogen receptor (ER), ...

Hillier, Shawn M. (Shawn Matthew)

2005-01-01T23:59:59.000Z

423

The Mechanism of Low Dose Radiation Risk Associated with Diagnostic X-rays,  

NLE Websites -- All DOE Office Websites (Extended Search)

Mechanism of Low Dose Radiation Risk Associated with Diagnostic X-rays, Mechanism of Low Dose Radiation Risk Associated with Diagnostic X-rays, PET, and Gamma-rays Douglas Boreham McMaster University Abstract The goal of this project was to investigate low dose ionizing radiation effects associated with exposure to diagnostic computed tomography (CT) or positron emission tomography (PET) scans. Biological effects were evaluated in wild type and Trp53+/- heterozygous females, following in vivo exposure to diagnostic CT (75kVp, 200µ) or PET (18F-FDG) scans. The short term biological effects following CT or PET scans were evaluated in order to understand biological modification of mechanisms, such as DNA repair processes and apoptosis, that might alter long term cancer risk. Corresponding life-time cancer risk studies are in progress. Short-term

424

Xiangchun Xuan Department of Mechanical  

E-Print Network (OSTI)

­liquid interface [13, 14]. Therefore, pumps, valves, and other mechanical moving parts are eliminated in electro April 20, 2007 Revised May 21, 2007 Accepted May 21, 2007 Review Joule heating in electrokinetic flow Joule heating in electrokinetic flow, which is known to cause temperature variations in liquids and draw

Xuan, Xiangchun "Schwann"

425

Mechanical scriber for semiconductor devices  

DOE Patents (OSTI)

A mechanical scriber using a scribing tip, such as a diamond, provides controlled scriber forces with a spring-loaded compound lever arrangement. The scribing force and range of scribing depth are adjusted by a pair of adjustable micrometer heads. A semiconductor device, such as a multilayer solar cell, can be formed into scribed strips at each layer. 5 figs.

Lin, P.T.

1985-03-05T23:59:59.000Z

426

Mechanical scriber for semiconductor devices  

DOE Patents (OSTI)

A mechanical scriber using a scribing tip, such as a diamond, provides controlled scriber forces with a spring-loaded compound lever arrangement. The scribing force and range of scribing depth are adjusted by a pair of adjustable micrometer heads. A semiconductor device, such as a multilayer solar cell, can be formed into scribed strips at each layer.

Lin, Peter T. (East Brunswick, NJ)

1985-01-01T23:59:59.000Z

427

Mechanical and Hydraulic Press Brakes  

Science Conference Proceedings (OSTI)

...drives, with mechanical linkages from motor to flywheel to clutch to gears to crankshaft to crank arm to ram (Fig. 4). They all have one thing in common: a crankshaft action that converts rotary motion into straight, reciprocating motion (Fig. 5). During a stroke cycle, the crank arm drives the ram down...

428

Battery Vent Mechanism And Method  

DOE Patents (OSTI)

Disclosed herein is a venting mechanism for a battery. The venting mechanism includes a battery vent structure which is located on the battery cover and may be integrally formed therewith. The venting mechanism includes an opening extending through the battery cover such that the opening communicates with a plurality of battery cells located within the battery case. The venting mechanism also includes a vent manifold which attaches to the battery vent structure. The vent manifold includes a first opening which communicates with the battery vent structure opening and second and third openings which allow the vent manifold to be connected to two separate conduits. In this manner, a plurality of batteries may be interconnected for venting purposes, thus eliminating the need to provide separate vent lines for each battery. The vent manifold may be attached to the battery vent structure by a spin-welding technique. To facilitate this technique, the vent manifold may be provided with a flange portion which fits into a corresponding groove portion on the battery vent structure. The vent manifold includes an internal chamber which is large enough to completely house a conventional battery flame arrester and overpressure safety valve. In this manner, the vent manifold, when installed, lessens the likelihood of tampering with the flame arrester and safety valve.

Ching, Larry K. W. (Littleton, CO)

2000-02-15T23:59:59.000Z

429

Propagators in Nonrelativistic Quantum Mechanics  

Science Conference Proceedings (OSTI)

A discussion of propagators (Green's functions) and methods for calculating them for the simplest systems in nonrelativistic quantum mechanics is given from several points of view. The relevance of such techniques to partition function calculations is pointed out. Finally

Laurent A. Beauregard

1966-01-01T23:59:59.000Z

430

SCIENCE CHINA Physics, Mechanics & Astronomy  

E-Print Network (OSTI)

SCIENCE CHINA Physics, Mechanics & Astronomy © Science China Press and Springer-Verlag Berlin for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. Sci China-Phys Mech Astron, 2013, 56: 207221, doi: 10.1007/s11433-012-4970-8 1 Introduction

Zhang, Guangyu

431

Student understanding of quantum mechanics  

Science Conference Proceedings (OSTI)

We investigate the difficulties of advanced undergraduate students toward the end of a full year upper-level quantum mechanics course with concepts related to quantum measurements and time development. Our analysis is based upon a test administered to 89 students from six universities and interviews with 9 students. Strikingly

Chandralekha Singh

2001-01-01T23:59:59.000Z

432

COMPUTATIONAL METHODS FOR FAST AND ACCURATE DNA FRAGMENT ASSEMBLY  

E-Print Network (OSTI)

.......................................................................................18 3. DNA Fluorescent-Trace Representation 2 0 3.1 Existing Representations. As shown in Figure 1-2, the underlying data is in the form of a set of four sequences of fluorescent-2. Fluorescent Trace Data. Sequences of fluorescent-dye intensities are used to call the sequence of bases

Shavlik, Jude W.

433

Coded DNA Self-Assembly for Error Detection/Location  

Science Conference Proceedings (OSTI)

This paper proposes a novel framework in which DNA self-assembly can be analyzed for error detection/ location. The proposed framework relies on coding and mapping functions that allow to establish the presence of erroneous bonded tiles based on the ... Keywords: Coding, Nano Manufacturing, Error Detection, Error Resilience

Zahra Mashreghian Arani; Masoud Hashempour; Fabrizio Lombardi

2009-10-01T23:59:59.000Z

434

Classification of co-expressed genes from DNA regulatory regions  

Science Conference Proceedings (OSTI)

The analysis of non-coding DNA regulatory regions is one of the most challenging open problems in computational biology. In this paper we investigate whether we can predict functional information about genes by using information extracted from their ... Keywords: Combinatorial and machine learning methods integration, Gene classification, Gene expression and bio-sequence data integration, Motif extraction and selection

Giulio Pavesi; Giorgio Valentini

2009-07-01T23:59:59.000Z

435

Exact and Approximation Algorithms for DNA Tag Set Design  

E-Print Network (OSTI)

in this thesis have already appeared in the following publications [31, 30]: 1. I.I. Mandoiu and D. Trinca. Exact available as ACM Computing Re- search Repository report cs.DS/0503057. 2. I.I. Mandoiu, C. Prajescu, and D Computing Research Repository report cs.DS/0502054. iii #12;Contents Abstract iii 1 Introduction 1 1.1 DNA

Mandoiu, Ion

436

Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring  

Science Conference Proceedings (OSTI)

Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

Gregory Stephanopoulos

2004-07-31T23:59:59.000Z

437

Iterative Dictionary Construction for Compression of Large DNA Data Sets  

Science Conference Proceedings (OSTI)

Genomic repositories increasingly include individual as well as reference sequences, which tend to share long identical and near-identical strings of nucleotides. However, the sequential processing used by most compression algorithms, and the volumes ... Keywords: Dictionary construction, compression, DNA, large data sets.

Shanika Kuruppu; Bryan Beresford-Smith; Thomas Conway; Justin Zobel

2012-01-01T23:59:59.000Z

438

Derivatized versions of ligase enzymes for constructing DNA sequences  

DOE Patents (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

439

Manipulating a single adsorbed DNA for a critical endpoint  

E-Print Network (OSTI)

We show the existence of a critical endpoint in the phase diagram of unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition of base pairing, adsorption and stretching by an external force leads to the critical end point. From exact results, the location of the critical end point is determined and its classical nature established.

Rajeev Kapri; Somendra M. Bhattacharjee

2008-03-24T23:59:59.000Z

440

Giant Protease TPP II's Structure, Mechanism Uncovered  

NLE Websites -- All DOE Office Websites (Extended Search)

Giant Protease TPP II's Structure, Mechanism Uncovered Giant Protease TPP II's Structure, Mechanism Uncovered Print Wednesday, 23 February 2011 00:00 Tripeptidyl peptidase II (TPP...

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


441

A Fundamental Mechanism in Anisotropic Nanocrystal Growth ...  

Science Conference Proceedings (OSTI)

In order to achieve this goal, it is necessary to understand the build block ( nanocrystal) growth mechanism. The oriented attachment (OA) mechanism originally...

442

Dynamic association of the replication initiator and transcription factor DnaA with the Bacillus subtilis chromosome during replication stress  

E-Print Network (OSTI)

DnaA functions as both a transcription factor and the replication initiator in bacteria. We characterized the DNA binding dynamics of DnaA on a genomic level. Based on cross-linking and chromatin immunoprecipitation data, ...

Grossman, Alan D.

443

Formation and Genotoxicity of Novel Oxidatively Generated Tandem DNA Lesions and N2-(1-carboxyethyl)-2'-deoxyguanosine  

E-Print Network (OSTI)

free and error-prone lesion bypass by human DNA polymerase ?free and error-prone lesion bypass by human DNA polymerase kfree and error-prone lesion bypass by human DNA polymerase

Jiang, Yong

2009-01-01T23:59:59.000Z

444

INTERACTION OF BENZO[a]PYRENE-7, 8-DIHYDRODIOL-9,10-OXIDE WITH SIMIAN VIRUS 40 DNA AND CHROMATIN  

E-Print Network (OSTI)

Diol Epoxide to DNA and Chromatin, 11 in 3rd InternationalSIMIAN VIRUS 40 DNA AND CHROMATIN Howard Byron Gamper, Jr. (Simian Virus 40 DNA and Chromatin By Howard Byron Gamper,

Gamper, Jr., Howard Byron

2012-01-01T23:59:59.000Z

445

Photonic Crystal Biosensor with In-Situ Synthesized DNA Probes for Enhanced Sensitivity  

Science Conference Proceedings (OSTI)

We report on a nearly 8-fold increase in multi-hole defect photonic crystal biosensor response by incorporating in-situ synthesis of DNA probes, as compared to the conventional functionalization method employing pre-synthesized DNA probe immobilization.

Hu, Shuren [Vanderbilt University, Nashville] [Vanderbilt University, Nashville; Zhao, Y. [Vanderbilt University, Nashville] [Vanderbilt University, Nashville; Retterer, Scott T [ORNL] [ORNL; Kravchenko, Ivan I [ORNL] [ORNL; Weiss, Sharon [Vanderbilt University, Nashville] [Vanderbilt University, Nashville

2013-01-01T23:59:59.000Z

446

A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase  

E-Print Network (OSTI)

Pro- cessivity of the DNA helicase activity of Escherichiaenzyme is a bipolar DNA helicase. Nature 423, 893897.translocation by single RecBCD helicase/nuclease molecules.

Spies, Maria; Bianco, Piero R; Dillingham, Mark S; Handa, Naofumi; Baskin, Ron J; Kowalczykowski, Stephen C

2003-01-01T23:59:59.000Z

447

Nano-Layered Microneedles for Transcutaneous Delivery of Polymer Nanoparticles and Plasmid DNA  

E-Print Network (OSTI)

Multilayer-coated microneedles achieve transcutaneous delivery of plasmid DNA to the viable epidermis. Cy3-labeled plasmid DNA encoding luciferase (yellow) is deposited on biodegradable microneedle arrays through multilayer ...

DeMuth, Peter Charles

448

On single-molecule DNA sequencing with atomic force microscopy using functionalized carbon nanotube probes  

E-Print Network (OSTI)

A novel DNA sequencing method is proposed based on the specific binding nature of nucleotides and measured by an atomic force microscope (AFM). A single molecule of DNA is denatured and immobilized on an atomically fiat ...

Burns, Daniel James

2004-01-01T23:59:59.000Z

449

Sensitive method for measurement of telomeric DNA content in human tissues  

DOE Patents (OSTI)

This research discloses a sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue. 5 figs.

Bryant, J.E.; Hutchings, K.G.; Moyzis, R.K.; Griffith, J.K.

1999-02-16T23:59:59.000Z

450

Control of the replication initiator DnaA by an anti-cooperativity factor  

E-Print Network (OSTI)

Proper coordination of DNA replication with cell growth and division is critical for production of viable progeny. In bacteria, coordination of DNA replication with cell growth is generally achieved by controlling activity ...

Merrikh, Houra

451

PCR template-DNA isolated quickly from monocot and dicot leaves without tissue homogenization.  

E-Print Network (OSTI)

1994, Vol. 22, No. 10 PCR template-DNA isolated quickly fromthe polymerase chain reaction (PCR). Because rice leaves arequantities of rice DNA for PCR (about 100 ng per half-

Williams, C E; Ronald, P C

1994-01-01T23:59:59.000Z

452

PCR template-DNA isolated quickly from monocot and dicot leaves without tissue homogenization.  

E-Print Network (OSTI)

1994, Vol. 22, No. 10 PCR template-DNA isolated quickly from5 6 Figure 1. Separation of PCR products on gels containing80C. DNA was used directly in PCR without quantification.

Williams, C E; Ronald, P C

1994-01-01T23:59:59.000Z

453

Understanding cell fate decisions in response to 0?-Methylguanine DNA lesions  

E-Print Network (OSTI)

The stability of the genome is constantly challenged by both endogenous and exogenous DNA damaging agents. DNA damage, if left unrepaired, can give rise to permanent genetic alterations that ultimately increase our risk ...

Noonan, Ericka Marie

2011-01-01T23:59:59.000Z

454

The biomechanical basis of DNA breakage in chronic myelogenous leukemia  

E-Print Network (OSTI)

in a replicative hexameric helicase. Nature 442: 270275.and implications for the helicase mechanism. Nat. Struct.Mechanisms of a ring shaped helicase. Nucl. Acid Res. 34:

Tu, Chi-Chiang

2010-01-01T23:59:59.000Z

455

Damage to DNA thymine residues in CHO cells by hydrogen peroxide and copper, ascorbate and copper, hypochlorite, or other oxidants: Protection by low MW polyethylene glycol  

SciTech Connect

Polyethylene glycol (PEG) MW 200-600, has been shown to protect animals against oxidant and radiation damage. In order to study the mechanism the authors examined the effect of PEG on damage to thymine residues in the DNA of living Chinese hamster ovary (CHO) cells. After growing to confluence in the presence of (methyl{sup 3}H)thymidine, the cells were treated, usually for 1 hr, with various combinations of H{sub 2}O{sub 2}, Cu{sup ++}, Fe{sup ++}, Ocl{sup {minus}}, ascorbate UV or X-irradiation, and PEG MW 300. The oxidants H{sub 2}O{sub 2}/Cu{sup ++}, and OCL{sup {minus}} released {sup 3}H into the medium from DNA thymine, and also formed thymine glycol residues in the DNA that were assayed by alkaline borohydride. The presence of 10% PEG during treatment significantly reduced the release of {sup 3}H into the medium but did not prevent formation of thymine glycol residues bound to the DNA. PEG at 10% had no effect on the cloning efficiency of CHO cells.

Schellenberg, K.A.; Shaeffer, J. (Eastern Virginia Medical School, Norfolk (United States))

1991-03-11T23:59:59.000Z

456

MOLECULAR MECHANISM OF SUPPRESSION OF NEOPLASTIC TRANSFORMATION BY LOW DOSES OF LOW LET RADIATION  

Science Conference Proceedings (OSTI)

We are currently funded (9/01-8/04) by the DOE Low Dose Radiation Research Program to examine mechanisms underlying the suppression of neoplastic transformation in vitro by low doses of low LET radiation. For the new studies proposed under Notice 04-21, we intend to follow up on our observation that upregulation of DNA repair may be an important factor and that its importance is dose-dependent. The experimental system will be the human hybrid cell neoplastic transformation assay that we are currently using. We propose to test the following hypothesis: Down-regulation of DNA dsb repair will abrogate the low dose suppression of neoplastic transformation. Using the technique of RNA silencing, it is proposed to test the effect of down-regulation of the two major DNA dsb repair pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ), on the dose response relationship for neoplastic transformation. Based on prior studies, we predict that this will result in abrogation of the suppressive effect at doses in the range 1 to 10 cGy, but not at lower doses. The proposed experiments will also help address the question as to which of the two DNA repair pathways may be the most important in causing suppression of transformation. HR is a pathway that is predominant in S and G2 phase cells and is known to be less error-prone than the NHEJ pathway that is predominant in G1 phase. We hypothesize that down-regulation of HR will result in the most effective abrogation of suppression. An important component of this study will be the determination of the how abrogation of DNA dsb repair impacts the spontaneous transformation frequency, presumably a consequence of endogeneous DNA damage. Experiments will be carried out using partially synchronized populations of cells enriched for G1 and S/G2 respectively. In addition to the endpoint of neoplastic transformation the impact of down-regulation of HR and NHEJ on the formation and disappearance of the DNA dsb marker, gamma-H2AX, will be studied.

J.LESIE REDPATH, PH.D.

2011-03-29T23:59:59.000Z

457

Raman-based system for DNA sequencing-mapping and other separations  

DOE Patents (OSTI)

DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated.

Vo-Dinh, Tuan (Knoxville, TN)

1994-01-01T23:59:59.000Z

458

Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free Energy  

E-Print Network (OSTI)

Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free of the solvent reorganization energy and free energy in the heterogeneous DNA environment. DNA is modeled represents water. Model calculations show the importance of including the reorganization energy and the free

Fayer, Michael D.

459

The cellular Mre11 protein interferes with adenovirus E4 mutant DNA replication  

SciTech Connect

Adenovirus type 5 (Ad5) relocalizes and degrades the host DNA repair protein Mre11, and efficiently initiates viral DNA replication. Mre11 associates with Ad E4 mutant DNA replication centers and is important for concatenating viral genomes. We have investigated the role of Mre11 in the E4 mutant DNA replication defect. RNAi-mediated knockdown of Mre11 dramatically rescues E4 mutant DNA replication in cells that do or do not concatenate viral genomes, suggesting that Mre11 inhibits DNA replication independent of genome concatenation. The mediator of DNA damage checkpoint 1 (Mdc1) protein is involved in recruiting and sustaining Mre11 at sites of DNA damage following ionizing radiation. We observe foci formation by Mdc1 in response to viral infection, indicating that this damage response protein is activated. However, knockdown of Mdc1 does not prevent Mre11 from localizing at viral DNA replication foci or rescue E4 mutant DNA replication. Our results are consistent with a model in which Mre11 interferes with DNA replication when it is localized at viral DNA replication foci.

Mathew, Shomita S. [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States); Bridge, Eileen [Department of Microbiology, 32 Pearson Hall, Miami University, Oxford OH 45056 (United States)], E-mail: BridgeE@muohio.edu

2007-09-01T23:59:59.000Z

460

Raman-based system for DNA sequencing-mapping and other separations  

DOE Patents (OSTI)

DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated. 11 figures.

Vo-Dinh, T.

1994-04-26T23:59:59.000Z

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461

Thermal deposition and electron beam patterning techniques for biopolymer thin films: dna complex and proteins  

Science Conference Proceedings (OSTI)

The properties and effects of deposition and patterning of bio-organic materials have been studied in this work. Thermal deposition of DNA:CTMA, DNA:CTMA/PEDOT, DNA:Eu complexes, bacteriorhodipsin, and Bombix mori silk thin films from ...

Robert Andrew Jones / Andrew J. Steckl

2007-01-01T23:59:59.000Z

462

Towards a System for Simulating DNA Computing with Whiplash PCR Akio Nishikawa and Masami Hagiya  

E-Print Network (OSTI)

Towards a System for Simulating DNA Computing with Whiplash PCR Akio Nishikawa and Masami Hagiya, hagiyag@is.s.u­tokyo.ac.jp Abstract­ Whiplash PCR, a reaction in which hairpin DNA structures are extended­ mented by this method. However, the feasibility of using whiplash PCR in a specific DNA algo­ rithm

Hagiya, Masami

463

Mechanics of Interfacial Composite Materials  

E-Print Network (OSTI)

Recent experiments and simulations have demonstrated that particle-covered interfaces can exist in stable non-spherical shapes as a result of the steric jamming of the interfacially trapped particles, which confers the interface with solid-like properties. We provide an experimental and theoretical characterization of the mechanical properties of these armored objects, with attention given to the two-dimensional granular state of the interface. Small inhomogeneous stresses produce a plastic response while homogeneous stresses produce a weak elastic response. Shear-driven particle-scale rearrangements explain the basic threshold needed to obtain the near-perfect plastic deformation that is observed. Furthermore, the inhomogeneous stress state of the interface is exhibited experimentally by using surfactants to destabilize the particles on the surface. Since the interfacially trapped particles retain their individual characteristics, armored interfaces can be recognized as a kind of composite material with distinct chemical, structural and mechanical properties.

Anand Bala Subramaniam; Manouk Abkarian; L. Mahadevan; Howard A. Stone

2006-05-25T23:59:59.000Z

464

Kinesin's backsteps under mechanical load  

E-Print Network (OSTI)

Kinesins move processively toward the plus end of microtubules by hydrolyzing ATP for each step. From an enzymatic perspective, the mechanism of mechanical motion coupled to the nucleotide chemistry is often well explained using a single-loop cyclic reaction. However, several difficulties arise in interpreting kinesin's backstepping within this framework, especially when external forces oppose the motion of kinesin. We review evidence, such as an ATP-independent stall force and a slower cycle time for backsteps, that has emerged to challenge the idea that kinesin backstepping is due to ATP synthesis, i.e., the reverse cycle of kinesin's forward-stepping chemomechanics. Supplementing the conventional single-loop chemomechanics with routes for ATP-hydrolyzing backward steps and nucleotide-free steps, especially under load, gives a better physical interpretation of the experimental data on backsteps.

Changbong Hyeon; Stefan Klumpp; Jos N. Onuchic

2009-04-18T23:59:59.000Z

465

Chemically assisted mechanical refrigeration process  

DOE Patents (OSTI)

There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator. 5 figs.

Vobach, A.R.

1987-11-24T23:59:59.000Z

466

Chemically assisted mechanical refrigeration process  

DOE Patents (OSTI)

There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer (11) at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer (11) to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator (10) to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing he evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator.

Vobach, Arnold R. (6006 Allentown Dr., Spring, TX 77379)

1987-01-01T23:59:59.000Z

467

Chemically assisted mechanical refrigeration process  

DOE Patents (OSTI)

There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer (11) at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer (11) to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator (10) to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator.

Vobach, Arnold R. (6006 Allentown Dr., Spring, TX 77389)

1987-01-01T23:59:59.000Z

468

Chemically assisted mechanical refrigeration process  

DOE Patents (OSTI)

There is provided a chemically assisted mechanical refrigeration process including the steps of: mechanically compressing a refrigerant stream which includes vaporized refrigerant; contacting the refrigerant with a solvent in a mixer at a pressure sufficient to promote substantial dissolving of the refrigerant in the solvent in the mixer to form a refrigerant-solvent solution while concurrently placing the solution in heat exchange relation with a working medium to transfer energy to the working medium, said refrigerant-solvent solution exhibiting a negative deviation from Raoult's Law; reducing the pressure over the refrigerant-solvent solution in an evaporator to allow the refrigerant to vaporize and substantially separate from the solvent while concurrently placing the evolving refrigerant-solvent solution in heat exchange relation with a working medium to remove energy from the working medium to thereby form a refrigerant stream and a solvent stream; and passing the solvent and refrigerant stream from the evaporator. 5 figs.

Vobach, A.R.

1987-06-23T23:59:59.000Z

469

The Schwinger mechanism and graphene  

E-Print Network (OSTI)

The Schwinger mechanism, the production of charged particle-antiparticle pairs in a macroscopic external electric field, is derived for 2+1 dimensional theories. The rate of pair production per unit area for four species of massless fermions, with charge $q$, in a constant electric field $E$ is given by $ \\pi^{-2} \\hbar^{-3/2} \\tilde{c}^{-1/2} (q E)^{3/2} $ where $\\tilde{c}$ is the speed of light for the two-dimensional system. To the extent undoped graphene behaves like the quantum field-theoretic vacuum for massless fermions in 2+1 dimensions, the Schwinger mechanism should be testable experimentally. A possible experimental configuration for this is proposed. Effects due to deviations from this idealized picture of graphene are briefly considered. It is argued that with present day samples of graphene, tests of the Schwinger formula may be possible.

Danielle Allor; Thomas D. Cohen; David A. McGady

2007-08-10T23:59:59.000Z

470

Bohmian Mechanics and Quantum Information  

E-Print Network (OSTI)

Many recent results suggest that quantum theory is about information, and that quantum theory is best understood as arising from principles concerning information and information processing. At the same time, by far the simplest version of quantum mechanics, Bohmian mechanics, is concerned, not with information but with the behavior of an objective microscopic reality given by particles and their positions. What I would like to do here is to examine whether, and to what extent, the importance of information, observation, and the like in quantum theory can be understood from a Bohmian perspective. I would like to explore the hypothesis that the idea that information plays a special role in physics naturally emerges in a Bohmian universe.

Sheldon Goldstein

2009-07-14T23:59:59.000Z

471

Mechanical Engineering Department Technical Review  

Science Conference Proceedings (OSTI)

The Mechanical Engineering Department Technical Review is published to inform readers of various technical activities within the Department, promote exchange of ideas, and give credit to personnel who are achieving the results. The report is presented in two parts: technical achievements and publication abstracts. The first is divided into seven sections, each of which reports on an engineering division and its specific activities related to nuclear tests, nuclear explosives, weapons, energy systems, engineering sciences, magnetic fusion, and materials fabrication.

Carr, R.B.; Denney, R.M. (eds.)

1981-07-01T23:59:59.000Z

472

MECHANICAL PROPERTIES OF ZIRCALOY-2  

DOE Green Energy (OSTI)

>The mechanical and physical properties of Zircaloy-2 were determined as a function of five test variables: temperature, grain size, direction to rolling, hydrgen content, and the presence or absence of a notch. The investigation included studies of the coefficient of thermal expansion, elastic moduius, tensile properties, creep properties, and low-cycle fatigue properties. Approximately 470 specimens from a single ingot were tested in the course of the investigation. (auth)