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  • 1
    Publication Date: 2012-02-17
    Description: We here characterize local conformations of site-specifically placed pairs of guanine (G) residues in RNA and DNA, using 6-methyl isoxanthopterin (6-MI) as a conformational probe. 6-MI is a base analog of G and spectroscopic signals obtained from pairs of adjacent 6-MI residues reflect base–base interactions that are sensitive to the sequence context, local DNA conformation and solvent environment of the probe bases. CD signals show strong exciton coupling between stacked 6-MI bases in double-stranded (ds) DNA; this coupling is reduced in single-stranded (ss) DNA sequences. Solvent interactions reduce the fluorescence of the dimer probe more efficiently in ssDNA than dsDNA, while self-quenching between 6-MI bases is enhanced in dsDNA. 6-MI dimer probes closely resemble adjacent GG residues, in that these probes have minimal effects on the stability of dsDNA and on interactions with solvent additive betaine. They also serve as effective template bases, although further polymerase-dependent extension of DNA primers past 6-MI template bases is significantly inhibited. These probes are also used to monitor DNA ‘breathing’ at model replication forks. The 6-MI dimer probe can serve in many contexts as a useful tool to investigate GG conformations at specific sites within the nucleic acid frameworks of functioning macromolecular machines in solution.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 1999-08-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alberts, B M -- Ayala, F J -- Botstein, D -- Frank, E -- Holmes, E W -- Lee, R D -- Macagno, E R -- Marrack, P -- Oparil, S -- Orkin, S H -- Rubenstein, A H -- Slayman, C W -- Sparling, P F -- Squire, L R -- von Hippel, P H -- Yamamoto, K R -- New York, N.Y. -- Science. 1999 Jul 30;285(5428):666-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10454921" target="_blank"〉PubMed〈/a〉
    Keywords: National Institutes of Health (U.S.)/*organization & administration ; *Peer Review, Research ; Public Policy ; Research ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2000-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- Jing, D H -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2435-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10766621" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA/*biosynthesis ; DNA Helicases/metabolism ; DNA Primase/*chemistry/*metabolism ; *DNA Replication ; DNA, Bacterial/biosynthesis ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Escherichia coli/enzymology/*metabolism ; Models, Biological ; Protein Structure, Tertiary ; RNA/*biosynthesis ; RNA, Bacterial/biosynthesis ; Templates, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1998-07-31
    Description: Recent findings now allow the development of an integrated model of the thermodynamic, kinetic, and structural properties of the transcription complex in the elongation, termination, and editing phases of transcript formation. This model provides an operational framework for placing known facts and can be extended and modified to incorporate new advances. The most complete information about transcriptional mechanisms and their control continues to come from the Escherichia coli system, upon which most of the explicit descriptions provided here are based. The transcriptional machinery of higher organisms, despite its greater inherent complexity, appears to use many of the same general principles. Thus, the lessons of E. coli continue to be relevant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 31;281(5377):660-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9685251" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/chemistry/metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; *Models, Genetic ; Promoter Regions, Genetic ; *RNA Editing ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics/*metabolism ; Templates, Genetic ; Thermodynamics ; Transcription Factors/metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1992-11-20
    Description: A synthetic RNA-DNA bubble duplex construct intended to mimic the nucleic acid framework of a functional transcription elongation complex was designed and assembled. The construct consisted of a double-stranded DNA duplex of variable length (the template and nontemplate strands) containing an internal noncomplementary DNA "bubble" sequence. The 3' end of an RNA oligonucleotide that is partially complementary to the template DNA strand was hybridized within the DNA bubble to form an RNA-DNA duplex with a non-complementary 5'-terminal RNA tail. The addition of either Escherichia coli or T7 RNA polymerase to this construct formed a complex that synthesized RNA with good efficiency from the hybridized RNA primer in a template-directed and processive manner, and displayed other features of a normal promoter-initiated transcription elongation complex. Other such constructs can be designed to examine many of the functional and regulatory properties of transcription systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daube, S S -- von Hippel, P H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Nov 20;258(5086):1320-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1280856" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/genetics ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/enzymology/genetics ; In Vitro Techniques ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Promoter Regions, Genetic ; RNA/genetics ; Structure-Activity Relationship ; Templates, Genetic ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1992-02-14
    Description: At any template position, the decision to extend the transcript by one residue or to release the nascent RNA represents a kinetic competition between elongation and termination pathways. This competition is discussed in terms of alternative Eyring transition state barriers; changes in termination efficiency correspond to small changes in the relative heights of these barriers. Elongation complexes are stable at nonterminator positions; a model is presented to explain the destabilization of these complexes at intrinsic termination sites. Functionally analogous effects can operate at rho-dependent terminators. Mechanisms for modulation of termination efficiency by regulatory proteins are described.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- Yager, T D -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 14;255(5046):809-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1536005" target="_blank"〉PubMed〈/a〉
    Keywords: Activation Analysis ; Escherichia coli/*genetics ; Gene Expression Regulation, Bacterial ; Models, Biological ; Models, Structural ; Templates, Genetic ; Thermodynamics ; Transcription, Genetic/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2004-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, Peter H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):350-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA. petevh@molbio.uoregon.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256661" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; DNA, Bacterial/*chemistry/*metabolism ; Diffusion ; Dimerization ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Bonding ; Kinetics ; Lac Operon ; Lac Repressors ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Static Electricity ; Thermodynamics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1994-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 11;263(5148):769-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303292" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 1993-11-05
    Description: Pre-steady state kinetics of misincorporation were used to investigate the addition of single nucleotides to nascent RNA by Escherichia coli RNA polymerase during transcription elongation. The results were fit with a branched kinetic mechanism that permits conformational switching, at each template position, between an activated and an unactivated enzyme complex, both of which can bind nucleotide triphosphates (NTPs) from solution. The complex exists most often in the long-lived activated state, and only becomes unactivated when transcription is slowed. This model permits multiple levels of nucleotide discrimination in transcription, since the complex can be "kinetically trapped" in the unactivated state in the absence of the correct NTP or if the 3' terminal residue is incorrectly matched. The transcription cleavage factor GreA (or an activity enhanced by GreA) increased the fidelity of transcription by preferential cleavage of transcripts containing misincorporated residues in the unactivated state of the elongation complex. This cleavage mechanism by GreA may prevent the formation of "dead-end" transcription complexes in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erie, D A -- Hajiseyedjavadi, O -- Young, M C -- von Hippel, P H -- GM-12915/GM/NIGMS NIH HHS/ -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 5;262(5135):867-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235608" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Endoribonucleases/metabolism ; Escherichia coli/enzymology ; *Escherichia coli Proteins ; Kinetics ; Models, Genetic ; Molecular Sequence Data ; Nucleotides/metabolism ; Peptide Elongation Factors/*metabolism ; Protein Conformation ; RNA, Messenger/*biosynthesis/metabolism ; Templates, Genetic ; Transcription Factors/*metabolism ; *Transcription, Genetic ; Uridine Triphosphate/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2010-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gleick, P H -- Adams, R M -- Amasino, R M -- Anders, E -- Anderson, D J -- Anderson, W W -- Anselin, L E -- Arroyo, M K -- Asfaw, B -- Ayala, F J -- Bax, A -- Bebbington, A J -- Bell, G -- Bennett, M V L -- Bennetzen, J L -- Berenbaum, M R -- Berlin, O B -- Bjorkman, P J -- Blackburn, E -- Blamont, J E -- Botchan, M R -- Boyer, J S -- Boyle, E A -- Branton, D -- Briggs, S P -- Briggs, W R -- Brill, W J -- Britten, R J -- Broecker, W S -- Brown, J H -- Brown, P O -- Brunger, A T -- Cairns, J Jr -- Canfield, D E -- Carpenter, S R -- Carrington, J C -- Cashmore, A R -- Castilla, J C -- Cazenave, A -- Chapin, F S 3rd -- Ciechanover, A J -- Clapham, D E -- Clark, W C -- Clayton, R N -- Coe, M D -- Conwell, E M -- Cowling, E B -- Cowling, R M -- Cox, C S -- Croteau, R B -- Crothers, D M -- Crutzen, P J -- Daily, G C -- Dalrymple, G B -- Dangl, J L -- Darst, S A -- Davies, D R -- Davis, M B -- De Camilli, P V -- Dean, C -- DeFries, R S -- Deisenhofer, J -- Delmer, D P -- DeLong, E F -- DeRosier, D J -- Diener, T O -- Dirzo, R -- Dixon, J E -- Donoghue, M J -- Doolittle, R F -- Dunne, T -- Ehrlich, P R -- Eisenstadt, S N -- Eisner, T -- Emanuel, K A -- Englander, S W -- Ernst, W G -- Falkowski, P G -- Feher, G -- Ferejohn, J A -- Fersht, A -- Fischer, E H -- Fischer, R -- Flannery, K V -- Frank, J -- Frey, P A -- Fridovich, I -- Frieden, C -- Futuyma, D J -- Gardner, W R -- Garrett, C J R -- Gilbert, W -- Goldberg, R B -- Goodenough, W H -- Goodman, C S -- Goodman, M -- Greengard, P -- Hake, S -- Hammel, G -- Hanson, S -- Harrison, S C -- Hart, S R -- Hartl, D L -- Haselkorn, R -- Hawkes, K -- Hayes, J M -- Hille, B -- Hokfelt, T -- House, J S -- Hout, M -- Hunten, D M -- Izquierdo, I A -- Jagendorf, A T -- Janzen, D H -- Jeanloz, R -- Jencks, C S -- Jury, W A -- Kaback, H R -- Kailath, T -- Kay, P -- Kay, S A -- Kennedy, D -- Kerr, A -- Kessler, R C -- Khush, G S -- Kieffer, S W -- Kirch, P V -- Kirk, K -- Kivelson, M G -- Klinman, J P -- Klug, A -- Knopoff, L -- Kornberg, H -- Kutzbach, J E -- Lagarias, J C -- Lambeck, K -- Landy, A -- Langmuir, C H -- Larkins, B A -- Le Pichon, X T -- Lenski, R E -- Leopold, E B -- Levin, S A -- Levitt, M -- Likens, G E -- Lippincott-Schwartz, J -- Lorand, L -- Lovejoy, C O -- Lynch, M -- Mabogunje, A L -- Malone, T F -- Manabe, S -- Marcus, J -- Massey, D S -- McWilliams, J C -- Medina, E -- Melosh, H J -- Meltzer, D J -- Michener, C D -- Miles, E L -- Mooney, H A -- Moore, P B -- Morel, F M M -- Mosley-Thompson, E S -- Moss, B -- Munk, W H -- Myers, N -- Nair, G B -- Nathans, J -- Nester, E W -- Nicoll, R A -- Novick, R P -- O'Connell, J F -- Olsen, P E -- Opdyke, N D -- Oster, G F -- Ostrom, E -- Pace, N R -- Paine, R T -- Palmiter, R D -- Pedlosky, J -- Petsko, G A -- Pettengill, G H -- Philander, S G -- Piperno, D R -- Pollard, T D -- Price, P B Jr -- Reichard, P A -- Reskin, B F -- Ricklefs, R E -- Rivest, R L -- Roberts, J D -- Romney, A K -- Rossmann, M G -- Russell, D W -- Rutter, W J -- Sabloff, J A -- Sagdeev, R Z -- Sahlins, M D -- Salmond, A -- Sanes, J R -- Schekman, R -- Schellnhuber, J -- Schindler, D W -- Schmitt, J -- Schneider, S H -- Schramm, V L -- Sederoff, R R -- Shatz, C J -- Sherman, F -- Sidman, R L -- Sieh, K -- Simons, E L -- Singer, B H -- Singer, M F -- Skyrms, B -- Sleep, N H -- Smith, B D -- Snyder, S H -- Sokal, R R -- Spencer, C S -- Steitz, T A -- Strier, K B -- Sudhof, T C -- Taylor, S S -- Terborgh, J -- Thomas, D H -- Thompson, L G -- Tjian, R T -- Turner, M G -- Uyeda, S -- Valentine, J W -- Valentine, J S -- Van Etten, J L -- van Holde, K E -- Vaughan, M -- Verba, S -- von Hippel, P H -- Wake, D B -- Walker, A -- Walker, J E -- Watson, E B -- Watson, P J -- Weigel, D -- Wessler, S R -- West-Eberhard, M J -- White, T D -- Wilson, W J -- Wolfenden, R V -- Wood, J A -- Woodwell, G M -- Wright, H E Jr -- Wu, C -- Wunsch, C -- Zoback, M L -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):689-90. doi: 10.1126/science.328.5979.689.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448167" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; Politics ; Public Policy ; Research/standards ; Research Personnel
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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