Journal of Biomolecular Structure and Dynamics, Volume 17, Issue sup1 (2000)

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Journal of Biomolecular Structure and Dynamics, Volume 17, Issue sup1 (2000)

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Proceedings of the Eleventh Conversation

Original Articles

Article
Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations
Jiří Šponer, Imre Berger, Nad'a Špačková, Jerzy Leszczynski & Pavel Hobza
Pages: 1-24
Published online: 15 May 2012
AbstractforAromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations | References | PDF (396.4 KB)
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Article
Molecular Biology of Light Transduction by the Mammalian Photoreceptor, Rhodopsin
H. G. Khorana
Pages: 1-16
Published online: 15 May 2012
AbstractforMolecular Biology of Light Transduction by the Mammalian Photoreceptor, Rhodopsin | References | PDF (661.8 KB)
  • 78 Views
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Article
Ligand Selectivity by Nuclear Hormone Receptors
Jean-Marie Wurtz & Dino Moras
Pages: 17-21
Published online: 15 May 2012
AbstractforLigand Selectivity by Nuclear Hormone Receptors | References | PDF (86.1 KB)
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Article
Aminoacylation at the Atomic Level in Class IIa Aminoacyl-tRNA Synthetases
John G. Arnez, Rajan Sankaranarayanan, Anne-Catherine Dock-Bregeon, Christopher S. Francklyn & Dino Moras
Pages: 23-27
Published online: 15 May 2012
AbstractforAminoacylation at the Atomic Level in Class IIa Aminoacyl-tRNA Synthetases | References | PDF (128.1 KB)
  • 77 Views
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Article
RNA Scaffolds for Minihelix-Based Aminoacyl Transfer: Design of “Transpeptizymes”
Niranjan Y. Sardesai, Scott M. Stagg, Margaret S. VanLoock, Stephen C. Harvey & Paul Schimmel
Pages: 29-37
Published online: 15 May 2012
AbstractforRNA Scaffolds for Minihelix-Based Aminoacyl Transfer: Design of “Transpeptizymes” | References | PDF (222.7 KB)
  • 34 Views
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Article
Structural Studies of Model RNA Helices with Relevance to Aminoacyl-tRNA Synthetase Specificity and HIV Reverse Transcription
Udo Heinemann, Uwe Mueller, Hermann Heumann & Mathias Sprinzl
Pages: 39-45
Published online: 15 May 2012
AbstractforStructural Studies of Model RNA Helices with Relevance to Aminoacyl-tRNA Synthetase Specificity and HIV Reverse Transcription | References | PDF (499.9 KB)
  • 17 Views
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Article
Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step
R. L. Jernigan, Ivet Bahar, David G. Covell, Ali Rana Atilgan, Burak Erman & Daniel T. Flatow
Pages: 49-55
Published online: 15 May 2012
AbstractforRelating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step | References | PDF (97.8 KB)
  • 25 Views
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Article
Solution Structure of an Antibody-Bound HIV-1IIIB V3 Peptide: A Cis Proline Turn Linking Two β-hairpin Strands
Vitali Tugarinov & Jacob Anglister
Pages: 57-63
Published online: 15 May 2012
AbstractforSolution Structure of an Antibody-Bound HIV-1IIIB V3 Peptide: A Cis Proline Turn Linking Two β-hairpin Strands | References | PDF (135.4 KB)
  • 21 Views
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Article
A Conserved Asparagine Makes an Essential Contact to an RNA Adenosine or Cytidine
Valerie Shipilov & Susan A. White
Pages: 75-78
Published online: 15 May 2012
AbstractforA Conserved Asparagine Makes an Essential Contact to an RNA Adenosine or Cytidine | References | PDF (129.6 KB)
  • 30 Views
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Article
Contribution of Salt Bridges Toward Protein Thermostability
Sandeep Kumar, Chung-Jung Tsai, Buyong Ma & Ruth Nussinov
Pages: 79-85
Published online: 15 May 2012
AbstractforContribution of Salt Bridges Toward Protein Thermostability | References | PDF (66.7 KB)
  • 205 Views
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Article
Globularity and Protein Function
Jannette Carey
Pages: 87-88
Published online: 15 May 2012
AbstractforGlobularity and Protein Function | References | PDF (11.9 KB)
  • 10 Views
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Article
Modeling Molecular Recognition: Theory and Application
Kristy Mardis, Ray Luo, Laurent David, Michael Potter, Amy Glemza, Greg Payne & Michael K. Gilson
Pages: 89-94
Published online: 15 May 2012
AbstractforModeling Molecular Recognition: Theory and Application | References | PDF (60 KB)
  • 30 Views
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Article
Aromatic Ring Currents at a Protein Surface: Use of 1H-NMR Chemical Shifts to Refine the Structure of a Naked β Sheet
Bing Wang, Alan S. Stern & Michael A. Weiss
Pages: 95-108
Published online: 15 May 2012
AbstractforAromatic Ring Currents at a Protein Surface: Use of 1H-NMR Chemical Shifts to Refine the Structure of a Naked β Sheet | References | PDF (493.2 KB)
  • 32 Views
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Article
How Do Hydrogen Bonds Contribute to Protein-DNA Recognition?
Surjit B. Dixit, Nidhi Arora & B. Jayaram
Pages: 109-112
Published online: 15 May 2012
AbstractforHow Do Hydrogen Bonds Contribute to Protein-DNA Recognition? | References | PDF (39.7 KB)
  • 54 Views
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Article
Structure and Dynamics of the Tetrameric Mnt Repressor and a Model for its DNA Complex
Irene M.A. Nooren, Gert E. Folkers, Robert Kaptein, Robert T. Sauer & Rolf Boelens
Pages: 113-122
Published online: 15 May 2012
AbstractforStructure and Dynamics of the Tetrameric Mnt Repressor and a Model for its DNA Complex | References | PDF (514.2 KB)
  • 25 Views
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Article
How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR
Kumaralal Kaluarachchi, David G. Gorenstein & Bruce A. Luxon
Pages: 123-133
Published online: 15 May 2012
AbstractforHow Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR | References | PDF (283.8 KB)
  • 13 Views
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Article
Role of the N- and C- Terminal Dimer Interfaces of 434 Repressor in Recognizing Sequence-Dependent DNA Structure
Gerald B. Koudelka, Amy L. Donner & Mihai Ciubotaru
Pages: 135-139
Published online: 15 May 2012
AbstractforRole of the N- and C- Terminal Dimer Interfaces of 434 Repressor in Recognizing Sequence-Dependent DNA Structure | References | PDF (37.1 KB)
  • 11 Views
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Article
Geometry of the DNA Substrates in Cre-loxP Site-Specific Recombination
Feng Guo, Deshmukh N. Gopaul & Gregory D. Van Duyne
Pages: 141-146
Published online: 15 May 2012
AbstractforGeometry of the DNA Substrates in Cre-loxP Site-Specific Recombination | References | PDF (1.1 MB)
  • 59 Views
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Article
A Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via Triple-Helical Intermediates
Guillaume Bertucat, Richard Lavery & Chantal Prévost
Pages: 147-153
Published online: 15 May 2012
AbstractforA Mechanism for RecA-Promoted Sequence Homology Recognition and Strand Exchange Between Single-Stranded DNA and Duplex DNA, via Triple-Helical Intermediates | References | PDF (97.4 KB)
  • 33 Views
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Article
DNA and RNA Folds in Transcription Complex as Evidenced by Iodine-125 Radioprobing
V. N. Karamychev, I. G. Panyutin, R. D. Neumann & V. B. Zhurkin
Pages: 155-167
Published online: 15 May 2012
AbstractforDNA and RNA Folds in Transcription Complex as Evidenced by Iodine-125 Radioprobing | References | PDF (1.4 MB)
  • 26 Views
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Article
DNA Structure and Polymerase Fidelity: A New Role for A-DNA
Youri Timsit
Pages: 169-176
Published online: 15 May 2012
AbstractforDNA Structure and Polymerase Fidelity: A New Role for A-DNA | References | PDF (1,012 KB)
  • 31 Views
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Article
Effects of Oxidation Agents and Metal Ions on Binding of p53 to Supercoiled DNA
M. Fojta, M. Brazdova, H. Cernocka, P. Pecinka, V. Brazda, J. Palecek, E. Jagelska, B. Vojtesek, S. Pospisilova, V. Subramaniam, T. M. Jovin & E. Palecek
Pages: 177-183
Published online: 15 May 2012
AbstractforEffects of Oxidation Agents and Metal Ions on Binding of p53 to Supercoiled DNA | References | PDF (681 KB)
  • 40 Views
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Article
The Atomic Structure of the Nucleosome Core Particle
K. Luger, A. Mäder, D. F. Sargent & T. J. Richmond
Pages: 185-188
Published online: 15 May 2012
First Page PreviewforThe Atomic Structure of the Nucleosome Core Particle | References | PDF (191.6 KB)
  • 132 Views
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Article
Crystal Structure of an RNA Duplex [r(gugcaca)dC]2 with 3′-Dinucleoside Overhangs Forming a Superhelix
Shome Nath Mitra, Roopa Biswas, Ke Shi & Muttaiya Sundaralingam
Pages: 189-194
Published online: 15 May 2012
AbstractforCrystal Structure of an RNA Duplex [r(gugcaca)dC]2 with 3′-Dinucleoside Overhangs Forming a Superhelix | References | PDF (172.1 KB)
  • 20 Views
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Article
The Early Folding Intermediates of the Tetrahymena Ribozyme are Kinetically Trapped
Corie Y. Ralston, Bianca Sclavi, Michael Brenowitz, Michael Sullivan & Mark R. Chance
Pages: 195-200
Published online: 15 May 2012
AbstractforThe Early Folding Intermediates of the Tetrahymena Ribozyme are Kinetically Trapped | References | PDF (114.8 KB)
  • 16 Views
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Article
Three-Dimensional RNA Structure-Based Drug Discovery
Thomas L. James, Kenneth E. Lind, Anton V. Filikov & Anwer Mujeeb
Pages: 201-205
Published online: 15 May 2012
AbstractforThree-Dimensional RNA Structure-Based Drug Discovery | References | PDF (585.2 KB)
  • 30 Views
  • 1 CrossRef citations
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Article
Bridging the Prebiotic and RNA Worlds: Prebiotic RNA Synthesis on Clay
Gözen Ertem, K. Joseph Prabahar, P. C. Joshi & James P. Ferris
Pages: 207-210
Published online: 15 May 2012
AbstractforBridging the Prebiotic and RNA Worlds: Prebiotic RNA Synthesis on Clay | References | PDF (41.5 KB)
  • 92 Views
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Article
Synthesis of Specifically Deuterated Nucleotides for NMR Studies on RNA
Jenny A.M.T.C Cromsigt, Jürgen Schleucher, Karin Kidd-Ljunggren & Sybren S. Wijmenga
Pages: 211-219
Published online: 15 May 2012
AbstractforSynthesis of Specifically Deuterated Nucleotides for NMR Studies on RNA | References | PDF (254.5 KB)
  • 60 Views
  • 10 CrossRef citations
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Article
An Earring for the Double Helix: Assembly of Topological Links Comprising Duplex DNA and a Circular Oligodeoxynucleotide
Heiko Kuhn, Vadim V. Demidov & Maxim D. Frank-Kamenetskii
Pages: 221-225
Published online: 15 May 2012
AbstractforAn Earring for the Double Helix: Assembly of Topological Links Comprising Duplex DNA and a Circular Oligodeoxynucleotide | References | PDF (97.1 KB)
  • 43 Views
  • 15 CrossRef citations
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Article
Targeting of Pu.Py Duplexes by GA and GT Rich Oligonucleotides on Microchip and in Solution
E. Khomyakova, J. Liquier, T. Huynh-Dinh, V. Florentiev, A. Mirzabekov & E. Taillandier
Pages: 227-235
Published online: 15 May 2012
AbstractforTargeting of Pu.Py Duplexes by GA and GT Rich Oligonucleotides on Microchip and in Solution | References | PDF (932.4 KB)
  • 13 Views
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Article
NMR Structural Studies on a DNA Four-Way Junction: Stacking Preference and Localization of the Metal-ion Binding Site
Bernd N.M. van Buuren, Jürgen Schleucher & Sybren S. Wijmenga
Pages: 237-243
Published online: 15 May 2012
AbstractforNMR Structural Studies on a DNA Four-Way Junction: Stacking Preference and Localization of the Metal-ion Binding Site | References | PDF (287.1 KB)
  • 27 Views
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Article
Intramolecular i-Motif Structures of Telomeric DNA
Anh Tuân Phan & Jean-Louis Leroy
Pages: 245-251
Published online: 15 May 2012
AbstractforIntramolecular i-Motif Structures of Telomeric DNA | References | PDF (495.8 KB)
  • 343 Views
  • 31 CrossRef citations
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Article
Two Dimensions and Two States in DNA Nanotechnology
Nadrian C. Seeman, Furong Liu, Chengde Mao, Xiaoping Yang, Lisa A. Wenzler, Ruojie Sha, Weiqiong Sun, Zhiyong Shen, Xiaojun Li, Jing Qi, Yuwen Zhang, Tsu-Ju Fu, Junghuei Chen & Erik Winfree
Pages: 253-262
Published online: 15 May 2012
AbstractforTwo Dimensions and Two States in DNA Nanotechnology | References | PDF (541.1 KB)
  • 105 Views
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Article
Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments
Erik Winfree
Pages: 263-270
Published online: 15 May 2012
AbstractforAlgorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments | References | PDF (728.8 KB)
  • 206 Views
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Article
Recent Highlights from Atomic Force Microscopy of DNA
Helen G. Hansma, Lía I. Pietrasanta, Roxana Golan, John C. Sitko, Mario B. Viani, George T. Paloczi, Bettye L. Smith, Douglas Thrower & Paul K. Hansma
Pages: 271-275
Published online: 15 May 2012
AbstractforRecent Highlights from Atomic Force Microscopy of DNA | References | PDF (707.7 KB)
  • 49 Views
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Article
Probing DNA Conductivity with Photoinduced Electron Transfer and Scanning Tunneling Microscopy
Eimer Tuite, Per Lincoln, Johan Olofsson, Hans-Christian Becker, Björn Önfelt, Donats Erts & Bengt Nordén
Pages: 277-283
Published online: 15 May 2012
AbstractforProbing DNA Conductivity with Photoinduced Electron Transfer and Scanning Tunneling Microscopy | References | PDF (502.4 KB)
  • 32 Views
  • 8 CrossRef citations
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Article
DNA-Mediated Electron Transfer: A Sensitive Probe of DNA-Protein Interactions
Scott R. Rajski & Jacqueline K. Barton
Pages: 285-291
Published online: 15 May 2012
AbstractforDNA-Mediated Electron Transfer: A Sensitive Probe of DNA-Protein Interactions | References | PDF (681.2 KB)
  • 40 Views
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Article
Long-Range Hole Transport in DNA
Stephan Wessely & Bernd Giese
Pages: 293-295
Published online: 15 May 2012
AbstractforLong-Range Hole Transport in DNA | References | PDF (52 KB)
  • 17 Views
  • 6 CrossRef citations
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Article
M-DNA: pH Stability, Nuclease Resistance and Signal Transmission
Palok Aich, Heinz-Bernhard Kraatz & Jeremy S. Lee
Pages: 297-301
Published online: 15 May 2012
AbstractforM-DNA: pH Stability, Nuclease Resistance and Signal Transmission | References | PDF (53.8 KB)
  • 89 Views
  • 5 CrossRef citations
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Article
NMR Studies of DNA Structures Containing Sheared Purine•Purine and Purine•Pyrimidine Base Pairs
Shan-Ho Chou
Pages: 303-313
Published online: 15 May 2012
AbstractforNMR Studies of DNA Structures Containing Sheared Purine•Purine and Purine•Pyrimidine Base Pairs | References | PDF (280.2 KB)
  • 22 Views
  • 3 CrossRef citations
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Article
DNA Bending and Sugar Switching
Shantaram Kamath, Mukti H. Sarma, Victor B. Zhurkin, Christopher J. Turner & Ramaswamy H. Sarma
Pages: 317-325
Published online: 15 May 2012
AbstractforDNA Bending and Sugar Switching | References | PDF (213.7 KB)
  • 26 Views
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Article
Nucleic Acid Structure Investigated by UV Resonance Raman Spectroscopy: Protonation Effects and A-Tract Structure
Liliana Sokolov, Kristi Wojtuszewski, Eliana Tsukroff & Ishita Mukerji
Pages: 327-334
Published online: 15 May 2012
AbstractforNucleic Acid Structure Investigated by UV Resonance Raman Spectroscopy: Protonation Effects and A-Tract Structure | References | PDF (123 KB)
  • 52 Views
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Article
Drug Self-Assembly on DNA: Sequence Effects with trans-bis-(4-N-methylpyridiniumyl)diphenyl Porphyrin and Hoechst 33258
Matthew A. Ismail, P. Mark Rodger & Alison Rodger
Pages: 335-348
Published online: 15 May 2012
AbstractforDrug Self-Assembly on DNA: Sequence Effects with trans-bis-(4-N-methylpyridiniumyl)diphenyl Porphyrin and Hoechst 33258 | References | PDF (303.9 KB)
  • 38 Views
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Article
Stabilization of Double Stranded Homologous Poly(dA)·Poly(dT) by Taxol
Gerlinde Bischoff, Ulrich Gromann, Sabine Lindau, Eckhard Birch-Hirschfeld, Robert Bischoff, Christian Bohley, Walter-Vesély Meister & Siegfried Hoffmann
Pages: 349-354
Published online: 15 May 2012
AbstractforStabilization of Double Stranded Homologous Poly(dA)·Poly(dT) by Taxol | References | PDF (90.8 KB)
  • 19 Views
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Article
DNA Sequence Recognition of a Cross-Linked Polyamide: CD Studies, Footprinting and Effects on the Activity of DNA Gyrase
Günther Burckhardt, Ingo Förtsch, Hannelore Simon, Eckhard Birch-Hirschfeld, Leonhard Kittler, Holger Schütz, Sanjay K. Sharma, J. William Lown & Christoph Zimmer
Pages: 355-363
Published online: 15 May 2012
AbstractforDNA Sequence Recognition of a Cross-Linked Polyamide: CD Studies, Footprinting and Effects on the Activity of DNA Gyrase | References | PDF (362.6 KB)
  • 17 Views
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Article
Pf1 Filamentous Phage as an Alignment Tool for Generating Local and Global Structural Information in Nucleic Acids
Mark R. Hansen, Paul Hanson & Arthur Pardi
Pages: 365-369
Published online: 15 May 2012
AbstractforPf1 Filamentous Phage as an Alignment Tool for Generating Local and Global Structural Information in Nucleic Acids | References | PDF (888.4 KB)
  • 71 Views
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Article
Anomalous Migration of Short Sequences of DNA: Comparison of Theory and Experiment
Udayan Mohanty, Tim Searls & Larry W. McLaughlin
Pages: 371-375
Published online: 15 May 2012
AbstractforAnomalous Migration of Short Sequences of DNA: Comparison of Theory and Experiment | References | PDF (202 KB)
  • 17 Views
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