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Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007
Showing 1 to 100 of 235 items.  Page: 1 3

A Structural and Functional Comparison of Yeast NTD (yNTD) and Human NTD (hNTD) of the TATA Binding Protein

Claire A. Adams, Michael G. Fried

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Cooperativity, Crosslinking, and Supercoiling in the Interaction of AGT with DNA

Claire Adams, Manana Melikishvili, Michael G. Fried

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Crystal Structure of a LexA Protein from Thermotoga Maritima

Adrianna Zhang, Arabela Grigorescu, Phoebe Rice

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DNA-Binding Mechanism of O6-Alkylguanine-DNA Alkyltransferase: Changes in DNA Twist and Base Stacking

Manana Melikishvili, Michael G. Fried

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Effect of Base Lesions on Duplex DNA

Amy Rumora, Anne Malhowski, Megan Nunez

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Human AP endonuclease 1: the Dynamics of Conformational Changes

Lyubov Yu. Pshenichnikova, Vladimir V. Koval, Dmitry O. Zharkov, Phyllis R. Strauss, Olga S. Fedorova

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NMR Characterization of DNA with a single carba-Fapy

Mark Lukin, Tatyana Zaliznyak, Sivaprasad Attaluri, Francis Johnson and , Carlos de los Santos

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Structural Basis for 3-Methyladenine Recognition and Removal by a Highly-specific DNA Glycosylase: The Crystal Structure of TAG in Complex with DNA

Audrey Herrin, Thomas Hollis, Brandt F. Eichman

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Structural Characterization of Clustered DNA Damage: Bistranded Oxidized Bases and Abasic Sites

Tatyana Zaliznyak, Francis Johnson, Carlos de los Santos

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Conformational Dynamics of Interactions of Escherichia coli Endonuclease VIII with DNA Substrates

N. A. Kuznetsov, D. O. Zharkov, O. S. Fedorova

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Crystallographic and Small-angle X-ray Scattering Analysis of DNA Ligase Interaction with the Protein Sliding Clamp, PCNA

John M. Pascal, Oleg V. Tsodikov, Greg L. Hura, John A. Tainer, Tom Ellenberger

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DNA bending by the non-canonical bZIP protein c-Maf

Mensur Dlakic

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DNA Fexibility Enhancement In Vivo

Nicole A. Becker, L. James Maher, III

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In vitro Effect of Modified TFO on the DNA-gyrase Activity and Binding with Target Duplex

Anna Gabrielian, Hannelore Simon, Günther Burckhardt, Christoph Zimmer

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Examination of the ATPase Mechanism of Saccharomyces cerevisiae Replication Factor C

Siying Chen, Manju Hingorani

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Primer-Template Recognition by the Mitochondrial DNA Polymerase Gamma

Aleksandr Treyer, Elena Yakubovskaya, Daniel F. Bogenhagen

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Structural Studies of Mcm10, An Essential Eukaryotic Replication Initiation Factor

Eric M. Warren, Audrey H. Metz, Antonin V. Tutter , Johannes C. Walterand , Brandt F. Eichman

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Structural view of the clamp-loading mechanism onto DNA

Kosuke Morikawa

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The Stoichiometry and EM Structure of Human DNA Polymerase gamma

Elena Yakubovskaya, Mark Lukin, Zhixin Chen, John Berriman, Caroline Kisker, Daniel F. Bogenhagen

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Multiprotein Machines for Gene Transcription

Patrick Cramer

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Homology Modeling and Molecular Dynamics Simulations of RNA Polymerases

Ivan Barvik , Kamil Malac

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Development of a Coarse Grain Model of the Nucleosome

Sachin Goyal, Apostol Gramada, Thomas C. Bishop

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MARs Incorporate Strong Nucleosome-positioning Sites with TopoII Binding in the Vicinity

Fedoseyeva V. B., Alexandrov A. A.

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Prediction of Nucleosome Positioning Using a Support Vector Machine

Eric Bishop and, Thomas D. Tullius

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Structural properties of GC-rich sequences may hinder nucleosome positioning in CpG islands

Michael Y. Tolstorukov , Victor B. Zhurkin, Wilma K. Olson

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Chicken and yeast nucleosomal DNA sequences differ at the ends: A possible relation to the linker histone binding

Feng Cui and Victor B. Zhurkin

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The ?Kink-and-Slide? folding of DNA in nucleosome is facilitated by asymmetric interactions of the histone arginines in the minor groove

Difei Wang, Feng Cui and , Victor B. Zhurkin

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Analysis of Modification at 966 and 967 Positions in Escherichia coli 16 S ribosomal RNA

Tek N. Lamichhane, Ashesh A. Saraiya, Christine S. Chow, Philip R. Cunningham

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Analysis of rRNA Dynamics as Inferred from Cryo-EM of Ribosomal Complexes

Joachim Frank, Jamie LeBarron, and, Haixiao Gao

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Antibiotic Binding to the Ribosome

Xiaoxia Ge, Benoît Roux

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Cooperative and pH Effects of Pseudouridine on Structure and Stability in Helix 69 of Escherichia coli 23 S rRNA

Sanjaya C. Abeysirigunawardena and Christine S. Chow

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Crystallographic and Biochemical Characterization of the GTPase and Ribosome Binding Properties of Salmonella Typhimuirum BipA

Raymond S. Brown, Megan A. deLivron, Victoria L. Robinson

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Discovery of Peptides that Target the Bacterial Decoding Region of 16S rRNA

Mei Li, Santosh K. Mahto, and Christine S. Chow

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High Performance Computing Simulations of tRNA Movement Through the Ribosome

Kevin Y. Sanbonmatsu

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New Insights into the Mechanism of Cleavage of Sarcin Ricin Loop (SRL) RNA

Swapan S. Jain, Orlando Suero, and, Thomas D. Tullius

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New Insights: Structure and behavior of the sarcin-ricin ribosomal RNA motif ? molecular dynamics simulations

Nada Spackova and, Jiri Sponer

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Ribosomal RNA Motifs and Segments have Salient Fexibilities

Jiri Sponer, Ali Mokdad, Filip Razga, Kamila Reblova, Nada Spackova

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Ribosomes Under Stress: Structural Variability of the 100S Particles Studied by Cryoelectron Tomography

Julio O. Ortiz, Stephanie Etchells, Andrew Leis, F. Ulrich Hartl, Wolfgang Baumeister

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Specific Interactions of Elongation Factor-G and Ribosome Recycling Factor on the 50S Subunit Revealed by Cryo-EM

Ning Gao, Andrey V. Zavialov, Mans Ehrenberg, Joachim Frank

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Structural Characterization of the Helix 31 Region of E. coli 16S rRNA and H. sapiens 18S rRNA Containing Different Post-transcriptional Modifications

Dinuka Abeydeera, Yu-Cheng Chang, Christine S. Chow

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Structures of eEF2-80S Ribosome Complexes Reveal the Role of GTP Hydrolysis in Translocation

Derek J. Taylor, Jakob Nilsson, A. Rod Merrill, Gregers Rom Andersen, Poul Nissen, Joachim Frank

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Study of Structure, Dynamics and Local Elasticity of 16S rRNA Helix 44 Using Molecular Dynamics Methods

Kamila Réblová, Filip Lankas, Jirí Sponer

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The Roles of RNA in the Peptidyl Transferase Reaction and its Inhibition by Antibiotics

Thomas A. Steitz

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The transfer RNA in the Hybrid P/E State

Wen Li and Joachim Frank

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Assembled Structure of the Mre11/Rad50/DNA Complex from X-ray Solution Scattering and Crystallography: Implications for Repair and Signaling

R. Scott Williams, David S. Shin, Gabriel Moncalian, Lynda M. Groocock, Jessica S. Williams, Charly Chahwan, Dana Cahill, James P. Carney, Paul Russell, John A. Tainer

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Deducing the multiple binding modes of p53 tetramer ? DNA interaction based on full-site palindrome of p53 response elements: convergence of sequence and geometry based recognitions

Buyong Ma , and , Arnold J. Levine

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Implications of Folding in the p53 Dimer

David J. Lubin, James S. Butlerand, Stewart N. Loh

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Mutant p53 Interactions with Supercoiled DNA

Brázdová, M., Nemcová, K., Cincárová, L., Sebesta, P., Pivonková, H., Brázda,V., Fojta,M., Palecek,E.

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p53 Tumour Suppressor: Structure, Function-Rescue

Alan Fersht

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p53-RNA Interactions: in vitro, in Yeast, and in Human Cells

Kasandra Riley, L. James Maher, III

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Sequence Dependence of DNA Bending upon p53 Binding: A Molecular Dynamics Simulation

Yongping Pan, Ruth Nussinov

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Solution Structure of the Human Pirh2 RING-H2 Domain and its Role in Self-ubiquitylation and Ubiquitylation of P53

Yi Sheng, Cheryl H. Arrowsmith

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Specific recognition of DNA by p53 and its dependence on DNA structural properties

Tali E. Haran

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Structural basis of restoring DNA binding activity to mutant p53 by a second-site suppressor mutation

Oded Suad , Haim Rozenberg and , Zippi Shakked

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Structural Studies on the tumor-suppressor protein p53 and its interaction with DNA

Zippi Shakked

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The p53-DNA binding in the chromatin context: p53-induced activation of the apoptotic and cell cycle arrest genes

Feng Cui, Michael Sirotin, Victor B. Zhurkin

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Towards a FRET-Based ATP Biosensor Using Quantum Dot/Aptamer-Based Complexes

Erika Revesz, Edward P.C. Lai, Maria C. DeRosa

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Alkynylpyrene Exciplex-based Split-probe Systems for the Detection of Mutation and Single Nucleotide Polymorphisms

Laura L. Etchells, Elena V. Bichenkova, Abdul Gbaj, Lindsey Walsh, Kenneth T. Douglas

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Application of Target-assembled Exciplex-based Probes for DNA Detection and Mismatch Discrimination in PCR Products and Plasmid DNA

Lindsey Walsh, Abdul Gbaj, Laura Etchells, Qingyong Li, Zhaolei Lang, Kenneth T. Douglas, Elena Bichenkova

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FRET and Beyond: High-Resolution Approaches Based on Target-Assembled Exciplexes for Nucleic Acid Detection

Kenneth T. Douglas, Elena V. Bichenkova

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SNP Detection of the Cytochrome P450 2C9*3 Mutation using DNA-assembled Exciplexes

Abdul Gbaj, Lindsey Walsh, Elena V. Bichenkova, Laura L. Etchells, Kenneth T. Douglas

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The Molecular Origins of the Specific Exciplex-promoting Solvent Effect of 80% (v/v) Trifluoroethanol for DNA-mounted Target-assembled Exciplexes in a Tandem Oligonucleotide System

Candelaria Rogert, Elena V. Bichenkova, Abdul Gbaj, Lindsey Walsh, Hannah E. Savage, Ali R. Sardarian, Laura L. Etchells, Kenneth T. Douglas

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Use of Locked Nucleic Acid Analogues in Exciplex-based Molecular FLuorescence Probes

Candelaria Rogert, Elena V. Bichenkova, Abdul Gbaj, Hannah E. Savage, Ali R. Sardarian, Kenneth T. Douglas

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A PM6 Study of the ?Hydration Shell? of Nucleic Acid Bases in Small Water Clusters

Victor I. Danilov, James J. P. Stewart, Tanja van Mourik

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An Electronic Structure Study of the ?Hydration Shell? of Adenine and Cytosine

Tanja van Mourik, Victor I. Danilov, Alexandra S. Deryabina, Eduardo Gonzalez, Valery I. Poltev

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Application of Differential Pulse Voltammetry Revealing the Peculiarities of EtBr-DNA Complexes

Poghos O. Vardevanyan, Ara P. Antonyan, Marine A. Parsadanyan, Kristine V. Pirumyan, Seyran H. Minasyan, Levon A. Tavadyan, Andranik M. Muradian, Armen T. Karapetian

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Are Micrococcal Nuclease Hypersensitive Sites the Centers of PREMELTONS Present in Naked DNA Molecules?

Henry M. Sobell

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Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines

Tumpa Sarkar, Iulia Vitoc, Ishita Mukerji and , Nicholas V. Hud

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Calculation of DNA-ligand Binding Characterized by the Infinite Radius of Interactions of Adsorbed Ligands

Dmitri Y. Lando, Alexander S. Fridman, Vladimir B. Teif

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Comparative Analysis of Electrostatic and Functional Properties of Some Synthetic A-Tracts Containing Promoters

Anatoly A. Sorokin, Alexander A. Osypov, Svetlana G. Kamzolova

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Comparative Analysis of the Structural and Dynamical Characteristics of AT and GC Base-pair Sequences in DNA Molecule

A. V. Kabanov, V. M. Komarov, L. A. Krasnobaeva, L. V. Yakushevich

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Competitive Interaction of Ethidium Bromide and Hoechst 33258 with DNA

Poghos H. Vardevanyan, Ara P. Antonyan, Karine Kh. Khachatryan, Marieta S. Mikaelyan, Zaruhi R. Boyajyan, Andranik M. Muradyan, Armen T. Karapetian

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DFT Study of B-like Conformations of Deoxydinucleoside Monophosphates

Valery I. Poltev, Victor M. Anisimov, Victor I. Danilov, Alexandra Deriabina, Eduardo Gonzalez, Agata Jurkiewicz, Andrzej Les, Nina Polteva

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DNA Binding Properties and Antiviral Activity of two Bis-Netropsins Containing Cis-Diammineplatinum(II) Group in the Linker Between Two Netropsin Moeties

A.N. Surovaya, S.L. Grokhovsky, V.L. Andronova , G.A. Galegov and , G.V. Gursky

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DNA Binding Properties of Dye Hoechst 33258 Derivatives Containing Bulky Substituents in the Phenyl Ring

I.Yu. Fyodorova, A.M. Nikitin, N.P. Bazhulina, S.A. Rodin, A.N. Surovaya, V.F. Pismensky, V. S. Archipova, R.F. Martin, G.V.Gursky

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DNA Melting Temperature Fluctuations Due to Adsorption and Desorption of Ligands

V. B. Arakelyan, Z. E. Navoyan

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Do Antioxidant Flavonoids Prevent DNA Damage: Fact or Fiction

H. A. Tajmir-Riahi, C. D. Kanakis, P. A. Tarantilis, M. G. PolissiouView Abstract

General Transfer Matrix Formalism to Calculate DNA-Protein Binding in Gene Regulation: Applications to the Lambda-Switch and Beyond

Vladimir B. Teif

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Hairpin Formation Affects the Electrophoretic Mobilities Observed for Single-stranded DNA Oligomers

Nancy C. Stellwagen, Arian Abdulla, Earle Stellwagen, Qian Dong

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Influence of Non-Thermal Millimetric Coherent Electromagnetic Radiation on Physical Properties of DNA Solutions

Yuri S. Babayan, Luiza R. Grigoryan, Hovhannes P. Vardevanyan, Marine A. Parsadanyan, Sergei N. Hakobyan, Alexan Sh. Markaryan

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Mechanisms of Mutagenic Action of 5BrU: Quantum Mechanical Study

Noriyuki Kurita, Victor I. Danilov, Victor M. Anisimov, Dmytro Hovorun, Taisuke Nakatsu, Kenishi Dedachi

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Modeling of the ?Hydration Shell? of Uracil and Thymine in Small Water Clusters by DFT and MP2 Methods

Victor I. Danilov, Tanja van Mourik, Valery I. Poltev

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New Highly Fluorescing bis-Hoechsts: Physicochemical, Biochemical and Cytological Studies

A. L. Zhuze, A. V. Gromyko, A. A. Ivanov, V. I. Salyanov, K. V. Popov, S.P. Korolev, M. B. Gottikh, V. A. Oleinikov, S. A. Streltsov

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Spectroscopic Investigations of DNA Dynamics and Relationship to HU DNA Interactions

A. Moreno, J. Knee, M. Hawkins , I. Mukerji

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DNA and RNA Branching: NMR structural studies

Sybren Wijmenga, Otmar Ottink, Sumientra Rampersad, Marco Tessari, Frank Nelissen, Hans Heus, Frederic Girard, Bin Wu, C.E. Pearson, and , Ramon van der Werf

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New Method of Mapping STructural INTeractions using in-cell NMR spectroscopy (STINT-NMR)

David. S. Burz, Alexander Shekhtman

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NMR Structures of the HIV-1 V3 Region Suggest a Mechanism for the Virus Phenotype Conversion

Jacob Anglister, Osnat Rosen, Michal Sharon, Vitali Tugarinov, Naama Kessler and, Rina Levy

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NMR studies of the structure, dynamics, and ligand interactions of polyubiquitin chains provide clues to functional diversity of polyubiquitin

David Fushman, Ranjani Varadan, Aydin Haririnia, Yaroslav Ryabov, Bryan Dickinson, Daoning Zhang, Ming-Yih Lai

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Pharmacophore Pattern Identification for NK-2 Receptor Agonists and Modeling of the Agonist-binding Site in NK-2 Receptor

Indu R. Chandrashekar, Gita Subba Rao, Sudha M. Cowsik

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Saturation Transfer Difference NMR Studies on the Binding of Pyrazinamide and 5-Chloropyrazinamide to Mycobacterium tuberculosis Fatty Acid Synthase I

H. Sayahi, S. S. Puttamadappa, S. C. Ngo, W. R. Jacobs, Jr, A. Shekhtman, J. T. Welch

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Structural Characterization of Neurokinin-3 Receptor Selective Peptide Agonist Scyliorhinin II Bound to DPC Micelles

Anjali Dike, Sudha M. Cowsik

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Vinblastine and Its Analogues: A Fluoremetric, NMR and Molecular Modeling Study for DNA Binding

Prateek Pandya, G. Suresh Kumar, Surat Kumar

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A new approach to an old problem: the crystal structure of a DNA- Co(III)⋅bleomycin-B2 complex

Kristie D. Goodwin, Mark A. Lewis , Eric C. Long , Millie M. Georgiadis

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A Strong Increase in DNA Destabilization Caused by Cisplatin Binding in Alkaline Medium

Elena N. Galyuk, Maryna M. Hauruk, Dmitri Y. Lando

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Chemistry and Biology of Platinum Anticancer Drugs at the Nucleosome Level

Matthias Ober, Dong Wang, Matthew A. Wallace, Stephen J. Lippard

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Cisplatin-RNA adducts: Crosslinking of a spliceosomal RNA subdomain by an anticancer compound

Victoria J. DeRose , Alethia Hostetter, and , Erich Chapman

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Direct excitation luminescence spectroscopy of lanthanide ions bound to DNA and RNA

Janet R. Morrow, Christopher M. Andolina, Ryan A. Mathews, Brooke Switala

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DNA Charge Transport Chemistry and Biology

Jacqueline K. Barton

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DNA-Threading Intercalation Rate Studies: Dynamics is an Efficient Mechanism for Biomolecular Structure Recognition

Bengt Nordén, Per Lincoln, Pär Nordell, Fredrik Westerlund, Marcus Wilhelmsson

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Electron hole flow patterns through DNA and nucleoprotein complexes yield unusual information about their structure and folding

Edward K. Y. Leung and , Dipankar Sen

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Showing 1 to 100 of 235 items.  Page: 1 3