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Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)
Showing 101 to 200 of 210 items.  Page: 2

A-minor I vs A-minor 0 tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis

Kamila Reblova,, Judit E. Sponer, Nada Spackova, Ivana Besseova, and Jiri Sponer

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Intrinsically Flexible Ribosomal RNA Segments. Family C 3-Way Junctions and their Possible Role in the Translation

Ivana Besseova, Kamila Reblova, Neocles B. Leontis, Jiri Sponer

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On the Geometry, Electronic Structure and Hydrolytic Stability of the As-DNA backbone

Arnost Mladek, Jiri Sponer, Bobby G. Sumpter, Miguel Fuentes-Cabrera, and Judit E. Sponer

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Role of Protonation States of G8 and A38 Nucleobases in Structure Stabilization and Catalysis of the Hairpin Ribozyme

Vojtěch Mlýnský, Pavel Banáš, Nils G. Walter, Jiří Šponer, Michal Otyepka

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Synthesis of a Disubstituted Purine Analog and its Binding Interactions with Xanthine Phosphoribosyl Transferase (xpt) Riboswitch

Angela Potenza, Rachit Neupane, Emily McLaughlin, Swapan S. Jain

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Computer-Aided Design of Novel HIV-1 Entry Inhibitors, Their Synthesis and Trials: Glycolipids Against the Envelope gp120 V3 Loop

Alexander M. Andrianov, Ivan V. Anishchenko, Mikhail A. Kisel, Vasiliy A. Nikolayevich, Vladimir F. Eremin, and Alexander V. Tuzikov

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Disclosure of Conserved Structural Motifs in the HIV-1 Third Variable (V3) Loop by Comparative Analysis of 3D V3 Structures for Different Virus Subtypes

Alexander M. Andrianov, Ivan V. Anishchenko, and Alexander V. Tuzikov, ,

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Hypothetical Mechanism of the Kissing to Extended Dimer Conversion for the HIV-1 Stem-Loop 1 RNA

Nikolai B. Ulyanov, Richard Tjhen, Christophe Guilbert, Thomas L. James

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Probing the Molecular Determinants of HIV Alternative Splicing: NMR and Thermodynamic Studies of UP1/ESS3

Blanton S. Tolbert, Clay Mishler, Jeff Levengood, Prashant Rajan

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An Evolutionary Tree Rooted in Actinobacteria

William L. Duax, Robert Huether, David Dziak, Courtney McEachon

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Emergence and evolutionary connections between enzymatic functions via prototypes of elementary functional loops

Alexander Goncearenco, and Igor N. Berezovsky

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Mechanisms of Protein Oligomerization, the Critical Role of Insertions and Deletions in Maintaining Different Oligomeric States

Kosuke Hashimoto, Anna R. Panchenko

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Recently Duplicated Human Genes: Basics of Evolution

Alexander Y. Panchin, Elena N. Shustrova, Irena I. Artamonova

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Ribosomal Paleontology and Resurrection: Molecular Fossils from before Coded Protein

Loren Dean Williams, Chiaolong Hsiao, Jessica C. Bowman, Chad R. Bernier, Jessica Peters, Dana M. Schneider, and Eric O’Neill

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Structural and Functional Evolution of Proteins by Conformational Diversity

T. J. Glembo, S.B. Ozkan

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Structure, Function and Evolutionary Relationship of the Leptin Receptor (OB – Rb)

R. Malathi , R. Raskin Erusan

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Development and Applications of the Fluorescent Tricyclic Cytosine Family - The First Nucleic Acid Base Analogue FRET-pair

Karl Börjesson , Søren Preus , Kristine Kilså , Afaf H. El-Sagheer , Tom Brown , Bo Albinsson , L. Marcus Wilhelmsson

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Peptide Nucleic Acid (PNA) - Artificial DNA with Many Faces

Peter E. Nielsen

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Sequence Specific Targeting Duplex DNA by Artificial DNA Analogs

Maxim D. Frank-Kamenetskii , Irina Smolina

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Two-step construction of base-modified nucleic acids for electrochemical DNA sensing

Miroslav Fojta, Petra Horakova, Hana Pivonkova, Ludek Havran, Peter Sebest, Jan Spacek, Petr Orsag, Milan Vrabel, Hana Macickova-Cahova, Lubica Kalachova, Jan Riedl, Veronika Raindlova, and Michal Hocek

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Efficient B-Z DNA Conformational Transition Induced by Ru(II) Complexes

Lv-Ying Li, Hui Chao, Li-Ping Weng, Liang-Nian Ji

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Role of Z-DNA forming silencer in the regulation of human ADAM-12 gene expression

Alpana Ray, Srijita Dhar, Arvind Shakya, and Bimal K. Ray

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Roles of Z-DNA Binding Proteins in Immunity and Infection

Alexander Rich, Ky Lowenhaupt , Jin-Ah Kwon

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G-Quadruplex, Telomere and Telomerase

K. W. Lim, A. T. Phan

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Platinum(II) Phenanthroimidazoles for G-quadruplex Targeting: The Effect of Structure on Binding Affinity, Selectivity and Telomerase Inhibition

Katherine Castor, Roxanne Kieltyka, Pablo Englebienne, Nathanael Weill, Johans Fakhoury, Johanna Mancini, Nicole Avakyan, Anthony Mittermaier, Chantal Autexier, Nicolas Moitessier, Hanadi F. Sleiman

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Structural Transition in the Human Telomeric DNA Sequence d[(TTAGGG)4] upon interaction With Putative Anticancer Agents, Sanguinarine And Ellipticine

Saptaparni Ghosh, Suman Kalyan Pradhan, Gautam Basu, Dipak Dasgupta

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Structure of Human Telomeric RNA G-quadruplexes

Herry Martadinata , Anh Tuan Phan

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Terminalia chebula Extract Enhances Fenton-reaction Mediated Nucleoside Damage

Indrani Kar , Rajagopal Chattopadhyaya

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Characterization of erp Operator DNA Binding by Borrelia burgdorferi Protein BpaB.

Claire Adams, Manana Melikishvili, Mike Fried, and Brian Stevenson

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Characterization of Fpg Protein Binding to DNA Lesions Using Pyrrolocytosine Fluorescence

Nikita A. Kuznetsov, Olga S. Fedorova

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Dynamic XPD & Mre11-Rad50-Nbs1 DNA Repair Complexes: Disease-causing Mutations and Biological Outcomes

John A. Tainer

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Dynamical Allosterism in the Mechanism of Action of DNA Mismatch Repair Protein MutS

Susan N. Pieniazek, Manju M. Hingorani, D. L. Beveridge

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Enzyme-catalyzed DNA Cytidine Deamination in Human Biology

Reuben S. Harris

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Kinetics of the Initial Step of Base Excision Repair in Trinucleotide Repeats

A.V. Endutkin, A.G. Derevyanko, D.O. Zharkov

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Post-synthetic Generation of Fapy-dG Lesion within Oligodeoxynucleotides: Differential Anomeric Impacts on DNA Duplex Properties

Mark Lukin , Conceição A. S. A. Minetti, David P. Remeta, Sivaprasad Attaluri, Francis Johnson, Kenneth J. Breslauer, Carlos de los Santos

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Search of Damaged Bases by DNA Repair Enzymes: Random Walks in One and Three Dimensions

Dmitry O. Zharkov, Grigory V. Mechetin, and Boris A. Veytsman

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Substrate Interactions of a Human DNA Alkyltransferase

Manana Melikishvili, Lance Hellman, Michael G. Fried

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The Good and the Bad of DNA Damage DNA Damage and Epigenetic Marks Drive Transcription and Repair

Enrico V. Avvedimento

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Base Excision Repair of Trinucleotide Repeat DNA

Kelly Schermerhorn , Sarah Delaney

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Incorporation of Oxidized Guanine Nucleotides into DNA

Craig J. Yennie , Sarah Delaney

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Investigation of Trinucleotide Repeats in Nucleosome Core Particles

Catherine Burke Volle , Sarah Delaney

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Kinetic Characterization of the Repair Enzyme OGG1 acting on Triplet Repeat DNA

Daniel A. Jarem, Kelly M. Schermerhorn, Nicole R. Wilson, Sarah Delaney

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Structure and Reactivity of Triplet Repeat Sequences Associated with Neurodegenerative Disorders

Amalia Ávila-Figueroa, Douglas Cattie , Sarah Delaney

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Substrate Binding, Catalytic Activity and Product Release by Human 8-Oxo-7,8-dihydroguanine Glycosylase (hOGG1) are Modulated by the Structural Context of 8-Oxo-7,8-dihydroguanine in a CAG Trinucleotide Repeat Sequence

Daniel A. Jarem, Nicole R. Wilson, Kelly M. Schermerhorn , Sarah Delaney

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A Genomic Code for Nucleosome Positioning from Archaebacteria to Man

Jonathan Widom

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Computational Approach to Unravel Molecular Events During Vitiligo

Khushhali Menaria

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Functional Nuclear Architecture Studied by High-Resolution Microscopy

Thomas Cremer, Marion Cremer, Yolanda Markaki, Barbara Hübner, Katharina Austen, Daniel Smets, Jacques Rouquette, Manuel Gunkel, Sven Beichmanis, Rainer Kaufmann, Heinrich Leonhardt, Lothar Schermelleh, Stanislav Fakan, Christoph Cremer

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How is a long strand of DNA compacted into a chromosome?

Kazuhiro Maeshima

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Mapping Oxidative Damage at High Resolution Throughout an Entire Genome

Sarah Bernard, Cheryl Chiang, Stephen C. J. Parker, Elliott H. Margulies, and Thomas D. Tullius

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The Impact of Interchromosomal Associations on the Functional State of the Human Genome

Ekaterina E. Khrameeva, Andrey A. Mironov, Mikhail S. Gelfand

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Three-Dimensional Genome Architecture Predicts the Distribution of Chromosomal Alterations in Human Cancers

Geoffrey Fudenberg, Leonid Mirny

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High-Throughput DNA Structural Analysis by Hydroxyl Radical Cleavage and Capillary Electrophoresis

Nicholas B. Hammond, Clare C. Rittschof, and Thomas D. Tullius

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A Topological View of Transcription-Replication Collisions

Virginia López, Estefanía Monturus de Carandini, María-Luisa Martínez-Robles, Pablo Hernández, Dora B. Krimer, and Jorge B. Schvartzman

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An Active Clamping Role for PCNA during Assembly and Function on DNA

Yayan Zhou, Manju M. Hingorani

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Electrostatic Properties of Bacteriophage T7 Early Promoters Recognized by E. coli RNA Polymerase.

S.G. Kamzolova, P.M. Beskaravainy, A.A. Sorokin

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Electrostatic Properties of T7 RNA Polymerase Specific Promoters

P.M. Beskaravainy, A.A. Osypov, G.G. Krutinin, E.A. Krutinina, S.G. Kamzolova

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Essential role of the Rep, UvrD and DinG Helicases and of the RecBC Recombination Complex upon Replication – Transcription Collisions in the E. coli Chromosome

Anne Langlois de Septenville, Stéphane Duigou, Hasna Boubakri, Enrique Viguera, and Bénédicte Michel

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The E. coli Replisome and Use of Clamps to Bypass Replication Barriers

Roxana E. Georgescu, Nina Y. Yao, Mike O’Donnell

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Transcription Blockage by Guanine-Rich DNA Sequences and Possible Effects on Transcription of Nascent RNA Binding to DNA

Boris P. Belotserkovskii, Richard Liu, Shayon Saleh, Silvia Tornaletti, Maria M. Krasilnikova Sergei M. Mirkin, and Philip C. Hanawalt

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Transcription-associated Mutagenesis and Top1 Activity in Budding Yeast

Nayun Kim, Jang-Eun Cho, Sue Jinks-Robertson

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When Replication Meets Transcription

Sergei M. Mirkin

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Strand Exchange Reaction Between Short Oligonucleotides Promoted by a Derivative of 1,3 – diazaadamantane.

Anna Gabrielian, Tatiana N. Bocharova, Elena A. Smirnova, Alexander A. Volodin, Gayane Harutjunyan

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Cis-Regulatory Modules: Identification in silico and Understanding of Gene Regulatory Networks

Ivan V. Kulakovskiy, Yulia A. Medvedeva, Vsevolod J. Makeev

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Dynamics of Two Combined Reversible Binding Ligands to DNA

Valery B. Arakelyan, Gohar G.Hovhannisyan, Poghos O.Vardevanyan

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Effect of Millimeter Electromagnetic Waves on the Water-Saline Solutions of DNA and DNA-Ligand Complexes

Poghos O.Vardevanyan, Ara P.Antonyan, Mariam A.Shahinyan, Margarita A.Torosyan, Armen T.Karapetian

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Investigation of Interaction of Podophyllotoxins with DNA

Ara P. Antonyan, Anna S.Ryazanova, Hrachik R.Vardapetyan

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Minor Groove Ligands Based on Dimeric Bisbenzimidazoles as Inhibitors of DNA-Dependent Enzymes

Alexander A. Ivanov , Sergey A. Streltsov, Victor I. Salyanov, Olga Yu. Susova, Elizaveta S. Gromova, Alexei L. Zhuze

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Preferred Pair Distance Templates for Identification of Functional Binding Sites for Interacting Transcription Factors

Ivan V. Kulakovskiy, Alexander A. Belostotsky, Vsevolod J. Makeev

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Promoter Islands: The Novel Elements In Bacterial Genomes

Konstantin S. Shavkunov, Maria N Tutukina, Irina S. Masulis, Olga N. Ozoline

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The Influence of Aliphatic Alcohols on Oligonucleotide Hybridization

Alexander A. Lomzov, Irina V. Khalo, Dmitrii V. Pyshnyi

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Transcription factor - DNA interactions: cis regulatory codes in the genome

Martha L. Bulyk

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In Silico Analysis of Structural Properties of Fungal DNA Sequences and Promoter Prediction

Manju Bansal , Venkata Rajesh Yella

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Yarrowia Lipolytica Yeast Possesses An Atypical Catabolite Repression

Igor G. Morgunov, Svetlana V. Kamzolova

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A Convenient Fluorescence Assay of Polyamide-DNA Interactions

Cynthia M. Dupureur, James K. Bashkin, Karl Aston, Kevin J. Koeller, Kimberly R. Gaston, and Gaofei He

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A Kinetic Code for SRY-Dependent Transcriptional Activation Based on DNA Intercalation

Joseph Racca, Yen-Shan Chen, Nelson Phillips, Agnes Jansco-Radek, Michael Weiss, Elisha Haas

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A Mechanism to Understand the Dynamics of Tryptophan Repressor

Balasubramanian Harish , Jannette Carey

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Coarse-Grained Model of Nucleic Acids

Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, and Harold A. Scheraga

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DNA Recognition in RNA Polymerase III Transcription

Nicholas Taylor , Gary Male , Christoph W. Müller

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DNA Shape Patterns and Evolutionary Constraint in Nucleosome Positioning Sequences

Stephen C. J. Parker , Sean M. West , Eric Bishop, Remo Rohs, Barry Honig, Thomas D. Tullius , Elliott H. Margulies

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Getting a Firm Grip on DNA: Understanding DNA Recognition at the Finger-Finger Interface of Zinc Finger Proteins

Ankit Gupta, Amy Rayla, Ryan G. Christiansen, Nathan D. Lawson, Gary D. Stormo, Scot A. Wolfe

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Indirect Readout by the P22 Repressor Protein: How Charge and Solvent Organization Aid Binding Site Discrimination

Lydia-Ann Harris , Gerald Koudelka

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New Insights into Protein-DNA Electrostatic interactions: Beyond Promoters to Transcription Factors Binding Sites

Eugenia A. Krutinina, Gleb G. Krutinin, Svetlana G. Kamzolova, Alexander A. Osypov

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Physicochemical Features of Protein-DNA Interactions and the Identification of Interface Region in DNA-Binding Proteins

Pinak Chakrabarti,, Sucharita Dey,, Arumay Pal,, Mainak Guharoy

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Protein Sliding and Jumping Along DNA

Yaakov (Koby) Levy

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Statistical Thermodynamics of DNA Sequences Based on a Two State Model for the Base Pair Steps

Garima Khandelwal, Rebecca A. Lee, B. Jayaram, and David L. Beveridge

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Temperature-Induced Unfolding Thermodynamics of DNA Hairpins Containing Internal Loops and Their targeting with Complementary Strands

Luis A. Marky, Iztok Prislan, Cynthia Lee, and Hui-Ting Lee

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The Mode of DNA Recognition and Dimerization Specificity of MITF Revealed by Three Crystal Structures

Vivian Pogenberg, Viktor Deineko, Morlin Milewski, Alexander Schepsky, Eirikur Steingrimsson, and Matthias Wilmanns

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The Role of Electrostatics in Protein-DNA Interactions in Phage Lambda

Gleb G. Krutinin, Eugenia A. Krutinina,, Svetlana G. Kamzolova, Alexander A. Osypov

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The Study of the Nucleic Acid Base-Stacking by Monte Carlo Method: Extended Cluster Approach

Victor I. Danilov, Vladimir V. Dailidonis, Tanja van Mourik, Herbert A. Früchtl

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Dimerization with Extradenticle Unlocks Latent DNA Binding Specificities that Discriminate Hox Proteins in Drosophila

Todd R. Riley , Matthew Slattery, Namiko Abe , Harmen J. Bussemaker, Richard S. Mann

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DNA Shape Patterns and Binding Specificities for Drosophila Hox Proteins

Dana R. Holcomb, Thomas D. Tullius

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Exploring the DNA Binding Specificities of Homeodomain Complexes Using SELEX-sequencing

Matthew Slattery, Todd R. Riley, Namiko Abe , Harmen J. Bussemaker, Richard S. Mann

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Intrinsic DNA Shape of Fis-DNA Binding Sites Determines Binding Affinity

Tianyin Zhou, Ana Carolina Dantas Machado , Remo Rohs

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Modulating DNA Binding Activity of p53 by Base Sequence Effects and Amino-Acid Mutations

H. Rozenberg, A. Eldar, M. Kitayner, Y. Diskin-Posner, A. Kapitkovsky, O. Suad, Z. Shakked,

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Protein-DNA interactions in the p53/DNA system

Itai Beno, Karin Rosenthal, Michael Levitine, Lihi Shaulov, and Tali E. Haran

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Structural determinants of DNA-binding specificity for Drosophila Hox proteins

Peng Liu, Remo Rohs, Richard S. Mann, Barry Honig

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Structural Studies of Nucleic Acid-Binding Proteins Involved in Regulating Cell Differentiation and Pluripotency

Udo Heinemann, Florian Mayr, and Anja Schuetz

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The Role of DNA Shape on Protein-DNA Binding Affinity and Specificity

Remo Rohs

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DNA Mechanics, Nucleosome Positioning and p53-DNA Recognition

Victor B. Zhurkin, Feng Cui, and Difei Wang

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Yeast Nucleosomes Mapped with High Resolution by Paired-end Sequencing Exhibit Strong Positioning Patterns

Feng Cui, Hope A. Cole, David J. Clark, and Victor B. Zhurkin

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