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Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005
Showing 1 to 100 of 185 items.  Page: 1

2D DNA Crystalline Sections as a Method to Test Structural Design in 3D

Pamela E. Constantinou, Tong Wang, Jens Kopatsch, Baoquan Ding, William B. Sherman, Jens J. Birktoft, Ruojie Sha, Chengde Mao, Nadrian C. Seeman

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A 1.7-kilobase Single-stranded DNA that Folds into a Nanoscale Octahedron

William M. Shih, Joel D. Quispe, Gerald F. Joyce

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A Model of Stop Codon Recognition in Eukariotes with Repulsive Guanine

Valery I. Ivanov

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A New DNA Quadruplex That Inhibits HIV-1 Integrase

A.T. Phan, V. Kuryavyi, J.B. Ma, A. Faure, M.L. Andréola, D.J. Patel

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A One Nanosecond Particle Mesh Ewald (PME) Periodic Boundary Solvated Molecular Dynamic Simulation of the Glucocorticoid Receptor Protein DNA Binding Domain in Complex with a Nucleosome DNA Model Containing Five Glucocorticoid Response Elements (GREs)

Lester F. Harris, Michael R. Sullivan

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A Ribosome-Like DNA Nanomechanical Device

Shiping Liao, Nadrian C. Seeman

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A Robust Sequence-Dependent Three-State DNA Nanomechanical Device

Banani Chakraborty, Ruojie Sha, Nadrian C. Seeman

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A Sequence-Specific DNA Alkylating Polyamide, Toward a Tailor-Made Antitumor Agent

Hiroshi Sugiyama

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A Survey of the Protein Folding Problem

Harold A. Scheraga

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A-tract Clustering, DNA Looping, and Bacterial Genome Packaging

Michael Y. Tolstorukov, Konstantin M. Virnik, Sankar Adhya, Victor B. Zhurkin

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Acceleration of De Novo DNA Synthesis by Restriction Enzymes

Xingguo Liang, Kari Jensen, Maxim D. Frank-Kamenetskii

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Accurate Interaction Energies of Base Pairing and Base Stacking. The Final Chapter

Jiri Sponer, Petr Jurecka, Pavel Hobza

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Adaptive Evolution in Alanyl-tRNA Synthetase

Manal A. Swairjo, Paul Schimmel

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Alteration in Content of Chromatin Phospholipids Under the Action of Hydrocortisone and Insulin

Emil S. Gevorgyan, Zhenya V. Yavroyan, Irina G. Artsruni, Karine S. Matinyan, Lusine O. Demirkhanyan, Nune R. Hakobyan, Artak G. Galstyan

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Analysis of Complexes Formed Between Anthrax Protective Antigen Monomers and Between Anthrax Protective Antigen and Models for the Human Anthrax Toxin Receptor

Linsey Stiles, Donald J. Nelson

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Analysis of the Chitosan-DNA Binding in Solutions of Different Ionic Strengths

E. A. Vorobyev, Yu. D. Nechipurenko, V. I. Salyanov, Yu. M. Yevdokimov

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Ancestral Module of TIM Barrel Protein Fold

Z. M. Frenkel, E. N. Trifonov

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Assembly and Characterization of Eight-Arm and Twelve-Arm DNA Branched Junctions

Xing Wang, Nadrian C. Seeman

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Base-Stacking and Base-Pairing Contributions to DNA Stability

Peter Yakovchuk, Ekaterina Protozanova, Maxim D. Frank-Kamenetskii

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Biological Protein Evolution from Two Aminoacyl-tRNA Synthetases?

C. W. Carter, Jr., L. Li, Y-P. Bao, A. Kim, J. M. Roach

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Biophysical Features Of Slipped CTG/CAG Structures And Their Biological Recognition

Mariana Kekis, Rachel Lau, S. Erin Montgomery, Kerrie Nichol Edamura, Yuh-Hwa Wang, Christopher E. Pearson

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Biosensing by Hybridization Chain Reaction

Niles A. Pierce

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CAG Expansion is Caused in the Process Of 8-Oxo-G Removal

Irina Kovtun, John Badger II, Magnar Borjas, Erling Seeberg, Arne Klugland, Lars Eide, Cynthia T. McMurray

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Catalytic Strategies of the Hepatitis Delta Virus Ribozyme as Probed by Molecular Dynamics Simulations

Maryna V. Krasovska, Jana Sefcikova, Nada Spackova, Jiri Sponer, Nils G. Walter

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Cationic Phosphoramidate α-oligonucleotides Target Double Stranded DNA: Molecular Dynamics Study

I. Barvik, Jr.

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Central Machinery of Life: Insights from Comparative Genomics

Andrei Osterman, Ross Overbeek

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Characterization of HU-cruciform DNA Interaction

Iulia Vitoc, Ishita Mukerji

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Characterization of Hydrogen Bonds in Double-Helical DNA Using H/D Fractionation Factors

Alicia E. Every, Daniel Coman, Irina M. Russu

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Complex Riboswitches

Ronald R. Breaker

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Compressed Backbone Hypothesis of B-DNA Fine Structure and Dynamics

Dimitri E. Kamashev, Alexey K. Mazur

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Condensation of Nicked and Gapped Duplexes: Potential Structures for Oligonucleotide Delivery

Tumpa Sarkar, Christine C. Conwell, Lilia C. Harvey, Catherine T. Santai, Nicholas V. Hud

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Conformational Model for the Human Immunodeficiency Virus Type 1 gp120 V3 Loop

Alexander M. Andrianov

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Conservation and Variation: A Balancing Act in the Genome

Samir K. Brahmachari

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Controlling Nucleic Acid Assembly by Small Molecule Binding: Formation of Antiparallel (dA)n·(dA)n Duplexes in the Presence of Coralyne

Ozgul Persil, Catherine T. Santai, Swapan S. Jain, Nicholas V. Hud

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Could We Consider a Cell as a Device with a Set of Right Organized Crystalline Ribosomes?

Karpova, E.A.

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Cryo-EM Study of the 80S Ribosome From Trypanosoma cruzi Reveals Novel rRNA Components

Haixiao Gao, Maximiliano Juri Ayub, Mariano J. Levin, Joachim Frank

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Crystal structure of a group I intron splicing intermediate

Scott Strobel

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Crystal Structure of an Active Group I Ribozyme-Product Complex

Barbara L. Golden

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Crystal Structure of Skp. A Prefoldin-like Chaperone that Prevents Protein Aggregation

Troy A. Walton, Marcelo C. Sousa

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Crystal Structure of the B-DNA - Z-DNA Junction Reveals Two Extruded Bases

Sung Chul Ha, Ky Lowenhaupt, Alexander Rich, Yang-Gyun Kim, Kyeong Kyu Kim

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Crystalline DNA Structures Stabilized by Transition Metals

N. Valls, J. A. Subirana

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Cyclization of Short DNA Fragments and Bending Fluctuations of the Double Helix

Quan Du, Chaim Smith, Nahum Shiffeldrim, Maria Vologodskaia, Alexander Vologodskii

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Damaged DNA and Repair Machines: Damage Recognition, Conformational Changes and the Structural Chemistry for DNA Repair Coordination

John A. Tainer

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Defining the ATPase Mechanism of Replication Factor C, the S.cerevisiae Clamp Loader

Siying Chen

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Design and construction of arbitrary two-dimensional DNA shapes

Paul W. K. Rothemund

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Deuterium Kinetic Isotope Effect Experiments on RNA Cleavage by the Hydroxyl Radical

Timothy Gay, Thomas Tullius

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DNA Charge Transport in Ruthenium-modified Assemblies

Katherine E. Augustyn, Matthias Pascaly, Jae Yoo, Jacqueline K. Barton

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DNA Deformability Energetic Changes Associated with Single Base Pair Mutants of CDE Binding Sites within S. cerevisiae Centromere DNAs Correlate with Measured Chromosomal Loss Rates

Brad Hennemuth, Kenneth A Marx

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DNA Flexibility

J. Widom

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DNA Nanostructures: Self-assembly and Pattern Transfer

Chengde Mao

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DNA Triads in the Context of DNA Quadruplexes

Vitaly Kuryavyi, Anh Tuan Phan, Dinshaw J. Patel

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DNA Triplex Bending Induced by Nonisomorphic Base Triplets

Thenmalarchelvi, R., Yathindra, N.

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Domain Architecture in a Homodimeric Multi-substrate Enzyme

Irina I. Protasevich, Heather M. McDonald, Wayne J. Brouillette, Christie G. Brouillette

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Doublesex: Structure and Function in Drosophila Sex Determination

James Bayrer, Wei Zhang, Yanwu Yang, Michael Weiss

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Duplex-passage Reaction Between Short Double-stranded DNA Regions Within Long Circular Single-stranded DNA Mediated by Type II Topoisomerases

Boris P. Belotserkovskii, Paola B. Arimondo, Nicholas R. Cozzarelli

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Effect of Association of Anticancer Antibiotics Upon Chromatin Structure

Dipak Dasgupta

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Electrostatic Map of E. coli Genome DNA. Specific Features of Electrostatic Potential of Promoter and Nonpromoter Regions

Anatoly A. Sorokin, Alexander A. Osypov, Petr M. Beskaravainy, Svetlana G. Kamzolova

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Electrostatic Polymer Condensation and the A/B Polymorphism in DNA

Alexey K. Mazur

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Energetics and Structure of DNA and RNA in Viral Capsids

Avinoam Ben-Shaul

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Evolution of Spliceosomal Introns: Insights From Comparative Genomics

Igor B. Rogozin, Vladimir N. Babenko

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Exploring the Flexibility of Nucleic Acids from Molecular Dynamics Simulations

Modesto Orozco

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Express-analysis of New Anti-tumor Compounds Binding with DNA

Yuri S. Babayan, Alexan Sh. Markaryan, Ruzan S. Kazaryan, Jasmin H. Sarkisyan, Ara. P. Antonyan, Anna B.Khachatryan

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Fidelity in Bacterial Signal Transduction

Kottayil I. Varughese

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Fluctuations of the Enzymatic Reaction Rate in the Case of Competing Inhibitor-Enzyme Bounding

Valery B. Arakelyan, Emil S. Gevorgyan, Tigran S. Sukiasyan, Aram E. Gevorgyan, Anush V.Arakelyan

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Free Dimer of E. coli RNA Polymerase α Subunit is a Potential Transcription Regulator

Yu.A. Purtov, A. Ishihama, O.N. Ozoline

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Functional Interplay of Structure-specific and Sequence-specific Elements in the Bacterial Promoters

O. N. Ozoline, A. A. Deev

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Functional Proteomics and Structural Dynamics of Mammalian Spliceosomes

Reinhard Luhrmann, Henning Urlaub, Holger Stark

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Generalized Model of Polypeptide Chain (GMPC) as One-Dimensional Potts-Like Model With Many-Particle Interactions and Theory of Helix-Coil Transition In Biopolymers

Vladimir F. Morozovz, Yevgeni Sh. Mamasakhlisov, Artem V. Badasyan, Arsen V. Grigoryan, Artem V. Tsarukyan

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Geometry of the Nucleosome's Superhelix: Ideal and Actual Structures

Thomas C. Bishop

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Guanine Quadruplex Invasion by Complementary and Homologous PNA Probes

Bruce A. Armitage

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Guanine Riboswitch Crystal Structure as a Basis for Ligand Specificity by a Natural RNA Aptamer

Sunny D. Gilbert, Sarah J. Wise, Crytstal Love, Rebecca K. Montange, Robert T. Batey

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Hinge-like Motions in RNA Kink-turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases

Filip Razga, Jaroslav Koca, Neocles B.Leontis, Jiri Sponer

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HU, Nucleoid Structure, and Transcription Profile

Sankar Adhya, Fusheng Guo, Sudeshna Kar

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In Planta Herbicide Detoxification with an Improved Bacterial Enzyme

Linda A. Castle, Daniel L. Siehl, Robert Keenan

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In Silico Structure-Based Design of a Potent and Selective Small Peptide Inhibitor of Protein Tyrosine Phosphatase 1B, A Novel Therapeutic Target for Type 2 Diabetes Mellitus and Obesity

Gita Subba Rao, Manoj V. Ramachandran, J.S. Bajaj

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Identification of Missing tRNA Modification Genes by Comparative Genomics

Valerie de Crecy-Lagard

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Introns are Inserted into Nucleosome DNA

Simon Kogan, Edward N. Trifonov

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Isolation and Characterization of the Proteins Recognizing Oxidatively Damaged DNA

Long Xu, Michael Lewis, Mahadevan Sethuraman, Thomas D. Tullius

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Kinking of Nicked DNA

Maxim D. Frank-Kamenetskii, Ekaterina Protozanova

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Ligand-Induced DNA Condensation: Choosing the Model

Vladimir Teif

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Local DNA Structural Features in the Contact Region with E.coli RNA Polymerase α Subunits Affect Transcription Complex Formation

E. G. Kostyanicina, I. S. Masulis, O. N. Ozoline

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Mechanism for the Disassembly of the Post-termination Complex Inferred from Cryo-EM Studies

Ning Gao, Andrey V. Zavialov, Wen Li, Jayati Sengupta, Mikel Valle, Richard P. Gursky, Måns Ehrenberg, Joachim Frank

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Melting Behavior of DNA Triplexes of the Pyrimidine Motif

Mahima Kaushik, Ronald Shikiya, Sarah Betzold, Rajkumar Ganugula, Ana Maria Soto, Luis A. Marky

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Model of a Pseudoknot Structure with a Triple-helical Stem from the Telomerase RNA of Kluyveromyces lactis

Nikolai B. Ulyanov, Kinneret Shefer, Valentin Gorkovoy, Tamar Nussbaum, Yogev Braun, Mira Abraham, Sivan Pearl, Deborah Shalev, Yehuda Tzfati

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Modular Assembly of a Multi-functional Homing Endonuclease

Marlene Belfort, Patrick Van Roey, Victoria Derbyshire

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Modulation and De Novo Design of Protein-Protein Interactions

Stephen L. Mayo

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Molecular Dynamics Simulation Studies on the Minor Groove Deformability of DNA

Martin Zacharias

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Molecular Insights into Intein Structure and Function

Kaori Hiraga, Tara Snyder, Patrick Van Roey, Marlene Belfort, Victoria Derbyshire

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Molecular Modeling for Biogenic Polyamines Bindings to B-DNA and A-RNA Duplex

H.A. Tajmir-Riahi, A. Ahmed Ouameur, S. Diamantoglou

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Molecular Modeling of a 30 Amino Acid Linker Connecting the DNA Binding Domain (DBD) and Ligand Binding Domain (LBD) of the Glucocorticoid Receptor (GR) Protein Using Secondary Structure Prediction, Model Building, Conformational Space Annealing, Energy M

Lester F. Harris, Michael R. Sullivan

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Monitoring Thymine Dimer Repair Electrically

Maria C. DeRosa, Aziz Sancar, Jacqueline K. Barton

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Multiple Conformational Changes in DNA Repair Enzymes During Substrate Recognition and Catalysis

O. Fedorova, G. Nevinsky, V. Koval, D. Zharkov, N. Kuznetsov, K. T. Douglas

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Multiple Open Reading Frames and Codon Bias in All Genomes

W.L. Duax, V. Pletnev, R. Huether, Lukas Habegger

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Multiplication Using DNA

Gang Wu, Nadrian C. Seeman

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Mutations By Error-Prone Repair Of Slipped-Strand DNAs Formed By Disease-Associated CTG/CAG Repeats

Gagan B. Panigrahi, Rachel Lau, Michelle Blondin, Christopher E. Pearson

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Nanoengineered Robotic Walkers from DNA

William B. Sherman, Nadrian C. Seeman

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NMR Solution Structure of a DNA Interstrand Cross-link Obtained via a Novel Furan Oxidation Strategy

Kristof Stevens, Annemieke Madder, Michael Petersen

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NMR Structural Study of Wild Type and Mutant U1A Proteins

Alina G. Britchi, Philip H. Bolton, Anne M. Baranger

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NMR Studies of Ribosomal Stem-loop RNA Recognized by an erm Methyltransferase

Katrine E. Nielsen, Michael Petersen

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Non-empirical Studies of the DNA Rare Base Pairs: The Molecular Mechanism of the Spontaneous Substitution Mutations Conditioned by Tautomerism of Bases

Victor I. Danilov, Noriyuki Kurita, Victor Anisimov

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Showing 1 to 100 of 185 items.  Page: 1