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Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003
Showing 101 to 200 of 201 items.  Page: 2

On the Role of DNA Looping in the Regulation of Lac operon in Escherichia coli

David Swigon, Wilma K. Olson, Bernard D. Coleman

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On the Structural ? Gene Transfer Activity Relationship of DNA-Dicationic Lipid Genosomes

A. S. Elkady, V. P. Tychinskii, Y. Sebyakin, A. Moskovetsov, R. Zhdanov, A.R.Khokhlov

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On the Structural and Kinematical Peculiarities of DNA-Vitamin D Complexes as Revealed by Atomic Force Microscopy and Molecular Mechanics

A. S. Elkady, R. I. Zhdanov

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Open Reading Frames (ORFs) and Codon Bias In The Genome Of Streptomycis coelicolor and the Origin and Evolution of the Genetic Code

R. Huether, L. Habegger, S. Connare, V. Pletnev, W. L. Duax

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Oxidative Damage by DNA-Mediated Charge Transport

Sarah Delaney, Jacqueline K. Barton

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Parallel Molecular Computation of Pair-wise XOR using DNA ?String Tile? Self-Assembly

Hao Yan, Liping Feng, Thomas H. LaBean, John H. Reif

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Parameterization of Na+ and Cl- Ions

David R. Langley

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Phosphorus Nuclear Spin Relaxation Results on Nuclec Acids and Phosphlipids Obtained with a Field Shuttling Device Attached to a Shared Commercial NMR

Mary F. Roberts, Alfred Redfield

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Physical Chemistry of the Unfolding of DNA Intramolecular Triplexes

Ronald Shikiya, Ganugula Ragkumar, Ana Maria Soto, Monica Torres, Luis A. Marky

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Polymer Model for the Relationship between Chromosomal Configurations/ Associations and Nuclear Size/Shape

Joseph Ostashevsky

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Pose Analysis of Structures of Alpha-Carbons in Proteins

Sangyoon Lee, Gregory S. Chirikjian

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Possible Mutual Arrangements of Guanine and Cytosine Bases. Comparison of the Results Obtained by Molecular Mechanics and Quantum Mechanics Calculations

V. I. Poltev, V. I. Danilov, A. Les, A. Jurkiewicz, A. S. Deriabina, E. Gonzalez

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Probing Molecular Recognition by Protein Kinases with Novel Peptide Mimics

Steve Flemer, Alexander Wurthmann, Amarnath Natarajan, Delmy Diaz, Christian Nickl, Kevin Foley, Wolfgang Dostmann, Jose Madalengoitia

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Probing the Interactions of a DNA Triple Helix with Metal Ions by Proton Exchange and NMR Spectroscopy

Daniel Coman, Irina M. Russu

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Promoter-search Algorithm Based on Canonical and Non-canonical Sequence Elements of E.coli Regulatory Regions.

O. N. Ozoline, A. S. Brok-Volchansky, A. A. Deev,

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Protein Folding and Unfolding

George Rose

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Protein Folding by Quasi-static-like Process ? A First Order State Transition

Chia-Ching Chang, Ya-Chi Su, Ming-Sung Cheng and, Lou-Sing Kan

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Protein Structure: Missing Basics to Proteomic Code

Igor N. Berezovsky

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Protonation Induced Structures of Homo-and Hetero-polymer of Guanine-cytosine and Their Binding to Berberine: Spectroscopic Studies

G. Suresh Kumar, S. Das, M. Maiti

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Regulation of Promoter Activity by Sequence-Specific Minor Groove Binding Ligands

S. V. Belikov, S. L. Grokhovsky, A. N. Surovaya, G.V. Gursky,

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Resolution of Undistorted Symmetric Immobile DNA Junctions by Vaccinia Topoisomerase I

Shiping Liao, Chengde Mao, Jens Birktoft, Stewart Shuman, Nadrian C. Seeman

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RNA Informatics: Discovery of RNA Structural Features by Computation

Shu-Yun Le, Jih-Hsiang Chen, Jacob V. Maizel, Jr.

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RNA Recognition by Threonyl-tRNA Synthetase

Dino Moras, A. Torres-Larios, B. Rees, R. Sankaranarayanan, A.C. Dock-Bregeon

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RNA Structure and Dynamics in Biology

Joseph D. Puglisi

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Role of Pseudouridine in Stabilizing the Pre-mRNA Branch Site Helix of the Eukaryotic Splicosome

Nancy L. Greenbaum, Meredith I. Newby

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Sequence-Dependent DNA Condensation and the Electrostatic Zipper Motif

Helen G. Hansma, John C. Sitko, Eduard M. Mateescu

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Sheared Ganti·Csyn Base Pair: A Unique d(GXC) Loop Closure Motif

Ko-Hsin Chin, Shan-Ho Chou

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Single Molecule Supercoiling and Denaturation in GalR/HU-mediated DNA Looping

Laura Finzi

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Single-molecule Fluorescence Microscopy of the Hairpin Ribozyme Reveals Elementary Principles of RNA Folding

Gregory Bokinsky, David Rueda, Vinod K. Misra, Miguel J. B. Pereira, Harold Kim, Hazen P. Babcock, Andrew Gordus, Maria M. Rhodes, Steven Chu, Xiaowei Zhuang, Nils G. Walter

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Site-Resolved Energetics in a DNA Unwinding Element

Daniel Coman, Irina M. Russu

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Site-Specific Nicking of Duplex DNA using PNAs and Restriction Endonucleases

Heiko Kuhn, Maxim D. Frank-Kamenetskii, Vadim V. Demidov

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Slow Kinetics of DNA/single Stranded Binding Protein SSB gp32 Interaction Studied by the Single Molecule DNA Stretching

Ioulia Rouzina, Mark Williams

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Small Interfering RNAs and MicroRNAs in Animal Systems

Javier Martinez, Agnieszka Patkaniowska, Mariana Lagos-Quintana, Jutta Meyer, Alexei Aravin, Sayda M. Elbashir, Jens Harborth, Klaus Weber, Abdullah Yalcin, Henning Urlaub, Reinhard Rauhut, Reinhard Luehrmann, Thomas Tuschl

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Some Characteristics of DNA Melting Curve

Yu. S. Babayan, A. Sh. Markaryan, S. Yu. Babayan, M. A. Parsadanyan, A. P. Antonyan, P. O. Vardevanyan

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Some New Insights into DNA Triplexes Formed by Non-isomorphous Base Triplets: Concept of Intrinsic ?Residual? Hoogsteen Twist and Sequence Dependent DNA Triplexes

R. Thenmalarchelvi, N. Yathindra

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Specific Features of Electrostatic Potential of E.coli Ribosomal Promoters

S. G. Kamzolova, A. A. Sorokin, T. R. Dzhelyadin, N. N. Ivanova, R. V. Polozov

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Spectroscopic Contributions to the Understanding of Hemoglobin Function: Implications for Structural Biology

Robert G. Shulman

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Strategies for Accurate NMR Structure Determination of Larger DNAs and RNAs. Application of Selective Labeling, Chemical Shifts and Phage-induced and/or Magnetic-field-induced Residual Dipolars

B. Wu, F. Girard, S. Flodell, J. Cromsigt, B. van Buuren, J. Cromsigt, J. Schleucher, K. Kidd-Ljunggren, M.Tessari, S. Wijmenga

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Structural Analysis of β-barrel Membrane Proteins

Vasanthi G, Krishnaswamy S

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Structural and Conformational Properties of the Functionally Essential Domains in Tetrahymena thermophilus Telomerase RNA

Lukas Trantirek, Carla A. Theimer, Juli Feigon

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Structural and Energetic Analysis of the DNA A-B Transition Using Spectroscopic and Computational Methods

Colin E. Aitken, Kelly M. Knee, Ishita Mukerji, David L. Beveridge

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Structural and Functional Proteomics

Cheryl H. Arrowsmith

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Structural Aspects of Gene Expression by Formation of High Order Protein Complexes on Promoter DNA: A Recent Progress

Tahir H. Tahirov

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Structural DNA Nanotechnology

Nadrian C. Seeman, Hao Yan, Chengde Mao, Ruojie Sha, Furong Liu, Xiaoping Zhang, Zhiyong Shen, Pamela E. Constantinou, Baoquan Ding, Wanqiu Shen, Shiping Liao, Lisa Israel, Philip Lukeman, Yariv Pinto, William Sherman, Jiwen Zheng, Jens Kopatsch, Loraine Foley, Xiaoping Yang, Weiqiong Sun, Yinli Wang, Shouming Du, Hui Wang, Tsu-Ju Fu, Yuwen Zhang, Hangxia Qiu, John E. Mueller, Junghuei Chen

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Structural Genomics of Human Proteins: Concept, Pitfalls, Achievements

Udo Heinemann

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Structural Proteomics of DNA-binding Proteins from Hyperthermophilic Sulfolobus Archaebacteria

Andrew H.-J. Wang

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Structural Weaknesses and Cation-π Interactions in Proteins. A Possible Link with 3D Domain Swapping

Yves Dehouck , Christophe Biot, Dimitri Gilis, Jean Marc Kwasigroch, Marianne Rooman

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Structure and Dynamics of Polyubiquitin Chains in Solution

Ranjani Varadan, Aydin Haririnia, Michael Assfalg, Olivier Walker, Cecile Pickart, David Fushman

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Structure and Energetics of a DNA Triple Helix Investigated by UV Resonance Raman Spectroscopy

Eliana Tsukroff, Lihong Jiang, Ishita Mukerji

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Structure and Energetics of a DNA Triple Helix
Investigated by UV Resonance Raman Spectroscopy

Eliana Tsukroff, Lihong Jiang, Ishita Mukerji

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Substrate Specificity in RNase H Family of Enzymes: Modeling the Interaction of (DNA:RNA) Hybrid With RNase H

G. Goldsmith, S. Raja, N. Yathindra

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Tailoring the Activity of DNA-processing Proteins via Sequence-directed DNA Looping

Ekaterina Protozanova, Vadim V. Demidov, Maxim D. Frank-Kamenetskii

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Temperature-induced Alterations Within E.coli RNA Polymerase α-subunit Contact Region with T7D Promoter Affect the Mode of Transcription Initiation

V. V. Chasov, I. S. Masulis, O. N. Ozoline

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The Design of Nucleic Acid Nanotubes

William B. Sherman, Nadrian C. Seeman

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The Difference Between Coding and Non-coding DNA Thermal Stability: A Large Scale Surrvey of 28 Eukaryotic Organisms of Varying (G+C) Composition Studied by Melting Simulation, Base Shuffling and DNA Frequency Analysis

Dang D. Long, Ivo Grosse, Kenneth A. Marx

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The Double Helix: A View 50 Years Later

Alexander Rich

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The Dynamics of the E. coli 70S Ribosome: An Application of Real-Space Refinement

Haixiao Gao, Jayati Sengupta, Mikel Valle, Andrei Korostelev, Narayanan Eswar, Scott M. Stagg, Patrick Van Roey, Rajendra K. Agrawal, Stephen C. Harvey, Andrej Sali, Michael S. Chapman, Joachim Frank

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The Effect of the Sequences Flanking the TATA Box on TBP/TATA Box Interaction

Hana Faiger, Keren-Or Amar, Tali E. Haran

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The Fluctuating Enzymes

Sunney Xie

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The Geometry of Canonical Watson-Crick DNA Base Pairs: Ab Initio Post-Hartree-Fock Theory Studies

V. I. Danilov, V. M. Anisimov

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The Minor Groove Binding SN-ligands? Influence On The Oligonucleotide Triplex-Duplex-Coil Transitions

Gabrielian Anna, Walter Axel, Schütz Holger, Birch-Hirshfeld Eckhard

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The Mu Transposition Enhancer and Path of DNA within the Mu Transpososome

Shailja Pathania, Makkuni Jayaram, Rasika M. Harshey

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The Nature of Actinomycin D Binding to Self-Complementary d(CXYGGCCY?X?G) Sequence Motifs

Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, Shan-Ho Chou

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The Nature of the Stability of Watson-Crick Nucleic Acids Base Pairs. Ab Initio Hartree-Fock and Post-Hartree-Fock Theory Studies

V. I. Danilov, V. M. Anisimov

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The Role of Both Negatively and Positively Charged Protein Residues on the Salt-Dependent Protein-Nucleic Acid Association Process

Marcia O. Fenley, Gerald S. Manning

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The Structure and Active Site of the VS Ribozyme

Daniel A. Lafontaine, David G. Norman, Timothy J. Wilson, Aileen McLeod, David M. J. Lilley

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Theory of the Dependence of Configurations of Intrinsically Curved DNA on Salt Concentration

Bernard D. Coleman, Yoav Biton, David Swigon,

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Three Dimensional Structures of Lipid Induced NK2 ? Selective Tachykinin Agonists

Indu R. Chandrashekar, M. Anil Kumar, Anjali Dike, Sudha M. Cowsik

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Three-dimensional Structure of a Gene Transfer Complex from Agrobacterium tumefaciens

Asmahan Abu-Arish, Sharon Grayer-Wolf, Vitaly Citovsky, Michael Elbaum

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Topics in the Polyelectrolyte Theory of DNA

Gerald S. Manning

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Towards the Prediction of Novel DNA-binding Protein Structures

Hugh Shanahan

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Translational Termination in E. coli by Class-I Release Factors: A Cryo-em Study

Urmila B. S. Rawat, A. Zavialov, J. Sengupta, M. Valle, E. Narayanan, R.A. Grassucci, R. Gursky, A. Sali, M. Ehrenberg, J. Frank

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Travelling with t-RNAs Through the Ribosome

Jayati Sengupta, Haixiao Gao, Mikel Valle, Joachim Frank

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Two Bottlenecks for ab initio Prediction of Protein Structures

Alexei V. Finkelstein, Gerrit Vriend

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Two Dimensional DNA Parallelogram Crystals

Lisa B. Israel, Nadrian C. Seeman

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UNCG or YNMG?

Nikolai B. Ulyanov, Zhihua Du, Jinghua Yu, Luis R. Comolli, William H. Gmeiner, T. L. James

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Understanding the Mechanisms of Protein Aggregation

Nikolay V. Dokholyan

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Unexpected Digestion of DNA in One-Base Mismatch PNA/DNA Duplex by Nuclease S1 and Its Application to SNPs Detection

Xingguo Liang, Sheng Ye, Yoji Yamamoto, Takafumi Tomita, Jing-Min Zhou, Makoto Komiyama

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Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of cis Watson-Crick A/G Base Pairs: The Role of Nonplanar Guanine Amino Group

J. Sponer, A. Mokdad, J. E. Sponer, N. Spackova, J. Leszczynski, N.B. Leontis

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Using Structural Motif Templates to Identify Proteins with DNA Binding Function

Susan Jones, Jonathan Barker, Irilenia Nobeli, Helen M. Berman, Janet M.Thornton

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Visualizing tmRNA Entry into the Stalled Ribosome

Sukhjit Kaur, Mikel Valle, Reynald Gillet, Anke Henne, V. Ramakrishnan, Joachim Frank

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Watson at Harvard (1956-1976)

Paul Doty

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23Na, 17O and 2H MRD Investigations of DNA Quadruplexes

Karim Snoussi, Bertil Halle

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A Unified Model for the Role of Cations in DNA Sequence-Directed Curvature

Nicholas V. Hud

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Cation-π Interactions at Protein-DNA Interfaces: Possible Role in the Charge Migration Along the DNA Stack

Christophe Biot, René Wintjens, Eric Buisine, Jacky Liévin, Marianne Rooman

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Cation-π Interactions at Protein-ligand Interfaces: In silico Free Energy Estimation and Environment Dependency

Christophe Biot, Eric Buisine, Marianne Rooman

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DNA-Metal Ion Interactions in Crystal Structures of Oligonucleotides

Martin Egli

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Effect of Nucleic Acid Oligomer Length on Salt Ion Accumulation; NLPB Analysis at Experimental Salt Concentrations

I. A. Shkel, M. T. Record, Jr.

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Electrostatic Shielding of DNA in Tris and Diethylmalonate Buffers, with and without Added Salt

Nancy C. Stellwagen, Earle Stellwagen

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Inter-relationships Between A-tracts, G-tracts and Divalent Ions and Their Effect on the Intrinsic Bending Phenomenon

Ayelet Merling, Nataliya Sagaydakova, Tali E. Haran

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Interactions of Metal Cations with Nucleic Acids: Quantum Chemical View

J. Sponer, J. E. Sponer, J. Leszczynski, J. V. Burda, B. Lippert

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Ions and DNA: The View from Molecular Dynamics Simulations

S. Ponomarev, K. M. Thayer, D. L. Beveridge

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Ions, Bonding and Bending in DNA/Protein Recognition

Richard E. Dickerson, Mary L. Kopka, Ann Maris, Gye-Won Han

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Ions, Solvent and Counter-ions in G-quadruplex Structures

Shozeb M Haider, Gary N Parkinson, Michael PH Lee, Stephen Neidle

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Na+ and Rb+ Bind to the Same Sites in the Minor Groove of B-DNA

Flaminia Cesare Marincola, Vladimir P. Denisov, Bertil Halle

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Perturbations in Structures of Backbone Modified DNA to Probe Cation-DNA Interactions

David Volk, XianBin Yang, David Power, Ekaterina V. Viazovkina, Elena V. Bichenkova, V. Thiviyanathan, Bruce A. Luxon, Elliot K.Gozansky, Alexander V. Lebedev, David G. Gorenstein

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Sequence Dependence of Counterion Binding to DNA Oligomers Containing A-Tracts

Nancy C. Stellwagen, Qian Dong

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Studying Ion Distributions Around DNA

Krystyna Zakrzewska, Peter Varnai

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Thallium(I) Binds to Major and Minor Grooves of DNA in Aqueous Solution

A. Ahmed Ouameur, Sh. Nafisi, N. Mohajerani, H. A. Tajmir-Riahi

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The Crystal Structure of the Human Papillomavirus E2 Binding Site: A High-resolution View of DNA Bending by an Adenine-thymine Tract

Haim Rozenberg, Yehuda Halfon, Yaacov Halfon, Jenny Hizver, Dov Rabinovich, Zippi Shakked

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Showing 101 to 200 of 201 items.  Page: 2