Workshop on DNA Sequence and Topology

Dates: April 19 - 20, 2001
DIMACS Center, Rutgers University, Piscataway, NJ

Wilma K. Olson, Rutgers University,
Bernard D. Coleman, Rutgers University,
Victor B. Zhurkin, NIH,
Presented under the auspices of both the DIMACS Special Focus on Computational Molecular Biology and The Center for Molecular Biophysics and Biophysical Chemistry at Rutgers University, and with support from PMMB (The Program on Mathematics and Molecular Biology based at Florida State University).

Preliminary Program:

Thursday, April 19, 2001

Morning Session I: DNA Sequence Effects and Their Origins 8:30-9:00 Breakfast and Registration 9:00-9:15 Welcome and Greeting Fred S. Roberts, Director, DIMACS 9:15-9:30 Introduction and General Overview Wilma K. Olson 9:30-10:15 DNA Conformation and Genomic Organization Masashi Suzuki, AIST-NIBHT Centre, Japan 10:15-10:45 Morning Break 10:45-11:30 Measurement of DNA Intrinsic Curvature in Solution Alexander V. Vologodskii, New York University 11:30-12:15 Ab Initio Quantum Mechanical Analysis of Nucleic Acid Components Alexander D. MacKerell, Jr., University of Maryland 12:30-2:00 Lunch Break Afternoon Session I: Intrinsic and Protein- Induced Deformations of DNA Structure 2:00-2:45 A Theory of DNA Elasticity that takes into Account the Dependence of Deformability on the Base-Pair Sequence David Swigon, Rutgers University 2:45-3:30 Structure of a Flp Recombinase DNA Complex Phoebe A. Rice, University of Chicago 3:30-4:00 Afternoon Break 4:00-4:45 Probing the Architecture of the Crossover Site Synapsis Promoted by Gd Resolvase Andrew Leschziner, Yale University 4:45-5:30 Earliest Evolutionary Signatures in DNA Sequences Edward N. Trifonov, Weizmann Institute of Science, Israel 6:00-9:00 Buffet Dinner Reception and Poster Session

Friday, April 20, 2001

Morning Session II: Topological Transitions and Local Structure 8:30-9:00 Breakfast and Registration 9:00-9:45 Topologically Driven Transitions in DNA Structure: Their Mathematical Analysis and Roles in Biology Craig J. Benham, Mount Sinai Medical Center 9:45-10:30 Single-Molecule Analysis of DNA Uncoiling By A Type II Topoisomerase Terence Strick, Cold Spring Harbor Laboratory 10:30-11:00 Morning Break 11:00-11:45 DNA Sequence-Structure Relationships Christopher A. Hunter, University of Sheffield 11:45-12:30 Extracting Localized Properties of the TATA-Box Via Continuum Modeling of Cyclization Experiments Robert Manning, Haverford College 12:30-12:45 Discussion 12:45-2:00 Lunch Break Afternoon Session II: Mesoscopic and Higher-Order Representations of DNA 2:00-2:45 Dynamic Simulations of Regulatory DNA/ Protein System Tamar Schlick, New York University 2:45-3:30 Large-Scale Chromatin Structure and Function Andrew S. Belmont, University of Illinois 3:30-4:00 Afternoon Break 4:00-4:45 Antiparallel DNA Loop in the Gal Repressosome Victor B. Zhurkin, National Cancer Institute, NIH 4:45-5:30 Nucleosome Positioning DNA Sequences Jonathan Widom, Northwestern University

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Document last modified on April 12, 2001.