Workshop on DNA Sequence and Topology

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

Organizers:

Wilma K. Olson, Rutgers University, olson@rutchem.rutgers.edu

Bernard D. Coleman, Rutgers University, bcoleman@stokes.rutgers.edu

Victor B. Zhurkin, NIH, zhurkin@nih.gov

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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