Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Ions and DNA: The View from Molecular Dynamics Simulations

Understanding base pair sequence effects on DNA structure and axis bending has been historically addressed in terms of conformational preferences intrinsic to the DNA molecule, including steric, electrostatic and stacking effects. However, the idea that environmental effects from solvent water and counterions might play a role has not been overlooked. Recently there is a lively discussion about the role of mobile counterions from crystallographic, NMR and computational modeling based on molecular dynamics (MD) simulations. How reliable is the information to date, and what are the limitations? In this presentation we provide some critical perspectives on the issue of ions and DNA based on MD simulations, and specifically with the issue of the convergence of MD description of counterion motions around DNA oligonucleotides on the nanosecond time frame. This research is supported by NIH GM-37909.

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

Chemistry Department
Molecular Biophysics Program
Wesleyan University
Middletown, CT 06459
*Phone: 860 685 2575 dbeveridge@wesleyan.edu