SUNY at Albany
June 19-23, 2001
Normal Mode Analysis of DNA in Terms of Base Pair Step Parameters
Computer simulation of the dynamic structure of DNA can be carried out at various levels of resolution. Detailed high-resolution information about the motions of DNA is obtained with computer-intensive methods that use the Cartesian coordinates of the constituent atoms as independent variables. Because such methods are computationally demanding, the size of the molecules that can be treated is currently limited to a few turns of the double helix. At low resolution, by contrast, the sequence-dependence of DNA is neglected and molecule is treated as an elastic rod. With such treatments, one can study the topological features of long DNA of a few thousand base pairs.
Our newly developed normal mode analysis of DNA in terms of base pair step parameters addresses the dynamic structure of the double helix at intermediate resolution. The use of six parameters per base-pair step--Tilt, Roll, Twist, Shift, Slide, and Rise--reduces the number of independent variables drastically, allowing us to study relatively long DNA, including circular molecules, at the mesoscopic level, i.e., a few hundred base pairs. Furthermore, when combined with knowledge-based force fields, sequence-dependent effects can be incorporated into the calculations. Results of the analysis for linear DNA will be presented.
Atsushi Matsumoto, Wilma K Olson
Department of Chemistry, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854