Conformational Correlations in DNA. Molecular Dynamics Studies

Abstract

A statistical, circular correlation model for conformational degrees of freedom in DNA is proposed. Correlation coefficients are computed for A and B DNA, as well as for transition processes between these forms, using microscopic MD simulation data. The correlations are interpreted and a minimal number of independent conformational degrees of freedom conserving basic static and dynamic properties of the right-handed DNA forms are found. The selected degrees of freedom form a hierarchical class and can constitute a base for a dynamical model using curvilinear degrees of freedom. In the most accurate representation one uses all backbone, torsional angles as well as pseudorotation parameters and glycosidic angles. In the second model one treats the backbone angles δi, and the glycosidic angles χi, as functions of the phases of pseudorotation, Pi. The third model assumes a functional dependence of other backbone angles ξi as functions of Pi.