Model simulations of DNA dynamics

Abstract

A simple physical model is developed to study some characteristics of DNA dynamics. The model uses only a few degrees of freedom so that DNA dynamics can be simulated over longer times and for larger sequences than is possible with all-atom simulations. The utility of the model is examined by comparing several qualitative and quantitative features of the model DNA dynamics with all-atom simulations. The model helix is stable at low temperatuers and gradually unwinds (melts) at high temperatures. The melting transition in this model seems to be fairly sharp in temeprature but the melting kinetics is rather slow in time. Localized fluctuations of the hydrogen bonds are commonly observed, especially in regions enriched with adenine-thymine pairs.