MODEL SIMULATIONS OF DNA DYNAMICS

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 i s examined by comparing several qualitative and quantitative features of the model DNA dynamics with all-stem simulations. The model helix i s stable at low temperatures and gradually unwinds (melts) at high tem peratures. The melting transition in this model seems to be fairly sha rp in temperature, but the melting kinetics is rather slow in time. Lo calized fluctuations of the hydrogen bonds are commonly observed, espe cially in regions enriched with adenine-thymine pairs.