MOLECULAR-DYNAMICS STUDIES OF DNA

Progress has recently been made towards the development of an accurate theoretical model of DNA structure and motions on the basis of molecu lar dynamics computer simulations. Recent quantitative comparisons bet ween calculated properties with those observed in crystal structure de terminations and nuclear magnetic resonance experiments allow improvem ent of modelling techniques. Current issues in molecular dynamics meth odology, particularly truncation of potentials, are discussed, followe d by a survey of results from in vacuo and in aquo treatments of solve nt. The results of recent in aquo DNA trajectories extended into the n anosecond regime, together with a comparison of calculated and observe d axis bending behavior, close the gap between the timescale of molecu lar dynamics simulation and NMR techniques. Examples illustrating the analysis of DNA molecular dynamics simulations are included and discus sed.