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 molecular dynamics computer simulations. Recent quantitative comparisons between calculated properties with those observed in crystal structure determinations and nuclear magnetic resonance experiments allow improvement of modelling techniques. Current issues in molecular dynamics methodology, particularly truncation of potentials, are discussed, followed by a survey of results from in vacuo and in aquo treatments of solvent. The results of recent in aquo DNA trajectories extended into the nanosecond regime, together with a comparison of calculated and observed axis bending behavior, close the gap between the timescale of molecular dynamics simulation and NMR techniques. Examples illustrating the analysis of DNA molecular dynamics simulations are included and discussed.