CONFORMATION AND DYNAMICS OF DEOXYRIBONUCLEIC ACIDS

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The hope of understanding relationships between structure and function is at the heart of research in structural biology. At the macromolecular level, only computer models are capable of handling the enormous number of interactions that determine structure and dynamics. This project is aimed at elucidating the principles that determine how DNA sequence affects DNA structure and how that structure is affected by biologically relevant environmental factors, such as closure into circles, supercoiling, and interactions with proteins and drug molecules. Computer models are being developed for investigating these problems. Among these is a general purpose program for predicting and analyzing DNA structure when the sequence is specified. Also under development is a new program for modeling DNA supercoiling in molecules up to about 5000 basepairs long, with structural resolution to the basepair level. It will be used to investigate the effects of sequence, supercoiling pressure, and protein binding on global and local structure. New algorithms are being developed for the treatment of electrostatic effects, for the simplified treatment of solvation, for modeling conformational transitions, and for carrying out molecular dynamics simulations on general purpose parallel computers.