SITE-SPECIFIC DYNAMICS IN DNA - THEORY

This chapter reviews recent progress in understanding duplex DNA dynam ics. The weakly bending rod model of Schurr and coworkers is described and compared to a model-free formulation of DNA dynamics. Numerical t rajectory methods for obtaining dynamic information are also discussed . The general principles of magnetic resonance relaxation are then rev iewed, and the methods by which molecular motions are incorporated int o the calculation of relaxation rates or the simulation of experimenta l NMR and EPR data are described. The impact that the time scale of th e dynamics exerts on various computational methods is considered, and in particular, the implementation of (a) the stochastic Liouville equa tion, (b) the RedField relaxation matrix, and (c) tensorial preaveragi ng is described. Expressions for direct and cross-relaxation processes are developed by expanding the density matrix in terms of an irreduci ble tenser basis set.