Site-specific dynamics in DNA: theory

Abstract

This chapter reviews recent progress in understanding duplex DNA dynamics. The weakly bending rod model of Schurr and coworkers is described and compared to a model-free formulation of DNA dynamics. Numerical trajectory methods for obtaining dynamic information are also discussed. The general principles of magnetic resonance relaxation are the reviewed, and the methods by which molecular motions are incorporated into the calculation of relaxation rates or the simulation of experimental NMR and EPR data are described. The impact that the time scale of the dynamics exerts on various computational methods is considered, and in particular, the implementation of (a) the stochastic Liouville equation, (b) the Redfield relaxation matrix, and (c) tensorial preaveraging is described. Expressions for direct and cross-relaxation processes are developed by expanding the density matrix in terms of an irreducible tensor basis set.