Pertinent Questions and Problems

Before delving into theoretical and experimental details, it is useful to consider some of the motivations for research in this area. The kinds of problems and questions addressed by such experiments can be classified into several categories from physical to biological, as follows. 

At present, the Brownian motions of isolated rigid macromolecules are quite well understood. The challenge now is to understand the Brownian deformations of nonrigid macromolecules and to ascertain the time scales on which the coupled motions of their subunits relax various experimental signals. 

A particular question of interest is whether the DNA torsional motions observed on the nanosecond time scale are overdamped, as predicted by simple Langevin theory, and as observed for Brownian motions on longer time scales, or instead are underdamped, so that damped oscillations appear in the observed correlation functions. A related question is whether the solvent water around the DNA exhibits a normal constant viscosity on the nanosecond time scale, or instead begins to exhibit viscoelastic behavior with a time-, or frequency-, dependent complex viscosity. In brief, are the predictions for 

It is conceivable that diffusion of kinks, or overdamped solitons, along the DNA could act to relax the FPA with a time dependence similar to that predicted for torsional deformation/31 32) High levels of intercalated dyes would be expected to alter both the equilibrium population of kinks and their mobility along the DNA. Hence, this question is addressed by examining the effect of intercalating dyes on the torsional dynamics. 

Ordering of water in the DNA grooves is a topical subject. 51,52) Whether water in the DNA grooves behaves like normal water or instead 

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