ON THE HYDRODYNAMIC DIFFUSION OF RIGID PARTICLES OF ARBITRARY SHAPE WITH APPLICATION TO DNA.

A general model for the diffusive dynamics of rigid particles in a viscous solvent is studied. The model applies to particles of arbitrary shape and allows for arbitrary cross- and self-coupling between translational and rotational degrees of freedom. Scaling and perturbation techniques are used to characterize the dynamics at time scales relevant to different classic experimental methods. It is shown that translational and rotational motion can be treated as independent at these time scales and can be described by simplified diffusion models, provided that certain geometric and hydrodynamic parameters associated with a particle are small. These parameters are estimated for DNA molecules of different length using a sequence-dependent geometric model based on x-ray crystallography and a numerical boundary element technique. Our results suggest that, for short DNA fragments up to about a persistence length, translational data can be accurately analyzed using a simplified model characterized by a scalar, orientationally averaged diffusion coefficient, but not rotational data. Indeed, the accurate analysis of rotational data may require a model which accounts for self-coupling and other possible effects at the rotational time scale. [ABSTRACT FROM AUTHOR]