Brownian dynamics simulation of the diffusion of rods and wormlike chains in a gel modeled as a cubic lattice: application to DNA.

The translational diffusion constant of a particle, D, in a congested medium or a gel can be written as the product of two terms that account for long-range hydrodynamic interaction between the gel or congested medium and the particle, DEM, and a short-range "steric" term, S. For particles of arbitrary shape, DEM has been examined previously within the framework of the effective medium, EM, model (S. Allison et al., J. Phys. Chem. B 2008, 112, 5858-5866). In the present work, we examine S for rod- and wormlike chain models of duplex DNA in the size range of 100 to over 2000 base pairs. The gel is modeled explicitly as a cubic lattice, and Brownian dynamics simulation is used to examine S for a wide range of rod/wormlike chain and gel parameters. For wormlike chains with P = 50 nm, an empirical formula is derived for S that should be valid over a wide range of wormlike chain/gel parameters. For duplex DNA in the size of several hundred to several thousand base pairs in an agarose gel of 2% or less, fair agreement between modeling and experiment is obtained. However, modeling overestimates the length dependence of D observed experimentally. Finally, the reduction of D of DNA (100 to over 1000 base pairs in length) in cytoplasm relative to water can be accounted for quite well using the effective medium plus steric correction approach.