Dynamics of DNA in entangled polymer solutions: An anisotropic friction model

Abstract

We studied the electrophoretic behavior of DNA chains in linear-polymer solutions using Brownian dynamics with an anisotropic friction model in a three-dimensional space and projected on the x axis. For the three-dimensional model with a chain segment equal to 1/8 of the Kuhn length, a chain migrates with U-shaped conformation with low anisotropy of friction. With high anisotropy of friction, a chain always migrates with linear-shaped conformation with high segment-density regions, which remain at the same positions in space. This migration mode agrees with the observation of DNA in highly entangled solutions [Ueda et al., Biophys. Chem. 71, 113 (1998)]. The projection model also reproduces the linear-shaped motion. We clarified that the essential conditions for linear shaped motion are the sufficient chain length of DNA, the small mesh size, and strong confinement by entanglement with solvent polymers.