A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA

The variation of the diffusion coefficient (D) of DNA molecules with their size and topology is an important problem. Experiments have elucidated key scaling factors for diffusion for DNA molecules in the size range of 5.9–287.1 kilo base pairs. In this Letter, we have investigated the dependence of D for both linear and supercoiled DNAs (from 300 to about 2300 base pairs) using Brownian dynamics simulation. We show that the dependence is similar for linear and supercoiled DNA, similar to larger DNA. Our calculated D values were, in general, in excellent agreement with experiments.