Brownian Dynamics Simulation of Biased Sinusoidal Field Gel Electrophoresis

Abstract

Brownian dynamics simulation of DNA in the biased sinusoidal field gel electrophoresis was performed. The time development of the velocity of the center of mass and the principal value of the gyration tensor was measured as a function of the chain length and the frequency of the applied field. It is found that (i) for short chains N < Nc(E), the mean migration velocity decreases monotonically with the frequency, and that (ii) for long chains N > Nc(E), the mean migration velocity shows local minimum and local maximum at characteristic frequencies f1 and f2, respectively. These results are in agreement with the experiment of Shikata et al. Analysis of the data indicates that the DNA takes the stretched V-conformation and compact conformation alternatively, while at the frequency f1 the DNA frequently takes the W-conformation.