BROWNIAN DYNAMICS SIMULATION OF BIASED SINUSOIDAL FIELD GEL-ELECTROPHORESIS

Brownian dynamics simulation of DNA in the biased sinusoidal field gel electrophoresis was performed. The time development of the velocity o f the center of mass and the principal value of the gyration tensor wa s measured as a function of the chain length and the frequency of the applied field. It is found that (i) for short chains N < N-c(E), the m ean migration velocity decreases monotonically with the frequency, and that (ii) for long chains N > N-c(E), the mean migration velocity sho ws local minimum and local maximum at characteristic frequencies f(1) and f(2), respectively. These results are in agreement with the experi ment of Shikata et al. Analysis of the data indicates that the DNA tak es the stretched V-conformation and compact conformation alternatively , while at the frequency f(1) the DNA frequently takes the W-conformat ion.