Brownian dynamics studies on DNA gel electrophoresis. II. “Defect” dynamics in the elongation-contraction motion Available to Purchase

By means of the Brownian dynamics (BD) method of simulations we have developed, we study the dynamics of individual DNA molecules which are undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the “defect” concept due to de Gennes in CFGE. The corresponding objects, which we call slack beads (s-beads), are explicitly introduced in our BD model. In equilibrium under a vanishing field, the distance between s-beads and their hopping range is found to be randomly distributed following a Poisson distribution. In strong fields, where a chain undergoes elongation-contraction motion, s-beads are observed to be alternately annihilated in elongation and created in the contraction of the chain. On the other hand, the distribution of hopping ranges of s-beads does not differ much from that in equilibrium. The results indicate that in the elongation-contraction motion of the chain, a large number of random movements of s-beads are involved. We have also confirmed that these features of s-beads agree qualitatively with those of s-monomers in the extended bond fluctuation model (EBFM) which we recently proposed. This agreement strongly supports the stochastic semilocal movement of s-monomers which we a priori introduced into the EBFM.