Brownian Dynamics Simulations of Electrophoretic DNA Separation in a Post Array By Pulsed Electric Field

Electrophoretic separation of DNA through a post array has been heavily investigated in both experiments and simulations. However, the efficiency of the post array for separating long DNA has been found decreased rapidly with increasing Peclet number (or electric field). The loss of resolution power is largely due to the onset of channeling phenomenon that DNA move through the hypothetical “channel” between posts without collisions with the posts. To improve the efficiency of separation at high Peclet number, we propose to use a pulsed electric field to replace the traditionally adopted constant electric field. When the electric field is turned off, DNA relax and diffuse, resulting in higher probability of collision with posts as the field is turned on. To test our idea, we have used Brownian dynamics simulations and computational fluid dynamics to simulate lambda-DNA(48.5 kbp) and T4GT7-DNA (166 kbp) under pulsed electric field through a hexagonal post array. It is found that the pulsed electric field does improve the resolving power of the post array at higher electric field due to the enhancement of the DNA-post collision.