Brownian dynamics simulations of electrophoretic DNA separations in a sparse ordered post array.

We use Brownian dynamics simulations to analyze the electrophoretic separation of lambda-DNA (48.5kbp) and T4-DNA (169kbp) in a hexagonal array of 1microm diameter posts with a 3microm center-to-center distance. The simulation method takes advantage of an efficient interpolation algorithm for the non-uniform electric field to reach an ensemble size (100 molecules) and simulation length scale (1mm) that produces meaningful results for the average electrophoretic mobility and effective diffusion (dispersion) coefficient of these macromolecules as they move through the array. While the simulated electrophoretic mobility for lambda-DNA is close to the experimental data, the simulation underestimates the magnitude of the corresponding dispersion coefficient. The simulations predict baseline resolution in a 15mm device after 7min using an electric field around 30V/cm, with the resolution increasing exponentially as the electric field further decreases. The mobility and dispersivity data point out two essential phenomena that have been overlooked in previous models of DNA electrophoresis in post arrays: the relaxation time between collisions and simultaneous collisions with multiple posts. Copyright 2010 Elsevier B.V. All rights reserved.