Abstract
We used Brownian dynamics simulations to compare DNA separations in microfabricated post arrays containing either hexagonal or lamellar lattices. Contrary to intuition, dense hexagonal arrays with frequent DNA post collisions do not yield the optimal separation. Rather, hexagonal arrays with pore sizes commensurate with the radius of gyration of the DNA lead to increased separation resolution due to a molecular weight dependent collision probability that increases with molecular weight. However, when the hexagonal array is too sparse, this advantage is lost due to the low number of collisions. Lamellar lattices, such as the DNA nanofence, appear to be superior to a hexagonal array at the same post density, since the lamellar lattice combines regions for DNA relaxation with locally dense post regions for collisions. The relative advantages of different post arrays designs are explained in terms of the statistics for the number of collisions and the holdup time, providing guidelines for designing post arrays for separating long DNA.