Mechanisms of DNA separation in entropic trap arrays: A Brownian dynamics simulation

Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a device has been designed and fabricated recently by Han et al. for the separation of DNA molecules (Science, 2000). Our simulation reproduces the experimental observation that the mobility increases with the length of the DNA. A detailed data analysis allows to identify the reasons for this behavior. Two distinct mechanisms contribute to slowing down shorter chains. One has been described earlier by Han et al.: the chains are delayed at the entrance of the constriction and escape with a rate that increases with chain length. The other, actually dominating mechanism is here reported for the first time: Some chains diffuse out of their main path into the corners of the box, where they remain trapped for a long time. The probability that this happens increases with the diffusion constant, i.e., the inverse chain length.