(248c) Collision of a Large DNA Molecule in An Array of Obstacles

We have investigated the electrophoretic collision of T4 DNA (169 kbp) in an array of obstacles using a recently developed Boundary Element Method/Brownian dynamics simulation routine. Starting from a relaxed configuration in the gap between the posts, the molecule is driven into the obstacle under the influence of a relatively strong electric field. The magnitude of the field and the array geometry (1 μm diameter posts arranged in a hexagonal array with a 3 μm pitch) are similar to those used in experiments. We found that, in contrast to a relatively short molecule such as λ-DNA (48.5 kbp), the ensemble of collisions for the longer T4 DNA is considerably more complex. In addition to the single post collision dynamics observed by Randall and Doyle, we observed two array-based collision modes that we refer to as ?A? and ?M? collisions. The latter modes require that the unraveling chain possess sufficient stored length so that one arm of the chain can collide with a second obstacle. We will discuss the role of these additional collision modes on modeling the electrophoretic mobility and effective diffusivity (dispersivity) of the DNA in an array.