Electrophoretic collision of a DNA molecule with a small elliptical obstacle

Abstract

We present a Brownian dynamics study of the collision and unhooking of a lambda-DNA molecule with an elliptical obstacle. The semi-major and semi-minor axes of the obstacle are comparable to the radius of gyration of the DNA, and the field is sufficiently strong to cause frequent hairpin formation upon collision. We focus on how the dynamics of a head-on collision (impact parameter of zero) are affected by the angle between the major axis of the ellipse and the direction of the electric field far from the elliptical surface. When this orientation angle breaks the symmetry of the system, we find that the collision dynamics are considerably more complicated than the cylindrical obstacle case. In particular, a higher strain rate at the stagnation point on an elliptical surface does not always lead to a higher hooking probability. As a result, elliptical obstacles should be less effective than cylindrical obstacles for DNA separations based on hairpin formation.