Brownian Dynamics Simulation of DNA Fragments in Strong Electric Fields

Brownian dynamics simulation is used to study the transient deformation of semiflexible polyions (specifically a 194 bp DNA fragment) in time varying electric fields. The polyion is represented as a string of beads, and the interaction of the polyion with the electric field is accounted for by placing effective charges on the subunits. Charge polarization effects are included by adapting the model of Szabo, Haleem, and Eden ( J. Chem. Phys. 1986, 85, 7422), which also accounts for the response time of the ion atmosphere to a time varying field. Simulation results are in qualitative agreement with transient electric dichroism experiments on short DNA fragment which exhibit “amplitude inversion”. Amplitude inversion is a consequence of a bowing deformation which results from the electrophoretic migration of the polyion. The model studies also show that the bowing deformation can be eliminated by replacing a constant electric field pulse (of duration T ) with a rapidly reversing square wave of period 2 T ‘, provided T ‘ is short compared to the coil deformation time of the fragment but long compared to the ion atmosphere relaxation time.