ELECTRIC DICHROISM AND BIREFRINGENCE DECAY OF SHORT DNA RESTRICTION FRAGMENTS STUDIED BY BROWNIAN DYNAMICS SIMULATION

Brownian dynamics simulation is used to study the electric dichroism (ED) and birefringence (EB) off-field decay of short DNA fragments 100-367 base pairs in length. The simulation results are compared to the ED experiments of Diekmann and co-workers (Diekmann, S.; et al. Biophys. Chem. 1982, 15, 263) and EB experiments of Lewis and co-workers (Lewis, R. J.; et al. Macromolecules 1986, 19, 134). It is found that a simple flexible wormlike chain model with a persistence length slightly larger than 50 nm is entirely consistent with the ED/EB decay of all fragments. Although rigid ensemble models are able to account reasonably well for the longest relaxation time, the faster decay process, which is particularly sensitive to chain flexibility, cannot be reproduced by such models. Averages appropriate for ED/EB decay are derived in an appendix (strictly valid at low field strengths) for an induced dipole and a saturation-induced dipole orienting mechanism, respectively. These averages are based on a simple form for the electric polarizability tensor which scales, in the case of a rodlike polyion, as the square of the molecular weight. ED/EB decays are compared for both cases and shown to be similar.