Berlin 2008 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Posters I

BP 7.1: Poster

Monday, February 25, 2008, 17:00–19:30, Poster A

Counterion Dynamics in DNA Electrophoresis — •Sebastian Fischer¹, Ali Naji², and Roland Netz¹ — ¹Physik Department, Technische Universität München, 85748 Garching, Germany — ²Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA

We present Brownian Dynamics simulations of a coarse grained model for DNA in aqueous NaCl solution, moving under the influence of an externally applied electric field. The electrophoretic DNA mobility obtained is shown to agree almost quantitatively with experimental data. As theoretically predicted, the DNA mobility is found to decrease logarithmically with increasing salt concentration due to partial screening of hydrodynamic interactions caused by the adverse motion of oppositely charged ions.

Apart from the DNA mobility we focus on the mobility of the counterions in the immediate vicinity of the polymer which we find to be negative, i.e. the Na⁺ ions are dragged along by the DNA, albeit at diffent speed. This result contrasts with a common theoretical concept where counterions in close proximity to the DNA polymer are assumed to move at the same velocity [2]. In contrast to the DNA mobility the Na⁺ mobility increases with increasing salt concentration. At some point, the direction of motion changes from aligned to adverse with respect to the polymer. For weakly charged polymers the salt concentration dependence of the counterion mobility can be calculated using Green’s function methods.

[1] G. S. Manning, J. Phys. Chem. 85, 1506 (1981)