Simulation of DNA electrophoresis through microstructures

Abstract

The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E ≈ 25 V/cm for the mobility of λ-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the electric field and the DNA lengths. The model and the associated phase diagram described here provide an explanation for the conflicting results reported by previous authors (Han et al. on the one hand, and Duong et al. and Inatomi et al. on the other) about the dependence of mobility on the DNA size in lattices near or below the radius of gyration. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.