Formation of hairpins and band broadening in gel electrophoresis of DNA

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Abstract
The dynamics of a long DNA molecule undergoing constant-field gel electrophoresis is considered theoretically on the basis of the reptation theory. A generalized theoretical approach taking into account the possibility of a branched tube structure is presented. It is shown that in a wide range of electric fields a branched conformation is more stable than a linear conformation assumed by the standard biased reptation model. The process of nucleation of a branched structure from a linear structure is considered analytically in detail. The field dependencies of both longitudinal and transverse diffusion constants are discussed within the framework of the proposed two-states model. It is predicted that the longitudinal diffusion constant shows a sharp maximum in the weak-field regime.