Theory of gel electrophoresis of DNA: orientational effects.

Some aspects of the reptation model of gel electrophoresis of DNA, with emphasis on the orientational effects, are considered. A master equation for the reptational dynamics with the end boundary conditions is proposed. Based on this equation, the orientation and dynamics of the persistent-chain are investigated. In particular, the role of trap conformations for this chain, which essentially reduce the chain mobility, was analyzed. A transient orientation of the chain during pulsed field gel electrophoresis is also discussed.