Pulsed electrophoresis: Some implications of reptation theories

Abstract

This is an attempt to provide some theoretical guidelines for understanding and developing the pulsed electrophoresis techniques proposed as powerful means for separating very large macromolecules such as chromosome‐sized DNA. We show that even a simple approach using recent theories for biased reptation and ignoring the detailed shape of relaxation functions leads to nontrivial predictions. These predictions are used to discuss the presently available pulsed electrophoresis methods. We focus on several practical limits imposed on experiments by the critical values of the parameters associated with different electrophoresis regimes, such as the limiting effective velocity, or the mobility gap associated with the drift resonance. Some conceptual problems that do not seem to have been considered yet are identified. In particular, we show that the early expectation that orthogonal‐field pulsed electrophoresis could be an efficient way to fight chain orientation is probably unpractical. We propose a different approach, emphasizing resonance aspects.