Theory of DNA electrophoresis: a look at some current challenges.

Although electrophoresis is one of the basic methods of the modern molecular biology laboratory, new ideas are being suggested at an accelerated rate, in large part because of the pressing demands of the biomedical community. Although we now have, at least for some methods, a fairly good theoretical understanding of the physical mechanisms that lead to the observed peak spacings, widths and shapes, this knowledge is often too qualitative to be used to guide further technical developments and improvements. In this article, we review some selected elements of the current state of our theoretical ignorance, focusing mostly on DNA electrophoresis, and we offer several suggestions for further theoretical investigations.

Theory of capillary electrophoretic separations of DNA-polymer complexes.

Electrophoretic separation of DNA molecules normally requires the use of an anticonvection, sieving polymer matrix such as a gel or an entangled polymer solution. Recently, it has been suggested that free-solution separation could be achieved in a capillary if an electrically neutral, friction-generating molecule is attached to the DNA molecules before electrophoresis is carried out. The electrophoretic mobilities are then predicted to be very large and the resulting separation is expected to yield excellent resolution. The size-dependence of the electrophoretic mobility is attributed to longer DNA molecules pulling the neutral molecule with a larger electric force, thus eluting earlier than shorter DNA molecules. In this article, we focus on the particular case where one attaches an uncharged, flexible polymer to the end of the DNA. Our self-consistent model takes into account the deformation and the hydrodynamic resistance of the polymer in the flow. We find various regimes, depending on the intensity of the electric field and the length of the polymer. The most favorable conditions for high-resolution separation of DNA are described.

The biased reptation model of DNA gel electrophoresis: a user guide for constant field mobilities.

The biased reptation model of DNA gel electrophoresis is simple enough to allow one to obtain detailed analytical and numerical predictions for experimentally relevant situations. Although it is not always applicable for explaining experimental results, the biased reptation model is usually a good starting point for data analysis. Unfortunately, the model is often reported as being incapable of explaining experimental data because the users have not analyzed the data properly or because they attempted to use the model outside its expected range of applicability. This article presents a detailed practical guide to the model and its limitations, as well as a complete description of its predictions regarding the analysis of constant field mobilities.