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.