Laurette C. McCormick

Diffusion coefficient of DNA molecules during free solution electrophoresis.

The free‐draining properties of DNA normally make it impossible to separate nucleic acids by free‐flow electrophoresis. However, little is known, either theoretically or experimentally, about the diffusion coefficient of DNA molecules during free‐flow electrophoresis. In fact, many authors simply assume that the Nernst‐Einstein relation between the mobility and the diffusion coefficient still holds under such conditions. In this paper, we present an experimental study of the diffusion coefficient of both ssDNA and dsDNA molecules during free‐flow electrophoresis. Our results unequivocally show that a simplistic use of Nernst‐Einsteins relation fails, and that the electric field actually has no effect on the thermal diffusion process. Finally, we compare the dependence of the diffusion coefficient upon DNA molecular size to results obtained previously by other groups and to Zimms theory.

The theory of DNA separation by capillary electrophoresis

The Human Genome has been sequenced in large part owing to the invention of capillary electrophoresis. Although this technology has matured enough to allow such amazing achievements, the physical mechanisms at play during separation have yet to be completely understood and optimized. Recently, new separation regimes and new physical mechanisms have been investigated. The use of free-flow electrophoresis and new modes of pulsed-field electrophoresis have been suggested, while we have observed a shift towards single nucleotide polymorphism analysis and microchip technologies. A strong theoretical basis remains essential for the efficient development of new methods.

Capillary electrophoretic separation of uncharged polymers using polyelectrolyte engines. Theoretical model.

We recently demonstrated that the molecular mass distribution of an uncharged polymer sample can be analyzed using free-solution capillary electrophoresis of DNA-polymer conjugates. In these conjugates, the DNA is providing the electromotive force while the uncharged polydisperse polymer chains of the sample retard the DNA engine with different amounts of hydrodynamic drag. Here we present a theoretical model of this new analytical method. We show that for the most favourable, diffusion-limited electrophoresis conditions, there is actually an optimal DNA size to achieve the separation of a given polymer sample. Moreover, we demonstrate that the effective friction coefficient of the polymer chains is related to the stiffness of the two polymers of the conjugate, thus offering a method to estimate the persistence length of the uncharged polymer through mobility measurements. Finally, we compare some of our predictions with available experimental results.

Deformation, Stretching, and Relaxation of Single‐Polymer Chains: Fundamentals and Examples

#From the forthcoming book, Soft Materials: Structure, and Dynamics, Marangoni, A. G. and Dutcher, J., Eds., Marcel Dekker, Inc., in press.

Electrophoresis in the presence of gradients: I. Viscosity gradients

In many cases, the resolution provided by capillary electrophoresis systems approaches that predicted for diffusion‐limited separations. Once all device‐related sources of band broadening have been eliminated or minimized, only thermal diffusion remains. In principle, peaks can be sharpened using gradients of various system characteristics such as gel concentration, buffer viscosity and electric field. However, it is not clear whether this can actually increase the resolution of the system. In this article, we focus our attention on viscosity gradients and we examine both continuous and step‐like variations. Our results indicate that the performance of electrophoretic systems cannot be improved by viscosity gradients. They may provide extra stacking, and thus improve the resolution, when the injection width is non‐negligible. However, for the systems considered here, the best resolution is obtained when the viscosity is uniform and the stacking is entirely performed at injection. We conclude by discussing the link between these results, the fundamental laws of thermodynamics, the nature of the detection process and the importance of having nonlinear effects in nonuniform systems.