The free-draining properties of DNA normally make it impossible to separate
nucleic acids by free-flow electrophoresis. However, little is known, eith
er theoretically or experimentally, about the diffusion coefficient of DNA
molecules during free-flow electrophoresis. In fact, many authors simply as
sume that the Nernst-Einstein relation between the mobility and the diffusi
on 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-Einstein's relation fails, and that the el
ectric field actually has no effect on the thermal diffusion process. Final
ly, we compare the dependence of the diffusion coefficient upon DNA molecul
ar size to results obtained previously by other groups and to Zimm's theory
.