On the "door-corridor" model of gel electrophoresis. III. The gel constant and resistance, and the net charge, friction, diffusion and electrokinetic force of the migrating molecules.

The door-corridor model of gel electrophoresis enabled an estimation of the net charge of DNA molecules run in various gels. When the runs were carried out in Trisacetate-EDTA buffer having a concentration from 10 to 120 mM, the net charge in 1% agarose gel varied from 1.1 to 0.58 e per base pair. The friction between migrating molecules and gel fibers was dependent on the gel type and concentration, as well as the electric field strength and temperature during electrophoresis. In the 123 to 1,474 bp size range, the friction in 1% agarose changed from 1.91 to 378.03 x 10(-10) N.m-1.s. It was found that the friction per 123 bp DNA segment is not constant, but raises with size. The gel resistance force increases at higher electric field strengths, indicating that elastic forces govern the migration of macromolecules through gels. In the gels studied, the friction, and therefore thermal diffusion, of DNA and protein-SDS complexes scale with from 2.20 to 2.32 power of size. The ratio of thermally induced diffusion and velocity in various gels shows that there is a profound reduction of diffusion compared to velocity with increasing DNA size. This is directly linked to the high exponent relating friction and size. The high resolving power of gel electrophoresis can be correlated to the difference between the frictional coefficients of a diffusing and migrating macromolecule.