On the "door-corridor" model of gel electrophoresis. I. Equations describing the relationship between mobility and size of DNA fragments and protein-SDS complexes.

In a gel, electrophoretic mobility of a DNA fragment and a protein-SDS complex is an exponential function of the ratio between two forces, the resisting force of the gel polymers and the electrokinetic force of the migrating macromolecule. It is also proportional to the mobility of unit size of the migrating molecule, mu 1. Each gel gives an optimal resolution of macromolecules of a defined size. That size must be such that the electrokinetic force of the migrating molecule equals the gel resistance force, so that the ratio of mobility and mu 1 becomes e-1. The optima for several poly[N-acryloyl-tris(hydroxymethyl)aminomethane], polyacrylamide and agarose gels are given. Only two constants are sufficient for description of the relationship between mobility and size of DNA fragments and protein-SDS complexes of the sizes close to that optimally resolved. One is mu 1 and the other, ks, is the slope of the straight line which can be obtained from the size versus reciprocal of the mobility plot. The experimentally observed sigmoidal curves in the plots including the logarithm of size follow directly from the developed equations. The use of mu 1 instead of mu 0 may provide a better interpretation of the Ferguson plots.