A semiempirical expression for the gel electrophoretic mobility of supercoiled DNA.

Abstract

Gel electrophoresis is a convenient technique for sepa- rating fragments of linear DNA differing in length or for separating the topoisomers of a supercoiled DNA from a mixture.'-4 A number of theoretical attempts have been made in order to understand the physical basis underlying the process of gel electrophoresis of linear DNA, employing mostly the idea of reptation?- However, in spite of con- siderable advances in the understanding of gel electro- phoresis of linear DNA, the physical mechanism behind the resolution of topoisomers by gel electrophoresis has been inadequately studied. The purpose of this commu- nication is to show that the reptation model may be suit- ably extended to describe the gel electrophoretic mobility of the topoisomers of supercoiled DNA molecules also. The reptation mechanism was originally developed to study the diffusion of macromolecules in a polymer net- work. The polymer segments of the network surrounding the chain molecule restrict the motion of the chain, ef- fectively confining it to a tube.I3 Lateral motion is con- strained and the chain molecule can diffuse only longi- tudinally along the tube. During diffusion it is assumed that the head, i.e., the leading end of the chain, creates a path through the network and the rest of the chain follows the head in a snake-like fashion. For describing the gel electrophoresis of linear DNA on the basis of the reptation mechanism, Lumpkin and Zimm' assumed that the DNA chain, which is essentially a polyion, moves through a tube in the gel matrix under the influence of the applied electric field. On its basis, they obtained a simple expression for the steady state mobility of the DNA chain as where