A Viscosity Model of Polyacrylamide Gel Electrophoresis

Abstract

In current theories of polyacrylamide gel electrophoresis, the idea prevails that molecular siev­ing relies on different accessibility of volume fractions and of cross-sectional area fractions (denot­ed “pores”) to different-sized ions due to the effect of “geometric exclusion”. This correlates with the assumption that all elements of a polyacrylamide network occupy fixed and unchangeable po­sitions thus forcing colliding macro-ions to diffuse laterally in order to find an “accessible pore” and to resume motion in direction of the electrical field. However, the alternative conception would be equally well justified, i. e. the assumption that polyacrylamide chains represent smooth obstacles cleared aside under the electrokinetic pressure of a macro-ion. This explanation would even be preferable with respect to the molecular sieving effects occuring in solutions of “liquid polyacrylamide”. Yet no theory exists as to describe such effects in quantitative terms.In the present article, a parameter is defined and discussed, which can be estimated by experi­ment, and which seems to be apt to characterize local resistivity of polymer structures against dis­location and deformation: the “fractional specific resistance”. Definition of this parameter is bas­ed on the model of a “viscosity-emulsion” composed of two interpenetrating liquid compartments which are characterized by different levels of hydrodynamic friction and the spatial dimensions of which are inferred from Ogston’s theory. This concept of “localized viscosity” may also serve as a link between theories of molecular sieving and of “macroscopic viscosity” of flexible polymers. The data of Morris, formerly taken as verifications of the “rigid-pore” concept, are now interpret­ed in terms of four factors responsible for sizediscrimination: collision frequency, duration of sin­gle contacts, size-dependent frictional force, and the extent of cooperation among fibres, due to crosslinking and to simultanous contacts of several fibres to a single macro-ion. Some functions rel­evant for problems of molecular weight determination by gel electrophoresis are discussed in rela­tion to the suggested model.