Adaptation of pulsed-field gel electrophoresis for the improved fractionation of spheres Original Research Article

During gel electrophoresis, proteins are fractionated by both size (radius, R, for a sphere) and average electrical surface charge density. The fractionation by size depends entirely on nonspecific steric and hydrodynamic effects (sieving) of the fibrous network that forms the gel. Previous studies have demonstrated the following aspects of sieving: (1) as a function of the radius of the effective pore of a gel (PE), electrophoretic mobility decreases in magnitude by a factor that has the form 1−a1(R/PE)+a2(R/PE)n; a1 and a2 are constants; a1 is always positive; a2 is usually positive. (2) For a nonspherical particle not preferentially oriented in the gel, the effective R is best approximated by the R of a sphere that has a surface area equal to that of the nonspherical particle. For spheres, resolution by R is progressively increased by lowering PE, but maintaining PE>R; this approach, however, progressively increases the time of electrophoresis. To improve fractionation of both proteins and multimolecular protein complexes, a ratcheting-based procedure of pulsed-field gel electrophoresis is introduced here for spherical particles. Successfully tested here with latex spheres 95–235 nm in R, this procedure bypasses limitations of conventional sieving-based separations. Even though all spheres are negatively charged, larger spheres can be made to migrate in a direction opposite to the direction in which smaller spheres migrate.