Molecular weight and kinetic parameters of DNA undergoing pulsed field gel electrophoresis

Functions relating DNA size to reorientation time (Tr) should improve the theoretical basis to design pulsed field gel electrophoresis experiments. We initially developed a quantitative approach to calculate Tr based on kinetic data: DNA migration per pulse (d), and pulse time duration. Using this procedure with some modifications and a computer controlled pulsed field electrophoresis switching unit, we obtained the Trs of several DNA molecules of known molecular weight and analyzed the functional dependence between these parameters. The function obtained was used to interpolate the Tr values of yeast (Saccharomyces cerevisiae) chromosomes. We also interpolated the sizes of yeast chromosomes I and VI, and compared them with those obtained by another independent method, using lambda-mers and polynomial functions relating lambda-mers migration and DNA sizes. The equation obtained should be useful to separate chromosomes by PFGE and to study the genomes of microorganisms, parasites and mammals. (Arch Med Res 1994; 25:193).