APPARENT PORE-SIZE OF POLYACRYLAMIDE GELS - COMPARISON OF GELS CAST AND RUN IN TRIS-ACETATE-EDTA AND TRIS-BORATE-EDTA BUFFERS

The electrophoretic mobilities of DNA molecules in three different mol ecular weight ladders were measured in polyacrylamide gels containing different acrylamide concentrations (%T) and cross-linker ratios (%C), cast and run in Tris-acetate-EDTA (TAE) buffer. The apparent pore rad ius of each gel was estimated from Ferguson plots of the relative mobi liteis of each of the DNA molecules, using the mobility of the monomer fragment in each molecular weight ladder as the reference mobility. T he effective size of each of the DNA molecules was estimated from its radius of gyration. The apparent gel pore radii calculated in this man ner ranged from 21 nm in gels containing 10.5%T, 5%C to 200 nm in gels with 4.6%T, 2%C, similar to the values observed for polyacrylamide ge ls cast and run in Tris-borate-EDTA (TBE) buffer (Holmes and Stellwage n, Electrophoresis 1991, 12, 612-619). Hence, the effective pore size of polyacrylamide gels is essentially independent of whether the gels are cast and run in TAE or TEE buffer.