Electrophoresis of small DNA molecules in agaroses with different electroendosmotic properties

The migration rate of DNA standards in agaroses with different electroendosmotic (EEO) properties was compared in order to find an alternative to polyacrylamide slab gels for the separation of small restriction fragments by electrophoresis. Slower migration of DNA molecules only a few hundred of base pairs in length was observed after raising the concentration of unmodified low EEO agarose in gels up to 6%. Resolution of low-molecular-weight DNA fragments was best achieved, however, with hydroxyethylated agaroses showing high or low EEO properties. An immediate application of the above results was to confirm the presence of the human cytomegalovirus BamH I-P subgenomic fragment (7.2 kb) in a recombinant pAT153 plasmid by restriction endonuclease analysis.