On the characteristics of migration of oligomeric DNA in polyacrylamide gels and in free solution

We review a model for the free-solution electrophoretic mobility of oligome ric double-stranded (ds) DNA. We have found that the free-solution mobility of ds DNA increases as the molecular weight of the fragment increases, up to a few hundred base pairs. This insight is combined with recent advances in the nature of counterion condensation theory of very short DNA fragments to describe quantitatively the electrophoretic mobility of oligomeric sing le-stranded DNA in polyacrylamide gels. The model predicts, in agreement wi th recent experiments, that significant anomalous migration exists with sho rt DNA sequences, the onset of which is dependent on the size of polyacryla mide gel pores. For terminal phosphate-labeled DNA fragments, the free-solu tion mobility is no longer proportional to the ratio of the total effective charge and the friction coefficient. These changes in properties affect th e characteristics of migration of end-labeled DNA fragments in polyacrylami de gels.