Anomalous Migration of Short Sequences of DNA: Comparison of Theory and Experiment

Abstract A new model to replace the Ogstron and tube reptation models for gel retardation of DNA is proposed that explicitly takes into account screening of the hydrodynamic interactions and polyelectrolyte effects. At short DNA sequence lengths, significant anomalous migration is predicted whose onset is dependent on the size of polyacrylamide gel pores. Thus, a 2-residue fragment has the same electrophoretic mobility as a 12-residue fragment for a polyacrylamide gel with a mesh size of 60Å. The oligonucleotide length at which anomalous migration is observed also depends on pore size. Experimental measurement of gel mobility for DNA fragments of the form N(pN)(n), where n = 1-11, 14 and 19 substantiate this phenomenon.