Mechanism of Migration of DNA and Protein-DNA Complexes in Gel and in Free Solution
Ogstron and "tube" reptation models are generalized to describe the mobility of ss oligomeric DNA in polyacrylamide gel. The model predicts that significant anomalous migration exists with sequences about six residues such that the electrophoretic mobility of a 3-residue fragment is comparable to a 14-residue fragment (1). Experimental measurement of gel mobility for DNA fragments of form N(pN)n, where n = 1-11, 14 and 19 have substantiated this phenomenon.
A model for the free solution electrophoretic mobility of oilgo ds DNA relevant to capillary electrophoresis is described that explicitly takes into account screening of the hydrodynamic interactions, counterion condensation, Coulombic end-effects, ionic strength and pH of the buffer solution. We find, in agreement with experiments that the free solution mobility of ds DNA increases as the molecular weight increases up to a few hundred bp (2, 3).
We have developed a model for gel retardation of intrinsically curved DNA molecules, such as the A-tracts, that takes into account in an approximate way the low and the high frequency viscoelastic response of the polyacrylamide gel matrix and the transverse frictional drag forces. Dynamical motions of the "probe" chain are accompanied by viscoelastic response of the "vicinal" matrix chains by reptation. In agreement with Crothers and coworkers, analysis shows that the gel mobility of DNA with a bend at the center is slower than that of the same molecule with a bend at its end (4). Finally, we generalize the model to describe gel-shift retardation assay of protein-DNA complexes in polyacrylamide gel.
(1) Mohanty, U.; Searls, T.; McLaughlin, L. W. J. Am. Chem. Soc.1998, 120,
8275-8276; Mohanty, U.; Searls, T.; McLaughlin, L. W. J. Am. Chem. Soc. in
press, 2000. ,
Eugene F. Merkert Chemistry Center,