Electrophoretic Mobility of DNA is Controlled by the Surface Charge Density, not the Linear Charge Density as Expected from Counterion Condensation Theory

Abstract

The free solution mobilities of small single- and double-stranded DNA molecules with variable charge densities have been measured by capillary electrophoresis. The charge density was modified either by appending charged groups to the thymine residues or by replacing some of the negatively charged phosphate internucleoside linkers with neutral or positively charged phosphoramidate linkers. Mobility ratios were calculated for each data set by dividing the mobility of the charge variant by the mobility of the unmodified parent DNA. Mobility ratios eliminate the effect of the background electrolyte on the observed mobility, making it possible to compare data obtained in different buffers. The mobility ratios observed for ss- and dsDNA charge variants increase logarithmically with increasing fractional charge density, as expected from Manning's theory of DNA electrophoresis. Surprisingly, however, the mobility ratios are directly related to the surface charge densities of the ss- and ds-DNA molecules, not the linear charge density as expected from counterion condensation theory. The results therefore suggest that surface charge density may play a role in counterion condensation, as well as in electrostatic interactions between DNA and other charged molecules in the cell.