Single-Stranded DNA Oligomers may have a Molten Globule-Like Conformation in Solution

Abstract

The electrophoretic mobility of any analyte, including DNA, is the quotient of its net charge divided by its frictional coefficient. Manning has derived an equation predicting DNA electrophoretic mobility, based on counterion condensation theory1. Besides universal constants, the only input parameters are the temperature, properties of the solvent such as viscosity and dielectric constant, the concentrations, conductivities and valences of the counterions and coions, and b, the charge spacing along the contour length of the polymer. The ionic strength dependence of the mobility of double-stranded DNA (dsDNA) is reasonably well predicted by this theory, using the usual b value of 1.7 A. However, the ionic strength dependence of the mobility of unstructured single-stranded DNAs (ssDNA) is poorly predicted by the theory if the spacing between phosphate charges is assumed to be 4.0 A or greater. If the value of b is assumed to be ∼2.0 A, only slightly greater than that of dsDNA, the ionic strength dependence of the mobility of ssDNA is well predicted by the Manning electrophoresis theory. A charge spacing of 2.0 A for ssDNA suggests that solutions of moderate ionic strength facilitate the collapse of ssDNAs into compact unstructured conformations not dissimilar to molten globules in the protein world.Supported in part by the Analytical and Surface Chemistry Program of the National Science Foundation.1 G. S. Manning (1981) J. Phys. Chem. 85, 1506–1615.