Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency

A computational investigation of the effects of moleculartopology,namely, linear and circular, as well as counterion valency, on theensuing pairwise effective interactions between DNA molecules in anunlinked state is presented. Umbrella sampling simulations have beenperformed through the introduction of bias potential along a reactioncoordinate defined as the distance between the centers-of-mass ofpairs of DNA molecules, and effective pair interaction potentialshave been computed by employing the weighted histogram analysis method.An interesting comparison can be drawn between the different DNA topologiesstudied here, especially with regard to the contrasting effects ofdivalent counterions on the effective pair potentials: while DNA-DNArepulsion in short center-of-mass distances decreases significantlyin the presence of divalent counterion-ions (as compared to monovalentions) for linear DNA, the opposite effect occurs for the DNA minicircles.This can be attributed to the fact that linear DNA fragments can easilyadopt relative orientations that minimize electrostatic and stericrepulsions by rotating relative to one another and by exhibiting morepronounced bending due to the presence of free ends.