Ion-Specific Modulation of the Conformation and Compactness of DNA Oligo-Catenanes

The scope of the work presented here is the computational investigation of the effects of counterion valency, on the ensuing pairwise effective interactions between topologically interlinked DNA ring molecules within the dilute solution regime. Atomistic molecular dynamics (MD) simulations were performed for double stranded DNA [2]-catenanes in low to moderate ionic strength solutions of monovalent sodium and divalent counterions calcium and magnesium solutions. Upon catenation, stiff DNA minicircles obtain more anisotropic, more aspherical and slightly more oblate shapes, compared to their noncatenated conformations. In-plane ring stretching is observed in the catenated structures, which facilitates the spreading out of charges and reduces steric hindrance. Prominent effects of the ion type on the separation of the center-of-masses of the individual minicircles, as well as their preferred relative orientations have been established. An interesting interplay arises upon increasing ionic strength of divalent counterions, depending on the contour length of the individual DNA minicircle constituents: short DNA minicircles give rise to a nonmonotonic behavior that comprises sequential elongation and contraction regimes of the catenane, but longer minicircles give rise only to contracted catenane conformations.