Counterion valency effects on 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 molecules within the dilute solution regime. For the investigation of the structure and dynamics at an atomistic level, detailed molecular dynamics simulations of interlinked double stranded DNA minicircles ranging in size from 65 to 180 bp were performed, in ionic aqueous solutions of  varying ionic strength, by considering either monovalent sodium, or divalent calcium, or magnesium counterions. Prominent effects of the ion type on the bending deformation profile of the individual minicircles, as well as their preferred relative orientations have been established. The major finding of this work is the ion-specific modulation of the conformation and compactness of DNA [2]-catenanes: an interesting interplay arises depending on the contour length of the individual DNA minicircle constituents, and can give rise to a non-intuitive, non-monotonic variation of the overall size of DNA-catenanes upon increasing ionic strength of divalent counterions.