Effective interactions between double-stranded DNA molecules in aqueous electrolyte solutions: effects of molecular architecture and counterion valency*

Spontaneous self-assembly of DNA molecules is ubiquitous in biological systems and DNA-DNA interactions are relevant to numerous biological processes, including genome compaction, and homologous recombination, as well as in emerging DNA nanotechnological applications, such as functionalized DNA origami, as well as natural and synthesized DNA-catenane structures [1]. Complementary to experimental and theoretical studies, simulations offer an appealing alternative route for the study of these systems at an atomistic level, allowing for the detailed observation of the microscopic molecular conformation of DNA and the ionic atmosphere. The scope of the work presented here is the computational investigation of the effects of DNA molecular topology, namely linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an un-linked and linked (catenated) state. Umbrella sampling simulations were performed, and effective potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, regarding the contrasting effects of divalent counterions on the effective potentials, and this effect can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending.