Inter-DNA Attraction Mediated by Divalent Counterions

Abstract

Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by Mg2+ ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [Mg2+] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.

DNA-DNA Recognition: From Tight Contact to Fatal Attraction

“…1a) are thermodynamically stable in solution in the presence of divalent cations. Consistent with recent theoretical and experimental observations of close DNA-DNA interactions in the presence of divalent cations (Qiu et al, 2007;Tan and Chen, 2006;Inoue et al, 2007), a short-range attraction of about -4 kcal mol -1 between the self-fitted duplexes was observed in the presence of divalent cations . Attractive forces at short-range stabilize the DNA-DNA association with inter-axial separation of helices less than 20 Å. Right-handed crossovers, however, dissociate in the presence of monovalent ions only.…”

“…In these conditions, the parallel packing of helices is only moderately influenced by the helical nature of DNA (Kornyshev and Leikin, 1998;Minsky, 2004;Kornyshev et al, 2005). However, recent theoretical and experimental studies have indicated that close DNA-DNA interactions can occur in the presence of divalent cations (Qiu et al, 2006;Tan and Chen, 2006;Inoue et al, 2007;Qiu et al, 2007). Indeed, crystallographic studies have shown that both DNA geometry and chirality has a more profound effect on the association of closely-packed DNA helices, as in tight crossover arrangements.…”

“…1b) are stable only in the crystallographic environment but appeared to be unstable in solution. (Qiu et al, 2007). Also, recent theoretical work that used the tightly bound ion model found that helices repel one other in the presence of monovalent ions while divalent cations are able to induce attraction between two DNA helices (Tan and Chen, 2006).…”

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

“…This difference is likely to influence their molecular recognition and folding properties and has the potential to further our understanding of the different roles played by DNA and RNA in cells. By using smFRET over a wide range of Mg 2þ and Na þ concentrations, we find that the apparent charge screening efficiency of Mg 2þ is anomalously large compared to Na þ in both ssRNA and ssDNA; comparable to previously measured ratios for double-stranded DNA (34). The strong interaction between Mg 2þ and unfolded nucleic acids challenges our understanding of how ions influence the folding process.…”

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions

“…They can drastically modify either interactions between the nucleic acid component of the virion, or the interaction between the capsomere subunits of the capsid. In both cases their effect could most probably be ascribed to a diminished repulsion or indeed net attraction between the similarly charged macromolecular subunits 207 . In the context of virus electrostatics these effects have not been analyzed yet and can be of several types that we address separately.…”