DNA Bending by Small, Mobile Multivalent Cations

AbstractWe propose a purely electrostatic mechanism by which small, mobile, multivalent cations can induce DNA bending. A multivalent cation binds at the entrance to the B-DNA major groove, between the two phosphate strands, electrostatically repelling sodium counterions from the neighboring phosphates. The unscreened phosphates on both strands are strongly attracted to the groove-bound cation. This leads to groove closure, accompanied by DNA bending toward the cationic ligand. We explicitly treat the dynamic character of the cation-DNA interaction using an adiabatic approximation, noting that DNA bending is much slower than the diffusion of nonspecifically bound, mobile cations. We make semiquantitative estimates of the free energy components of bending—electrostatic (with a sigmoidal distance-dependent dielectric function), elastic, and entropic cation localization—and find that the equilibrium state is bent B-DNA stabilized with a self-localized cation. This is a bending polaron, formation of which should be critically dependent on the strength of electrostatic interaction and the concentration of highly mobile cations available for self-localization. We predict that the resultant bend will be large (∼20–40°), smooth (because it is spread over 6 bp), and infrequent. The stability of such a bend can be variable, from transient to highly stable (static) bending, observable with standard curvature-measuring techniques. We further predict that this bending mechanism will have an unusual sequence dependence: sequences with less binding specificity will be more bent, unless the specific binding site is in the major groove