Electrostatic free energy landscapes for DNA helix bending

¹ University of Missouri-Columbia
² University Of Missouri-Columbia

^* To whom correspondence should be addressed. E-mail: chenshi{at}missouri.edu.

Submitted on September 19, 2007
Revised on October 23, 2007
Accepted on 30 November 2007

	Abstract

Nucleic acids are highly charged polyanionic molecules, thus, the ionic conditions are crucial for the nucleic acid structural changes such as bending. We use the tightly bound ion (TBI) theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency and size. In a Na⁺ solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na⁺ concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in a Mg²⁺ solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction towards the minor groove. The microscopic analysis on ion-binding distribution reveals that the divalent ion-induced helix bending attraction may come from the correlated distribution of the ions across the grooves in the bending direction.

Key Words: DNA, RNA folding, ion electrostatics