Ion-Mediated Nucleic Acid Helix-Helix Interactions

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

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

Submitted on March 1, 2006
Revised on March 23, 2006
Accepted on 14 April 2006

	Abstract

Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an inter-helix distance around 26-36 Å, and the strength of the attractive force can reach -0.37 k_BT/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.

Key Words: RNA folding, folding thermodynamics, ion correlations, nucleic acid

This article has been cited by other articles:

				T. R. Sosnick Kinetic barriers and the role of topology in protein and RNA folding Protein Sci., August 1, 2008; 17(8): 1308 - 1318. [Abstract] [Full Text] [PDF]

				Z.-J. Tan and S.-J. Chen Salt Dependence of Nucleic Acid Hairpin Stability Biophys. J., July 15, 2008; 95(2): 738 - 752. [Abstract] [Full Text] [PDF]

				B. A. Todd, V. A. Parsegian, A. Shirahata, T. J. Thomas, and D. C. Rau Attractive Forces between Cation Condensed DNA Double Helices Biophys. J., June 15, 2008; 94(12): 4775 - 4782. [Abstract] [Full Text] [PDF]

				Z.-J. Tan and S.-J. Chen Electrostatic Free Energy Landscapes for DNA Helix Bending Biophys. J., April 15, 2008; 94(8): 3137 - 3149. [Abstract] [Full Text] [PDF]

				Q. Zhao, D. A. Jayawardhana, and X. Guan Stochastic Study of the Effect of Ionic Strength on Noncovalent Interactions in Protein Pores Biophys. J., February 15, 2008; 94(4): 1267 - 1275. [Abstract] [Full Text] [PDF]

				Z.-J. Tan and S.-J. Chen RNA Helix Stability in Mixed Na+/Mg2+ Solution Biophys. J., May 15, 2007; 92(10): 3615 - 3632. [Abstract] [Full Text] [PDF]

				Z.-J. Tan and S.-J. Chen Electrostatic free energy landscapes for nucleic acid helix assembly Nucleic Acids Res., December 1, 2006; (2006) gkl810v1. [Abstract] [Full Text] [PDF]