Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length

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

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

Submitted on July 19, 2005
Revised on August 17, 2005
Accepted on 1 November 2005

	Abstract

Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, inter-ion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann (PB) theory ignores these effects while the recently developed Tightly Bound Ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg²⁺) than PB. In the present study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.

Key Words: electrostatics, folding thermodynamics

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