Salt dependence of nucleic acid hairpin stability
Zhi-Jie Tan 1 and Shi-Jie Chen 2*
1 University of Missouri
2 University Of Missouri-Columbia
* To whom correspondence should be addressed. E-mail: chenshi{at}missouri.edu.
Submitted on February 15, 2008
Revised on March 17, 2008
Accepted on 31 March 2008
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Abstract |
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Single-stranded junctions/loops are frequently occurring structural motifs in nucleic acid structures. Due to the polyanionic nature of the nucleic acid backbone, metal ions play a crucial role in the loop stability. Here we use the tightly bound ion theory, which can account for the possible ion correlation and ensemble (fluctuation) effects, to predict the ion-dependence of loop and stem-loop (hairpin) free energies. The predicted loop free energy is a function of the loop length, the loop end-to-end distance, and the ion (Na+ and Mg2+ in the present study) concentrations. Based on the statistical mechanical calculations, we derive a set of empirical formulas for the loop thermodynamic parameters as functions of Na+ and Mg2+ concentrations. For three specific types of loops, namely, hairpin, bulge, and internal loops, the predicted free energies agree with the experimental data. Further applications of these empirical formulas to RNA and DNA hairpin stability lead to good agreements with the available experimental data. Our results indicate that the ion-dependent loop stability makes significant contribution to the overall ion-dependence of the hairpin stability.
Key Words:
DNA helix, RNA folding, ion electrostatics, thermodynamics
