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Nucleic Acids Research 2004 32(13):3967-3976; doi:10.1093/nar/gkh723
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Published online 28 July 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation

Peter J. Mikulecky and Andrew L. Feig*

Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA

* To whom correspondence should be addressed. Tel: +1 812 856 5449; Fax: +1 812 855 8300; Email: afeig{at}indiana.edu

Received April 16, 2004; Revised and Accepted July 8, 2004

In proteins, empirical correlations have shown that changes in heat capacity ({Delta}CP) scale linearly with the hydrophobic surface area buried upon folding. The influence of {Delta}CP on RNA folding has been widely overlooked and is poorly understood. In addition to considerations of solvent reorganization, electrostatic effects might contribute to {Delta}CPs of folding in polyanionic species such as RNAs. Here, we employ a perturbation method based on electrostatic theory to probe the hot and cold denaturation behavior of the hammerhead ribozyme. This treatment avoids much of the error associated with imposing two-state folding models on non-two-state systems. Ribozyme stability is perturbed across a matrix of solvent conditions by varying the concentration of NaCl and methanol co-solvent. Temperature-dependent unfolding is then monitored by circular dichroism spectroscopy. The resulting array of unfolding transitions can be used to calculate a {Delta}CP of folding that accurately predicts the observed cold denaturation temperature. We confirm the accuracy of the calculated {Delta}CP by using isothermal titration calorimetry, and also demonstrate a methanol-dependence of the {Delta}CP. We weigh the strengths and limitations of this method for determining {Delta}CP values. Finally, we discuss the data in light of the physical origins of the {Delta}CPs for RNA folding and consider their impact on biological function.


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