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Mg²⁺-RNA Interaction Free Energies and Their Relationship to the Folding of RNA Tertiary Structures

Dan Grilley, Ana Maria Soto and David E. Draper
Proceedings of the National Academy of Sciences of the United States of America
Vol. 103, No. 38 (Sep. 19, 2006), pp. 14003-14008
Stable URL: http://www.jstor.org/stable/30051976
Page Count: 6
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Since scans are not currently available to screen readers, please contact JSTOR User Support for access. We'll provide a PDF copy for your screen reader.
Mg²⁺-RNA Interaction Free Energies and Their Relationship to the Folding of RNA Tertiary Structures
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Abstract

Mg²⁺ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg²⁺ that it is difficult to separate free energies of Mg²⁺- RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg²⁺-induced RNA folding, it is necessary to independently determine Mg²⁺-RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg²⁺-RNA interactions are derived from an assay that measures the effective concentration of Mg²⁺ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg²⁺-induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg²⁺ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg²⁺ and in the free energy of their interactions with Mg²⁺. From these results, it appears that any comprehensive framework for understanding Mg²⁺-induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg²⁺.

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