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Entropy 2011, 13(11), 1958-1966; doi:10.3390/e13111958
Article

Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs

Physics Department, Williams College, Williamstown, MA 01267, USA
Received: 1 October 2011 / Revised: 10 November 2011 / Accepted: 18 November 2011 / Published: 24 November 2011
(This article belongs to the Special Issue Loop Entropy)
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Abstract

The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations.
Keywords: RNA; coaxial stacking; tertiary structure; secondary structure; multibranch loops; Hairpin loops; polymer simulations RNA; coaxial stacking; tertiary structure; secondary structure; multibranch loops; Hairpin loops; polymer simulations
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Aalberts, D.P. Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs. Entropy 2011, 13, 1958-1966.

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