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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

Received: 1 October 2011; in revised form: 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 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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

AMA Style

Aalberts DP. Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs. Entropy. 2011; 13(11):1958-1966.

Chicago/Turabian Style

Aalberts, Daniel P. 2011. "Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs." Entropy 13, no. 11: 1958-1966.


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