Next Article in Journal
Thermodynamics of Regular Cosmological Black Holes with the de Sitter Interior
Next Article in Special Issue
Quantitative Comparison of Conformational Ensembles
Previous Article in Journal
A Characterization of Entropy in Terms of Information Loss
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 / Revised: 10 November 2011 / Accepted: 18 November 2011 / Published: 24 November 2011
(This article belongs to the Special Issue Loop Entropy)
Download PDF [119 KB, 24 February 2015; original version 24 February 2015]

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.

Share & Cite This Article

Further Mendeley | CiteULike
Export to BibTeX |
EndNote
MDPI and ACS Style

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

View more citation formats

Article Metrics

Comments

Citing Articles

[Return to top]
Entropy EISSN 1099-4300 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert