Loop entropy assists tertiary order: loopy stabilization of stacking motifs

DOI10.3390/E13111958MaRDI QIDQ400961zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Daniel P. Aalberts

Publication date 26 August 2014

Published in Entropy (Search for Journal in Brave)

Full work available at URL https://doi.org/10.3390/e13111958

zbMATH Keywords

coaxial stackinghairpin loopsmultibranch loopspolymer simulationsRNAsecondary structuretertiary structure

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Measures of information, entropy (94A17)

Review text

Summary: 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.

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