Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs
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 loop...
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| Format: | Article |
| Language: | English |
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MDPI AG
2011-11-01
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| Series: | Entropy |
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| Online Access: | http://www.mdpi.com/1099-4300/13/11/1958/ |
| 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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| ISSN: | 1099-4300 |