Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs.
Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs.
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DOI：
10.3390/e13111958
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发表时间：
2011-11-24
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影响因子：
--
通讯作者：
Aalberts DP
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作者：
Aalberts DP
RNA折叠的自由能是有利的碱基配对和堆叠相互作用与形成环路的熵成本相竞争的组合。这里我们展示了循环熵如何，令人惊讶地，可以促进三级秩序。用基于聚合物物理的理论推导了形成多分支和其他RNA环的自由能的一般公式。我们还推导出了在环的情况下同轴叠加的自由能公式。仿真结果支持解析公式。通过仿真研究了不配对碱基的叠加效应。
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.