THE EQUILIBRIUM PARTITION-FUNCTION AND BASE PAIR BINDING PROBABILITIES FOR RNA SECONDARY STRUCTURE
THE EQUILIBRIUM PARTITION-FUNCTION AND BASE PAIR BINDING PROBABILITIES FOR RNA SECONDARY STRUCTURE
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DOI：
10.1002/bip.360290621
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发表时间：
1990-05-01
期刊：
影响因子：
2.9
通讯作者：
MCCASKILL, JS
中科院分区：
文献类型：
--
作者：
MCCASKILL, JS
一种新的应用程序的动态规划的RNA折叠问题，使之能够计算完整的平衡分配函数的二级结构和各种子结构的概率。特别地，所有碱基对的配分函数和概率都通过序列长度N中的多项式阶数N3的递归方案来计算。配分函数的温度依赖性给出了关于二级结构的熔化行为的信息。对结合概率，其计算取决于配分函数，直观地总结在一个“盒矩阵”显示，这提供了一个有用的工具，用于检查可能的替代平衡结构的完整合奏。该集成表示的计算允许适当的应用和评估的预测能力的二级结构方法，并产生重要的信息替代品和中间体除了本地信息碱基对开放和滑动。结果显示代表性的tRNA，5S RNA，自我复制和自我剪接的RNA分子，并允许与酶结构探针的直接比较。平衡系综上的热力学参数的变化的影响提供了进一步的灵敏度检查的预测。
A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a "box matrix" display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage. The results are illustrated for representative tRNA, 5S RNA, and self-replicating and self-splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.