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首页> 外文期刊>Biochemistry >Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches
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Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches

机译：RNA的完整序列对称串联错配的完整热力学表征和用于预测序列非对称串联错配的自由能贡献的改进模型

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摘要

Because of the availability of an abundance of RNA sequence information, the ability to rapidly and accurately predict the secondary structure of RNA from sequence is becoming increasingly important. A common method for predicting RNA secondary structure from sequence is free energy minimization. Therefore, accurate free energy contributions for every RNA secondary structure motif are necessary for accurate secondary structure predictions. Tandem mismatches are prevalent in naturally occurring sequences and are biologically important. A common method for predicting the stability of a sequence asymmetric tandem mismatch relies on the stabilities of the two corresponding sequence symmetric tandem mismatches [Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) J. Mol. Biol. 288,911-940]. To improve the prediction of sequence asymmetric tandem mismatches, the experimental thermodynamic parameters for the 22 previously unmeasured sequence symmetric tandem mismatches are reported. These new data, however, do not improve prediction of the free energy contributions of sequence asymmetric tandem mismatches. Therefore, a new model, independent of sequence symmetric tandem mismatch free energies, is proposed. This model consists of two penalties to account for destabilizing tandem mismatches, two bonuses to account for stabilizing tandem mismatches, and two penalties to account for A-U and G-U adjacent base pairs. This model improves the prediction of asymmetric tandem mismatch free energy contributions and is likely to improve the prediction of RNA secondary structure from sequence.
机译：由于可获得大量的RNA序列信息，因此从序列中快速准确地预测RNA二级结构的能力变得越来越重要。根据序列预测RNA二级结构的常用方法是最小化自由能。因此，对于每个RNA二级结构基序而言，准确的自由能贡献对于准确的二级结构预测是必要的。串联错配在自然发生的序列中普遍存在，并且在生物学上很重要。预测序列不对称串联错配的稳定性的常用方法取决于两个相应的序列对称串联错配的稳定性[Mathews，DH，Sabina，J.，Zuker，M.，and Turner，DH（1999）J. Mol 。生物学288,911-940]。为了改善对序列不对称串联错配的预测，报道了22个先前未测得的序列对称串联错配的实验热力学参数。但是，这些新数据并不能改善对序列不对称串联错配的自由能贡献的预测。因此，提出了一种独立于序列对称串联不匹配自由能的新模型。该模型包括两个罚则，一个用于解决不稳定的串联错配;两个奖金，一个用于解决稳定的串联错配，以及两个惩罚，用来解决A-U和G-U相邻碱基对。该模型提高了对不对称串联错配自由能贡献的预测，并可能从序列提高了RNA二级结构的预测。

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