Free energy cost of stretching mRNA hairpin loops inhibits small RNA binding.
Free energy cost of stretching mRNA hairpin loops inhibits small RNA binding.
复制标题
拉伸 mRNA 发夹环的自由能量消耗会抑制小 RNA 结合。
DOI：
10.1016/j.bpj.2012.12.017
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发表时间：
2013
影响因子：
3.4
通讯作者：
Aalberts,DanielP
中科院分区：
文献类型：
--
作者：
Meng,Yuzhong;Aalberts,DanielP
小RNA-mRNA结合是RNA干扰的重要步骤，RNA干扰是重要的细胞调控过程。结合自由能的计算已被用于结合位点的预测，但当小RNA-mRNA双链体形成时拉伸mRNA环的成本需要进一步探索。在这里，使用聚合物物理理论和模拟，我们估计拉伸mRNA环的自由能。我们发现环拉伸显著增加了3′补充/补偿miRNA结合和siRNA结合mRNA发夹环的自由能。我们还观察到，3′补充结合的位点可能仅在种子处结合，并且在mRNA发夹中，环拉伸通常有利于仅种子结合而不是种子加3′补充结合。
Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer physics theory and simulations, we estimate the free energy of a stretched mRNA loop. We find loop stretching significantly increases the free energy of 3′ supplementary/compensatory miRNA binding and siRNA binding to mRNA hairpin loops. We also make the observation that sites where 3′ supplementary binding is available may bind at the seed only, and that loop stretching often favors seed-only binding over seed plus 3′ supplementary binding in mRNA hairpins.