Thermodynamic characterization of naturally occurring RNA tetraloops
Thermodynamic characterization of naturally occurring RNA tetraloops
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DOI：
10.1261/rna.1773110
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发表时间：
2010-02-01
期刊：
影响因子：
4.5
通讯作者：
Znosko, Brent M.
中科院分区：
文献类型：
--
作者：
Sheehy, Justin P.;Davis, Amber R.;Znosko, Brent M.
虽然四环是RNA中最常见的二级结构基序之一，但在30种最常见的RNA四环中，只有不到三分之一的结构得到了鉴定。因此，将含有常见四环的24个茎环序列进行光学解链，并测定每个茎环的热力学参数Δ H-0、Δ S-0、Δ G（37）（o）和T-M。这些新的实验值平均与使用Vecenie CJ，Morrow CV，Zyra A，Serra MJ提出的模型预测的这些四环素的值相差0.7 kcal/mol。2006.生物化学45：1400-1407。然后将本文报告的24个四环的数据与先前发表的28个四环的数据相结合。一个新的模型，独立的终端失配数据，推导出预测自由能的贡献，以前未测量的tetraloops。测量值和使用该模型预测的值之间的平均绝对差为0.4千卡/摩尔。这种新的实验数据和更新的预测模型允许更准确地计算含有四环的RNA茎环的自由能，并且还应该允许改进从序列预测二级结构。还表明，序列5 ′-GCCNNNNNGGC-3 ′内的四环比序列5 ′-GGCNNNNGCC-3 ′内的相同四环平均稳定0.6千卡/摩尔。需要更系统的研究来确定非最近邻效应对四环稳定性的全部影响。
Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters Delta H-o, Delta S-o, Delta G(37)(o), and T-M for each stem-loop were determined. These new experimental values, on average, are 0.7 kcal/mol different from the values predicted for these tetraloops using the model proposed by Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Biochemistry 45: 1400-1407. The data for the 24 tetraloops reported here were then combined with the data for 28 tetraloops that were published previously. A new model, independent of terminal mismatch data, was derived to predict the free energy contribution of previously unmeasured tetraloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.4 kcal/mol. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem-loops containing tetraloops and, furthermore, should allow for improved prediction of secondary structure from sequence. It was also shown that tetraloops within the sequence 5'-GCCNNNNGGC-3' are, on average, 0.6 kcal/mol more stable than the same tetraloop within the sequence 5'-GGCNNNNGCC-3'. More systemic studies are required to determine the full extent of non-nearest-neighbor effects on tetraloop stability.