Thermodynamic characterization of tandem mismatches found in naturally occurring RNA
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA
复制标题
DOI：
10.1093/nar/gkp465
复制
发表时间：
2009-08-01
影响因子：
14.9
通讯作者：
Znosko, Brent M.
中科院分区：
文献类型：
--
作者：
Christiansen, Martha E.;Znosko, Brent M.
尽管所有序列对称串联错配和一些序列不对称串联错配已得到热力学表征，并且已经提出了一个模型来预测以前未测量的序列不对称串联错配的稳定性[Christiansen，M.E.和兹诺斯科，B.M. (2008) Biochemistry, 47, 4329-4336]，缺乏频繁发生的串联错配的实验热力学数据。由于实验数据优于预测模型，因此确定了 25 种频繁发生的串联错配的热力学参数。这些新的实验值平均与使用先前模型对这些不匹配的预测值有 1.0 kcal/mol 的差异。然后将此处报告的序列不对称串联错配的数据与之前发表的 72 个序列不对称串联错配的数据相结合，并更新用于预测先前未测量的序列不对称串联错配的热力学的参数。测量值与使用这些更新参数预测值之间的平均绝对差为 0.5 kcal/mol。这个更新的模型改进了对串联失配的预测，而之前的模型预测得相当差。这个新的实验数据和更新的预测模型允许更准确地计算包含串联错配的RNA双链体的自由能，此外，应该允许改进对序列二级结构的预测。
Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329-4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence.