Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
Biochemistry. 2012 Apr 24;51(16):3508-22. doi: 10.1021/bi3002709. Epub 2012 Apr 10.
Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates a prior penalty assumed for terminal GU pairs. Six additional duplexes with the 5'GG/3'UU motif were added to the single representation in the previous database. This revises the ΔG°(37) for the 5'GG/3'UU motif from an unfavorable 0.5 kcal/mol to a favorable -0.2 kcal/mol. Similarly, the ΔG°(37) for the 5'UG/3'GU motif changes from 0.3 to -0.6 kcal/mol. The correlation coefficients between predicted and experimental ΔG°(37), ΔH°, and ΔS° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.
GU 对的热力学参数对于预测 RNA 的二级结构以及寻找编码结构 RNA 的基因组序列非常重要。为了改进预测螺旋稳定性的近邻参数，我们测量了 29 个含有 GU 对的 RNA 双链体的光学熔融曲线。更新后的模型消除了先前对末端 GU 对的假设惩罚。在以前的数据库中，我们增加了另外 6 个具有 5'GG/3'UU 基序的双链体。这将 5'GG/3'UU 基序的 ΔG°(37)从不利的 0.5 kcal/mol 修正为有利的-0.2 kcal/mol。类似地，5'UG/3'GU 基序的 ΔG°(37)从 0.3 变为-0.6 kcal/mol。扩展数据库中预测和实验 ΔG°(37)、ΔH°和 ΔS°之间的相关系数分别为 0.95、0.89 和 0.87。这些结果应该会提高 RNA 二级结构预测的准确性。
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