Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA.
Department of Chemistry and Biochemistry, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
Nucleic Acids Res. 2022 May 20;50(9):5251-5262. doi: 10.1093/nar/gkac261.
Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5'GGUC3' paired to 3'CUGG5' separately from other 5'GU3'/3'UG5' stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37°C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.
用于估计 RNA 二级结构折叠稳定性的最近邻参数被广泛应用。对于螺旋结构，当前的参数会惩罚末端 AU 碱基对，而不是末端 GC 碱基对。我们整理了一个扩展的螺旋稳定性数据库，这些数据是通过光学融解实验确定的。对更新后的数据库的分析表明，末端惩罚取决于相邻倒数第二个碱基对的序列同一性。新的最近邻参数包含了这种额外的序列依赖性，可以准确预测更新后的数据库中 271 个螺旋的测量值，相关系数为 0.982。这种对螺旋末端的精细理解有助于与 GU 对拟合碱基对堆叠的项。之前的参数集将 5'GGUC3'与 3'CUGG5'配对与其他 5'GU3'/3'UG5'堆叠分别处理。然而，对螺旋末端稳定性的理解的提高使得这种分别处理变得不必要。通过三个光学融解实验测试了引入额外项的效果。这三个含有末端相邻 AU 和 GU 对的双链体在 37°C 时的测量和预测自由能变化之间的平均绝对差异从 1.38 降低到 0.27 kcal/mol。这证实了模型中需要额外的序列依赖性。
