Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs
Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs
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DOI：
10.1021/jp068732m
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发表时间：
2007-06-21
影响因子：
3.3
通讯作者：
Kennedy, Scott D.
中科院分区：
文献类型：
--
作者：
Chen, Gang;Kierzek, Ryszard;Kennedy, Scott D.
沃森-克里克样isoG-isoC（iGiC）对，氨基和羰基相对于沃森-克里克GC对转置，为理解塑造核酸结构的相互作用提供了扩展的字母表。在此，侧接iGiC对的串联GA对的热力学稳定性与RNA自身互补双链体（GCiGGAiCGCA）（2）和（GGiCGAiGCCA）（2）的NMR结构一起沿着报道。在（GCiGGAiCGCA）（2）中形成剪切GA配对，并且在（GGiGGAiGCCA）（2）中形成亚氨基GA配对。该结构与RNA自身互补双链体（GCGGACGC）（2）和（GGCGAGCC）（2）中分别由GC对侧接的串联亚氨基和剪切GA对的形成形成对比。在两种iGiC双链体中，在IG和iC之间形成Watson-Crick样氢键，并且iGiC取代导致不太有利的环稳定性。这些结果为测试RNA三维结构的分子相互作用的计算提供了基准。
The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)(2) and (GGiCGAiGCCA)(2). A sheared GA pairing forms in (GCiGGAiCGCA)(2), and an imino GA pairing forms in (GGiGGAiGCCA)(2). The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)(2) and (GGCGAGCC)(2), respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure.