NMR structures of r(GCA(G)under-barGC(G)under-barUGC)2 and determinants of stability for single guanosine-guanosine base pairs
NMR structures of r(GCA(G)under-barGC(G)under-barUGC)2 and determinants of stability for single guanosine-guanosine base pairs
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DOI：
10.1021/bi000720i
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发表时间：
2000-09-26
期刊：
影响因子：
2.9
通讯作者：
Turner, DH
中科院分区：
文献类型：
--
作者：
Burkard, ME;Turner, DH
RNA中非沃森-克里克配对的核苷酸形成识别或催化的独特结构，但这些结构的决定因素及其稳定性尚不清楚。两个鸟苷(G)的单个非规范对比其他非规范对更稳定，并且可能以四种不同的方式与两个氢键形成配对结构。本文利用光学熔融和核磁共振研究了不同序列背景下单个GG对的能量学和结构。G4和G7成对的r（5’gcaggcgugc3’）(2)的数据与G4和G7在双氢键对中交替形成同步糖苷构象的模型一致。这两种不同的结构是通过核奥弗豪瑟效应的光谱距离约束和AMBER 95力场的模拟退火得到的。在每个结构中，反G的亚胺质子和氨基质子分别与正G的O6和N7受体成氢键。一个额外的氢键将syng氨基与5'非桥接的前r -p磷酸氧连接起来。GG对很适合沃森-克里克螺旋结构。在r(5'GCAGGCGUGC3')(2)中，G4（反），G7（同步）结构优于G4（同步），G7（反）结构。在其他情况下，对于单个GG对，交换过程使光谱解释更加困难，但对也是G(syn)， G（anti）。各种含有G、肌苷和7-去氮鸟苷对的双链化合物的热力学数据与r（5’gcaggcgugc3’）的结构和能量解释一致(2)，表明它们具有相似的GG构象。
Nucleotides in RNA that are not Watson-Crick-paired form unique structures for recognition or catalysis, but determinants of these structures and their stabilities are poorly understood. A single noncanonical pair of two guanosines (G) is more stable than other noncanonical pairs and can potentially form pairing structures with two hydrogen bonds in four different ways. Here, the energetics and structure of single GG pairs are investigated in several sequence contexts by optical melting and NMR. The data for r(5'GCAGGCGUGC3')(2), in which G4 and G7 are paired, are consistent with a model in which G4 and G7 alternate syn glycosidic conformations in a two-hydrogen-bond pair. The two distinct structures are derived from nuclear Overhauser effect spectroscopic distance restraints coupled with simulated annealing using the AMBER 95 force field. In each structure, the imino and amino protons of the anti G are hydrogen bonded to the O6 and N7 accepters of the syn G, respectively. An additional hydrogen-bond connects the syn G amino group to the 5' nonbridging pro-R-p phosphate oxygen. The GG pair fits well into a Watson-Crick helix. In r(5'GCAGGCGUGC3')(2), the G4(anti), G7(syn) structure is preferred over G4(syn), G7(anti). For single GG pairs in other contexts, exchange processes make interpretation of spectra more difficult but the pairs are also G(syn), G(anti). Thermodynamic data for a variety of duplexes containing pairs of G, inosine, and 7-deazaguanosine flanked by GC pairs are consistent with the structural and energetic interpretations for r(5'GCAGGCGUGC3')(2), suggesting similar GG conformations.