Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G•U wobble base pairs
Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G•U wobble base pairs
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DOI：
10.1093/nar/27.7.1728
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发表时间：
1999-04-01
影响因子：
14.9
通讯作者：
Hogle, JM
中科院分区：
文献类型：
--
作者：
Trikha, J;Filman, DJ;Hogle, JM
邻G。小RNA基序的原子结构有助于更好地理解各种串联错配对双链结构和稳定性的影响，从而为RNA结构预测和验证提供更好的规则。含有序列r(GGUAGC-UACC)(2)的RNA双链的晶体结构已在2.1埃分辨率下用实验相求解。为了建立正确的溶剂模型，需要新颖的改进策略。这是目前唯一含有5'-U-U-3'/3‘-G-G-5’非对称串联G的短RNA双工结构。U摆动碱基对。在14mer双链结构中，6个中心碱基对都偏离了螺旋轴，从而在局部主链构象、螺旋参数和电荷分布上产生了显著的变化，这可能为生物相关配体结合提供了特定的识别位点。与a型螺旋结构最大的偏差发生在摇摆碱基对的鸟嘌呤在相反链的嘌呤上重叠的地方。在此附近，链内磷酸盐距离显著增加，主槽宽度增加至3埃。与其它含有对称串联G的短双链的结构比较。U或G。T摆动碱基对表明，最近邻序列依赖关系控制螺旋扭转和交叉链嘌呤堆积的发生。
Adjacent G . U wobble base pairs are frequently found in rRNA, Atomic structures of small RNA motifs help to provide a better understanding of the effects of various tandem mismatches on duplex structure and stability, thereby providing better rules for RNA structure prediction and validation. The crystal structure of an RNA duplex containing the sequence r(GGUAGC-UACC)(2) has been solved at 2.1 Angstrom resolution using experimental phases. Novel refinement strategies were needed for building the correct solvent model. At present, this is the only short RNA duplex structure containing 5'-U-U-3'/3'-G-G-5' non-symmetric tandem G . U wobble base pairs. In the 14mer duplex, the six central base pairs are all displaced away from the helix axis, yielding significant changes in local backbone conformation, helix parameters and charge distribution that may provide specific recognition sites for biologically relevant ligand binding, The greatest deviations from A-form helix occur where the guanine of a wobble base pair stacks over a purine from the opposite strand. In this vicinity, the intra-strand phosphate distances increase significantly, and the major groove width increases up to 3 Angstrom. Structural comparisons with other short duplexes containing symmetrical tandem G . U or G . T wobble base pairs show that nearest-neighbor sequence dependencies govern helical twist and the occurrence of cross-strand purine stacks.