Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA
Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA
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DOI：
10.1021/bi952697k
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发表时间：
1996-05-28
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：
Fountain, MA;Serra, MJ;Turner, DH
发夹环GUAAUA经常出现在核糖体RNA中。光学解链研究表明，r（GGCGUAAUAGCC）折叠成含有这个环的发夹。通过NMR和分子模拟确定了r（GGCGUAAUAGCC）发夹的结构特征。从G4-H1'到A9-H2和从A9-H2到G10-H1'的NOE表明，G4和A9形成具有两个氢键的剪切碱基对：A-N7到G-NH 2和A-NH 6到G-N3。一维NOE数据显示U 5和Us的亚氨基质子之间没有NOE，但在U 5-H1'与U8-H6和U8-H5之间观察到NOE，从而使U8亚氨基质子远离U 5。因此，U 5和U8不形成亚氨基氢键U。U对。U 5-H2'对A6-H8和A7-H8都表现出NOE，并且U 5和A6的3'磷共振向低场移动。这表明螺旋转角在U 5和A6核苷酸之间。J（H1 ′-H2 ′）和J（H3 ′-H4 ′）偶合常数表明该环是动态的，特别是在35 ℃时，远低于63 ℃的解链温度。使用75个距离和46个二面角约束生成结构。在这些结构中，U 5碱基堆叠在由G4和A9形成的剪切碱基对上，并且可以启动类似于在tRNA的反密码子环中观察到的尿苷转角。A6、A7和U8碱基可以彼此堆叠，它们的氢键表面暴露在溶剂中，这表明它们可用于rRNA中的三级相互作用或蛋白质识别。然而，一系列循环结构与数据一致。缺乏形成一个美国。U错配与最近的模型一致，该模型基于环中的闭合碱基对和第一错配预测六个核苷酸的发夹环的稳定性[Serra，M. J.，Axenson，T. J.，&特纳，D. H.（1994）Biochemistry 33，14289-14296]。
The hairpin loop GUAAUA occurs frequently in ribosomal RNA. Optical melting studies show that r(GGCGUAAUAGCC) folds into a hairpin containing this loop. The structural features of the r(GGCGUAAUAGCC) hairpin have been determined by NMR and molecular modeling. NOEs from G4-H1' to A9-H2 and from A9-H2 to G10-H1' show that G4 and A9 form a sheared base pair with two hydrogen bonds: A-N7 to G-NH2 and A-NH6 to G-N3. One-dimensional NOE data show no NOEs between the imino protons of U5 and Us, but NOEs are observed between the U5-H1' and the U8-H6 and U8-H5, thus orienting the U8 imino proton away from U5. Thus U5 and U8 do not form an imino hydrogen-bonded U . U pair. The U5-H2' exhibits NOEs to both the A6-H8 and A7-H8, and the 3' phosphorus resonances of U5 and A6 are shifted downfield. This suggests that the helix turn is between the U5 and A6 nucleotides. The J(H1'-H2') and J(H3'-H4') coupling constants indicate that the loop is dynamic, particularly at 35 degrees C, well below the melting temperature of 63 degrees C. Structures were generated using 75 distance and 46 dihedral angle restraints. In these structures, the U5 base is stacked on the sheared base pair formed by G4 and A9 and can initiate a uridine turn similar to that observed in the anticodon loop of tRNA. The A6, A7, and U8 bases can stack on one another with their hydrogen-bonding surfaces exposed to the solvent, suggesting that they are available for tertiary interactions or protein recognition in rRNA. A range of loop structures are consistent with the data, however. The lack of formation of a U . U mismatch is consistent with a recent model that predicts the stability of hairpin loops of six nucleotides on the basis of the closing base pair and first mismatch in the loop [Serra, M. J., Axenson, T. J., & Turner, D. H. (1994) Biochemistry 33, 14289-14296].