Holbrook S R, Cheong C, Tinoco I, Kim S H
Lawrence Berkeley Laboratory, University of California, Berkeley 94720.
Nature. 1991 Oct 10;353(6344):579-81. doi: 10.1038/353579a0.
The crystal structure of the RNA dodecamer duplex (r-GGACUUCGGUCC)2 has been determined. The dodecamers stack end-to-end in the crystal, simulating infinite A-form helices with only a break in the phosphodiester chain. These infinite helices are held together in the crystal by hydrogen bonding between ribose hydroxyl groups and a variety of donors and acceptors. The four noncomplementary nucleotides in the middle of the sequence did not form an internal loop, but rather a highly regular double-helix incorporating the non-Watson-Crick base pairs, G.U and U.C. This is the first direct observation of a U.C (or T.C) base pair in a crystal structure. The U.C pairs each form only a single base-base hydrogen bond, but are stabilized by a water molecule which bridges between the ring nitrogens and by four waters in the major groove which link the bases and phosphates. The lack of distortion introduced in the double helix by the U.C mismatch may explain its low efficiency of repair in DNA. The G.U wobble pair is also stabilized by a minor-groove water which bridges between the unpaired guanine amino and the ribose hydroxyl of the uracil. This structure emphasizes the importance of specific hydrogen bonding between not only the nucleotide bases, but also the ribose hydroxyls, phosphate oxygens and tightly bound waters in stabilization of the intramolecular and intermolecular structures of double helical RNA.
已确定RNA十二聚体双链体（r-GGACUUCGGUCC）2的晶体结构。十二聚体在晶体中首尾相连堆积，模拟了无限的A-型螺旋，只是磷酸二酯链中有一处断裂。这些无限螺旋在晶体中通过核糖羟基与各种供体和受体之间的氢键结合在一起。序列中间的四个非互补核苷酸并未形成内环，而是形成了一个包含非沃森-克里克碱基对G·U和U·C的高度规则的双螺旋结构。这是在晶体结构中首次直接观察到U·C（或T·C）碱基对。每个U·C碱基对仅形成一个碱基-碱基氢键，但通过一个在环氮之间桥连的水分子以及在大沟中连接碱基和磷酸的四个水分子而得以稳定。U·C错配在双螺旋中未引入扭曲，这可能解释了其在DNA中修复效率较低的原因。G·U摆动碱基对也通过一个在未配对鸟嘌呤氨基和尿嘧啶核糖羟基之间桥连的小沟水分子得以稳定。该结构强调了不仅核苷酸碱基之间，而且核糖羟基、磷酸氧和紧密结合的水分子之间特定氢键在稳定双螺旋RNA分子内和分子间结构中的重要性。
