A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes
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DOI：
10.1093/nar/gkg350
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发表时间：
2003-05-15
影响因子：
14.9
通讯作者：
Dumas, P
中科院分区：
文献类型：
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作者：
Ennifar, E;Walter, P;Dumas, P
已知金属离子，特别是镁，通过稳定二级和三级结构参与RNA折叠，并且作为辅因子参与RNA酶活性。我们对亚型A和亚型B天然序列的HIV-1 RNA二聚化起始位点的双链体形式的阳离子结合进行了系统的晶体学分析。结果表明，11种离子（K+，Pb ~（2+），Mn ~（2+），Ba ~（2+），Ca ~（2+），Cd ~（2+），Sr ~（2+），Zn ~（2+），Co ~（2+），Au ~（3+）和Pt ~（4+））和两种六胺[Co（NH_3）（6）]（3+）和[Ru（NH_3）（6）]（3+）与DIS双链结构结合。虽然这两个序列非常相似，但它们的阳离子结合性质存在很大差异。二价阳离子结合几乎完全，作为Mg 2+，在'Hoogsteen'网站的鸟嘌呤残基，与阳离子依赖的亲和力为每个网站。值得注意的是，给定的阳离子对于同一分子内的先验等价位点可以具有非常不同的亲和力。令人惊讶的是，使用的两种六胺中没有一种能够有效地替代六水合镁。相反，[Co（NH3）（4）]（3+）通过内球配位与RNA结合。这引起了一些关于[Co（NH3）（6）]（3+）作为[Mg（H2O）（6）]（2+）模拟物的实际应用的问题。也非常出乎意料的是，在鸟嘌呤碱基的N1强制性去质子化后，小的Au 3+阳离子恰好在G-C碱基对的沃森-克里克位点之间结合。使用X射线晶体学对金属离子结合的广泛研究显著丰富了我们对中重金属离子与RNA结合的知识，特别是与镁相比。
Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)(6)](3+) and [Ru (NH3)(6)](3+) were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)(4)](3+) was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)(6)](3+) as a [Mg (H2O)(6)](2+) mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.