反向Watson-CrickG:C碱基对(G:CW:WTrans)经常出现在不同的功能RNA中。这是其气相优化的隔离几何形状与相应的实验几何形状不一致的少数碱基对之一。一些早期的研究表明,通过转录后修饰,直接质子化,或与Mg2+协调,鸟嘌呤N7附近的正电荷积累可以稳定实验几何形状。有趣的是,最近的研究表明,假定结合的Mg2+的位置存在显著差异。这个,结合最近对鸟嘌呤亚氨基氮附近的一些Mg2分配的怀疑,暗示该碱基对存在多种Mg2结合模式。我们对高分辨率RNA晶体结构中Mg2结合的G:CW:WTrans对的详细研究表明,它们存在于14种不同的环境中,其中八个在鸟嘌呤的Hoogsteen边缘显示Mg2结合。在这八种情况下对事件的进一步检查导致了三种不同的Mg2结合模式的表征:1)通过N7配位直接结合,2)通过O6配位直接结合,和3)通过与第一壳水分子的氢键相互作用结合。在晶体结构中,后两种模式与基底的屈曲和螺旋桨扭曲几何形状有关。有趣的是,这些不同的Mg2+结合模式(使用六个不同的DFT官能度优化)的各自优化的几何形状与它们对应的实验几何形状一致。随后在MP2级的相互作用能计算,以及其成分的分解,建议对于G:CW:WTrans,Mg2+结合可以微调碱基对几何形状而不损害其稳定性。我们的结果,因此,强调Mg2+离子结合模式在塑造RNA结构中的重要性,折叠和功能。
Reverse Watson-Crick G:C basepairs (G:C W:W Trans) occur frequently in different functional RNAs. This is one of the few basepairs whose gas-phase-optimized isolated geometry is inconsistent with the corresponding experimental geometry. Several earlier studies indicate that through post-transcriptional modification, direct protonation, or coordination with Mg2+, accumulation of positive charge near N7 of guanine can stabilize the experimental geometry. Interestingly, recent studies reveal significant variation in the position of putatively bound Mg2+. This, in conjunction with recently raised doubts regarding some of the Mg2+ assignments near the imino nitrogen of guanine, is suggestive of the existence of multiple Mg2+ binding modes for this basepair. Our detailed investigation of Mg2+-bound G:C W:W Trans pairs occurring in high-resolution RNA crystal structures shows that they are found in 14 different contexts, eight of which display Mg2+ binding at the Hoogsteen edge of guanine. Further examination of occurrences in these eight contexts led to the characterization of three different Mg2+ binding modes: 1) direct binding via N7 coordination, 2) direct binding via O6 coordination, and 3) binding via hydrogen-bonding interaction with the first-shell water molecules. In the crystal structures, the latter two modes are associated with a buckled and propeller-twisted geometry of the basepair. Interestingly, respective optimized geometries of these different Mg2+ binding modes (optimized using six different DFT functionals) are consistent with their corresponding experimental geometries. Subsequent interaction energy calculations at the MP2 level, and decomposition of its components, suggest that for G:C W:W Trans , Mg2+ binding can fine tune the basepair geometries without compromising with their stability. Our results, therefore, underline the importance of the mode of binding of Mg2+ ions in shaping RNA structure, folding and function.