School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
RNA. 2011 Feb;17(2):291-7. doi: 10.1261/rna.2390311. Epub 2010 Dec 20.
Magnesium plays a special role in RNA function and folding. Although water is magnesium's most common first-shell ligand, the oxyanions of RNA have significant affinity for magnesium. Here we provide a quantum mechanical description of first-shell RNA-magnesium and DNA-magnesium interactions, demonstrating the unique features that characterize the energetics and geometry of magnesium complexes within large folded RNAs. Our work focuses on bidentate chelation of magnesium by RNA or DNA, where multiple phosphate oxyanions enter the first coordination shell of magnesium. These bidentate RNA clamps of magnesium occur frequently in large RNAs. The results here suggest that magnesium, compared to calcium and sodium, has an enhanced ability to form bidentate clamps with RNA. Bidentate RNA-sodium clamps, in particular, are unstable and spontaneously open. Due to magnesium's size and charge density it binds more intimately than other cations to the oxyanions of RNA, so that magnesium clamps are stabilized not only by electrostatic interactions, but also by charge transfer, polarization, and exchange interactions. These nonelectrostatic components of the binding are quite substantial with the high charge and small interatomic distances within the magnesium complexes, but are less pronounced for calcium due to its larger size, and for sodium due to its smaller charge. Additionally, bidentate RNA clamps of magnesium are more stable than those with DNA. The source of the additional stability of RNA complexes is twofold: there is a slightly attenuated energetic penalty for ring closure in the formation of RNA bidentate chelation complexes and elevated electrostatic interactions between the RNA and cations. In sum, it can be seen why sodium and calcium cannot replicate the structures or energetics of RNA-magnesium complexes.
镁在 RNA 功能和折叠中起着特殊的作用。尽管水是镁最常见的第一壳层配体，但 RNA 的含氧阴离子对镁具有显著的亲和力。在这里，我们提供了一个对第一壳层 RNA-镁和 DNA-镁相互作用的量子力学描述，展示了特征化大折叠 RNA 中镁配合物的能量学和几何形状的独特特征。我们的工作集中在镁通过 RNA 或 DNA 的双齿螯合上，其中多个磷酸含氧阴离子进入镁的第一配位壳。这些双齿 RNA 夹的镁在大型 RNA 中经常出现。这里的结果表明，与钙和钠相比，镁具有增强的能力，能够与 RNA 形成双齿夹。特别是双齿 RNA-钠夹是不稳定的，会自发打开。由于镁的大小和电荷密度，它比其他阳离子更紧密地与 RNA 的含氧阴离子结合，因此镁夹不仅通过静电相互作用稳定，而且通过电荷转移、极化和交换相互作用稳定。这些结合的非静电成分对于镁配合物来说非常重要，因为它们具有高电荷和小的原子间距离，但对于钙来说由于其较大的尺寸，以及对于钠来说由于其较小的电荷，这些成分的影响就不那么明显。此外，镁的双齿 RNA 夹比 DNA 的更稳定。RNA 配合物额外稳定性的来源有两个方面：在形成 RNA 双齿螯合配合物时，环闭的能量惩罚略有减弱，并且 RNA 和阳离子之间的静电相互作用升高。总之，可以看出为什么钠和钙不能复制 RNA-镁配合物的结构或能量学。
