Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain.
Biophys Chem. 2013 Oct-Nov;180-181:110-8. doi: 10.1016/j.bpc.2013.07.003. Epub 2013 Jul 20.
RNA oligonucleotides exhibit a large tendency to bend and form a loop conformation which is a major motif contributing to their complex three-dimensional structure. This is in contrast to DNA molecules that predominantly form the double-helix structure. In this paper we investigate by molecular dynamics simulation, as well as, by its combination with the replica-exchange method, the propensity of RNA chains containing the GCUAA pentaloop to form spontaneously a hairpin conformation. The results were then compared with those of analogous hybrid oligonucleotides in which the ribose groups in the loop-region were substituted by deoxyriboses. We find that the RNA oligomers exhibit a marginal excess stability to form loop structures. The equilibrium constant for opening the loop to an extended conformation is twice as large in the hybrid than it is in the RNA chain. Analyses of the hydrogen bonds indicate that the excess stability for forming a hairpin is a result of hydrogen bonds the 2'-hydroxyls in the loop region form with other groups in the loop. Of these hydrogen bonds, the most important is the hydrogen bond donated from the 2'-OH at the first position of the loop to N7 of adenine at the forth position. RNA and DNA backbones are characterized by different backbone dihedral angles and sugar puckering that can potentially facilitate or hamper the hydrogen bonds involving the 2'-OH. Nevertheless, the sugar puckerings of all the pentaloop nucleotides were not significantly different between the two chains displaying the C3'-endo conformation characteristic to the A-form double helix. All of the other backbone dihedrals also did not show any considerable difference in the loop-region except of the δ-dihedral. In this case, the RNA loop exhibited bimodal distributions corresponding to, both, the RNA and DNA backbones, whereas the loop of the hybrid chain behaved mostly as that of a DNA backbone. Thus, it is possible that the behavior of the δ-dihedrals in the loop-region of the RNA adopts conformations that facilitate the intra-nucleotide hydrogen bondings of the 2'-hydroxyls, and consequently renders loop structures in RNA more stable.
RNA 寡核苷酸表现出很大的弯曲和形成环构象的趋势，这是导致其复杂三维结构的主要模式。这与主要形成双螺旋结构的 DNA 分子形成对比。在本文中，我们通过分子动力学模拟以及将其与复制交换方法相结合来研究含有 GCUAA 五聚环的 RNA 链自发形成发夹构象的趋势。然后将结果与类似的杂交寡核苷酸进行比较，其中环区的核糖基被脱氧核糖基取代。我们发现，RNA 寡聚物形成环结构的稳定性略有增加。与 RNA 链相比，杂交体中打开环形成伸展构象的平衡常数大两倍。氢键分析表明，形成发夹的额外稳定性是环区 2'-羟基与环中其他基团形成氢键的结果。在这些氢键中，最重要的是来自环的第一个位置的 2'-OH 与第四个位置的腺嘌呤的 N7 之间的氢键。RNA 和 DNA 骨架的特征在于不同的骨架二面角和糖构象，这可能有利于或阻碍涉及 2'-OH 的氢键。尽管如此，两条链的所有五聚环核苷酸的糖构象都没有明显差异，显示出 A 型双螺旋特征的 C3'-endo 构象。除了 δ-二面角外，环区的所有其他骨架二面角也没有显示出任何明显的差异。在这种情况下，RNA 环表现出双峰分布，对应于 RNA 和 DNA 骨架，而杂交链的环主要表现为 DNA 骨架。因此，RNA 环区的 δ-二面角的行为可能采用有利于 2'-羟基内核苷酸氢键的构象，从而使 RNA 中的环结构更加稳定。
