School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
J Am Chem Soc. 2010 Sep 15;132(36):12679-89. doi: 10.1021/ja104387k.
In RNA, A-form helices are commonly terminated by tetraloops or 3' dangling ends. Aside from helices themselves, these helix-breaking motifs appear to be among the most frequent and repetitive structural elements of large folded RNAs. We show here that within a frequent type of tetraloop, cGNRAg (G is guanine, N is any base, R is purine, A is adenine), a tension exists between the backbone torsional energy of the loop and the energy contributed by molecular interactions (stacking and pairing). A model in which favorable bond rotamers are opposed by favorable stacking and pairing interactions is consistent with our observation that release of torsional restraints upon conversion of one or more loop riboses to more flexible trimethylene phosphate(s) contributes favorably to the enthalpy of folding. This effect presumably results from improved stacking and hydrogen-bonding interactions upon release of torsional restraints. The most obvious possibility for improving molecular interactions is a repositioning of A, which is proximal to the unfavorable torsion angles in native cGNRAg tetraloops, and which is unstacked on the 3' side and unpaired (it forms a single hydrogen bond with the opposing G). This tension between favorable bond rotamers and favorable molecular interactions may be representative of a general evolutionary strategy to prevent achievement of deep and irreversible thermodynamic wells in folded RNAs. Finally, we observe a simple stacking substructure with conserved geometry and sequence that forms a scaffold for both tetraloops and 3' dangling ends. It seems that simple substructures can build RNA motifs, which combine to establish the fundamental architecture of RNA.
在 RNA 中，A 型螺旋通常由四环或 3' 悬垂末端终止。除了螺旋本身之外，这些破坏螺旋的模体似乎是大型折叠 RNA 中最常见和重复的结构元件之一。我们在这里表明，在一种常见的四环类型 cGNRAg（G 是鸟嘌呤，N 是任何碱基，R 是嘌呤，A 是腺嘌呤）中，环的骨架扭转能和分子相互作用（堆积和配对）所贡献的能量之间存在张力。一个模型认为，有利的键旋转异构体受到有利的堆积和配对相互作用的反对，这与我们的观察结果一致，即在将一个或多个环核糖转换为更灵活的三亚甲基磷酸盐时，释放扭转约束有利于折叠的焓。这种效应可能是由于释放扭转约束后改善了堆积和氢键相互作用。改善分子相互作用的最明显可能性是 A 的重新定位，A 靠近天然 cGNRAg 四环中不利的扭转角，并且在 3' 侧未堆积且未配对（它与对面的 G 形成一个氢键）。有利的键旋转异构体和有利的分子相互作用之间的这种张力可能代表了一种防止折叠 RNA 中达到深和不可逆热力学势阱的一般进化策略。最后，我们观察到一个具有保守几何形状和序列的简单堆积亚结构，它为四环和 3' 悬垂末端提供了支架。似乎简单的亚结构可以构建 RNA 模体，这些模体结合起来建立 RNA 的基本结构。
