Blose Joshua M, Proctor David J, Veeraraghavan Narayanan, Misra Vinod K, Bevilacqua Philip C
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
J Am Chem Soc. 2009 Jun 24;131(24):8474-84. doi: 10.1021/ja900065e.
Hairpins are common RNA secondary structures that play multiple roles in nature. Tetraloops are the most frequent RNA hairpin loops and are often phylogenetically conserved. For both the UNCG and GNRA families, CG closing base pairs (cbps) confer exceptional thermodynamic stability but the molecular basis for this has remained unclear. We propose that, despite having very different overall folds, these two tetraloop families achieve stability by presenting the same functionalities to the major groove edge of the CG cbp. Thermodynamic contributions of this molecular mimicry were investigated using substitutions at the nucleobase and functional group levels. By either interrupting or deleting loop-cbp electrostatic interactions, which were identified by solving the nonlinear Poisson-Boltzmann (NLPB) equation, stability changed in a manner consistent with molecular mimicry. We also observed a linear relationship between DeltaG(o)(37) and log[Na(+)] for both families, and loops with a CG cbp had a decreased dependence of stability on salt. NLPB calculations revealed that, for both UUCG and GAAA tetraloops, the GC cbp form has a higher surface charge density, although it arises from changes in loop compaction for UUCG and changes in loop configuration for GAAA. Higher surface charge density leads to stronger interactions of GC cbp loops with solvent and salt, which explains the correlation between experimental and calculated trends of free energy with salt. Molecular mimicry as evidenced in these two stable but otherwise unrelated tetraloops may underlie common functional roles in other RNA and DNA motifs.
发夹是常见的RNA二级结构，在自然界中发挥多种作用。四环是最常见的RNA发夹环，并且在系统发育上常常是保守的。对于UNCG和GNRA家族而言，CG封闭碱基对（cbp）赋予了异常的热力学稳定性，但其分子基础仍不清楚。我们提出，尽管这两个四环家族的整体折叠非常不同，但它们通过向CG cbp的大沟边缘呈现相同的功能来实现稳定性。利用核碱基和官能团水平的取代研究了这种分子模拟的热力学贡献。通过中断或删除通过求解非线性泊松 - 玻尔兹曼（NLPB）方程确定的环 - cbp静电相互作用，稳定性以与分子模拟一致的方式发生变化。我们还观察到两个家族的ΔG°（37）与log[Na⁺]之间存在线性关系，并且具有CG cbp的环对盐的稳定性依赖性降低。NLPB计算表明，对于UUCG和GAAA四环，GC cbp形式具有更高的表面电荷密度，尽管它源于UUCG的环压缩变化和GAAA的环构型变化。更高的表面电荷密度导致GC cbp环与溶剂和盐之间的相互作用更强，这解释了实验和计算的自由能与盐趋势之间的相关性。这两个稳定但不相关的四环中所证明的分子模拟可能是其他RNA和DNA基序中常见功能作用的基础。
