Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, People's Republic of China.
NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, People's Republic of China.
Phys Chem Chem Phys. 2021 May 5;23(17):10636-10649. doi: 10.1039/d0cp06438f.
Recently, RNA aptamers activating small-molecule fluorophores have been successfully applied to tag and track RNAs in vivo. It is of significance to investigate the molecular mechanism of the fluorophore-RNA aptamer bindings at the atomic level to seek a possible pathway to enhance the fluorescence efficiency of fluorophores. In this work, multiple replica molecular dynamics (MRMD) simulations, essential dynamics (ED) analysis, and hierarchical clustering analysis were coupled to probe the effect of A22U mutation on the binding of two fluorophores, TO1-Biotin (TO1) and TO3-Biotin (TO3), to the Mango-II RNA aptamer (Mango-II). ED analysis reveals that A22U induces alterations in the binding pocket and sites of TO1 and TO3 to the Mango-II, which in turn tunes the fluorophore-RNA interface and changes the interactions of TO1 and TO3 with separate nucleotides of Mango-II. Dynamics analyses also uncover that A22U exerts the opposite impact on the molecular surface areas of the Mango-II and sugar puckers of nucleotides 22 and 23 in Mango-II complexed with TO1 and TO3. Moreover, the calculations of binding free energies suggest that A22U strengthens the binding ability of TO1 to the mutated Mango-II but weakens TO3 to the mutated Mango-II when compared with WT. These findings imply that point mutation in nucleotides possibly tune the fluorescence of fluorophores binding to RNA aptamers, providing a possible scheme to enhance the fluorescence of fluorophores.
最近，激活小分子荧光团的 RNA 适体已成功应用于体内标记和追踪 RNA。在原子水平上研究荧光团 - RNA 适体结合的分子机制对于寻找增强荧光团荧光效率的可能途径具有重要意义。在这项工作中，采用了多种复制品分子动力学（MRMD）模拟、本征动力学（ED）分析和层次聚类分析来探究 A22U 突变对两种荧光团 TO1-Biotin（TO1）和 TO3-Biotin（TO3）与 Mango-II RNA 适体（Mango-II）结合的影响。ED 分析表明，A22U 诱导 TO1 和 TO3 与 Mango-II 的结合口袋和结合位点发生变化，从而调节荧光团-RNA 界面并改变 TO1 和 TO3 与 Mango-II 上单独核苷酸的相互作用。动力学分析还揭示，A22U 对与 TO1 和 TO3 结合的 Mango-II 的分子表面积以及 Mango-II 中核苷酸 22 和 23 的糖环构象产生相反的影响。此外，结合自由能的计算表明，与野生型相比，A22U 增强了 TO1 与突变 Mango-II 的结合能力，但削弱了 TO3 与突变 Mango-II 的结合能力。这些发现表明，核苷酸的点突变可能会调节荧光团与 RNA 适体结合的荧光，为增强荧光团的荧光提供了一种可能的方案。
