Department of Chemistry, University of Waterloo , 200 University Ave West, Waterloo, ON N2L3G1, Canada.
Biochemistry. 2013 Sep 24;52(38):6575-83. doi: 10.1021/bi400549s. Epub 2013 Sep 11.
Adaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. The malachite green aptamer (MGA) has been shown to bind several closely related triphenyl dyes with planar and nonplanar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA-ligand interaction. The results of these studies reveal that binding of one ligand can reduce the ability of the aptamer pocket to adapt to another ligand, even if this second ligand has a significantly higher affinity to the free aptamer. A similar effect is observed in the presence of Mg(2+) ions which stabilize the binding pocket in a more ligand bound-like conformation.
自适应结合，即分子能够围绕配体的结构折叠自身并将其纳入其三维折叠的能力，是大多数 RNA 适体的关键特征。已显示孔雀石绿适体 (MGA) 以这种方式结合几个具有平面和非平面结构的密切相关的三苯基染料。使用等温滴定量热法和停流动力学进行竞争性结合研究，目的是了解 RNA-配体相互作用的适应性。这些研究的结果表明，即使第二个配体与游离适体具有更高的亲和力，结合一个配体也可以降低适体口袋适应另一个配体的能力。在存在稳定结合口袋的 Mg(2+)离子的情况下会观察到类似的效应，使其处于更类似于配体结合的构象。
