Iowa State University, Ames, Iowa 50011, United States.
Ames National Laboratory, Ames, Iowa 50011, United States.
J Phys Chem B. 2022 Sep 22;126(37):7114-7125. doi: 10.1021/acs.jpcb.2c04649. Epub 2022 Sep 12.
RNA aptamers are single-stranded oligonucleotides that bind to specific molecular targets with high affinity and specificity. To design aptamers for new applications, it is critical to understand the ligand binding mechanism in terms of the structure and dynamics of the ligand-bound and apo states. The problem is that most of the NMR or X-ray crystal structures available for RNA aptamers are for ligand-bound states. Available apo state structures, mostly characterized by crystallization under nonphysiological conditions or probed by low resolution techniques, might fail to represent the diverse structural variations of the apo state in solution. Here, we develop an approach to obtain a representative ensemble of apo structures that are based on RNA 3D structure prediction and experiments that characterize base stacking. Using the neomycin-B aptamer as a case study, an ensemble of structures for the aptamer in the apo (unbound) state are validated and then used to investigate the ligand-binding mechanism for the aptamer in complex with neomycin-B.
RNA 适体是与特定分子靶标具有高亲和力和特异性结合的单链寡核苷酸。为了针对新的应用设计适体，关键是要了解配体结合机制，包括配体结合和无配体状态的结构和动力学。问题是，大多数可用于 RNA 适体的 NMR 或 X 射线晶体结构都是配体结合状态的。可用的无配体状态结构，主要通过非生理条件下的结晶或低分辨率技术来探测，可能无法代表溶液中无配体状态的多种结构变化。在这里，我们开发了一种方法来获得代表无配体状态的构象集合，该方法基于 RNA 三维结构预测和表征碱基堆积的实验。我们以新霉素 B 适体为例，验证了适体在无配体（未结合）状态下的构象集合，并将其用于研究适体与新霉素 B 复合物的配体结合机制。
