A transient conformation facilitates ligand binding to the adenine riboswitch

Lin Wu; Dian Chen; Jienyu Ding; Yu Liu

doi:10.1016/j.isci.2021.103512

A transient conformation facilitates ligand binding to the adenine riboswitch

iScience. 2021 Nov 25;24(12):103512. doi: 10.1016/j.isci.2021.103512. eCollection 2021 Dec 17.

Authors

Lin Wu¹, Dian Chen¹, Jienyu Ding², Yu Liu¹

Affiliations

¹ State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
² Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.

Abstract

RNAs adopt various conformations to perform different functions in cells. Incapable of acquiring intermediates, the key initiations of ligand recognition in the adenine riboswitch have not been characterized. In this work, stopped-flow fluorescence was used to track structural switches in the full-length adenine riboswitch in real time. We used PLOR (position-selective labeling of RNA) to incorporate fluorophores into desired positions in the RNA. The switching sequence P1 responded to adenine more rapidly than helix P4 and the binding pocket, followed by stabilization of the binding pocket, P4, and annealing of P1. Moreover, a transient intermediate consisting of an unwound P1 was detected during adenine binding. These events were observed in both the WT riboswitch and a functional mutant. The findings provide insight into the conformational changes of the riboswitch RNA triggered by a ligand.

Keywords: Biochemistry; Biological sciences; Molecular biology; Structural biology.