Strategies for understanding RNA recognition by X-ray crystallography and NMR methods

Aiai Sun; Kaiyi Huang; Luqian Zheng; Aiming Ren

doi:10.1016/bs.mie.2019.05.024

Strategies for understanding RNA recognition by X-ray crystallography and NMR methods

Methods Enzymol. 2019:623:229-248. doi: 10.1016/bs.mie.2019.05.024. Epub 2019 Jun 6.

Authors

Aiai Sun¹, Kaiyi Huang¹, Luqian Zheng¹, Aiming Ren²

Affiliations

¹ Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
² Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China. Electronic address: aimingren@zju.edu.cn.

PMID: 31239048
DOI: 10.1016/bs.mie.2019.05.024

Abstract

One class of non-coding RNA molecules, termed riboswitches, are the regulatory elements with ability to control gene expression by sensing different cellular metabolites. Specific recognition of the corresponding ligand induced the conformation rearrangement of riboswitch, and thus turned on/off the down-stream gene expression. In this chapter, we will focus on two principal methods that are currently used to investigate the recognition mechanism of riboswitches, including X-ray crystallography and NMR spectroscopy. First, we present that how to get the diffraction-quality crystals of riboswitches in specific functional states. Then we focus on how to use NMR spectroscopy as a tool to learn the dynamics of riboswitches. Detailed protocols are listed below.

Keywords: Ligand; NMR; RNA; Recognition; Riboswitch; Structure; X-ray crystallography.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Crystallization / methods
Crystallography, X-Ray / methods*
Nuclear Magnetic Resonance, Biomolecular / methods*
Nucleic Acid Conformation
Riboswitch*

Substances

Riboswitch