RNA Dynamics by NMR Spectroscopy

Abstract

An ever‐increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so‐called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined—Lego like—than in proteins, hence the numerous revelations of RNA excited states.

The molecular structure of long non-coding RNAs: emerging patterns and functional implications

“…For reference, the largest RNA structure determined by NMR so far is the HIV-1 core packaging signal, which counts 155 nt [PDB id 2N1Q, (Keane et al 2015)]. As a consequence, at least in the immediate future, the contribution that NMR will offer to the characterization of lncRNA will remain limited to structure determination of short motifs and their dynamics (Marusic et al 2019).…”

A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints

“…As one might have noticed, these exchange regimes loosely correspond to the motional tiers described in 1.1.3, therefore a comparison can be made with the conformational transition described above with the following experimental probing techniques. The NMR methods and application examples mentioned below were recently reviewed by our group in a comprehensive work on the subject 109 .…”

“…The spectrum results in two distinct peaks for A and B, each corresponding to its own chemical environment and with characteristic Ω A and Ω B . However, the lineshape of the peaks is generally not affected by the process and the intensities are a direct readout of the relative populations 109 . This regime corresponds to seconds or slower exchange rates and the peaks corresponding to the two states resonating at Ω A and Ω B are readily observable in fingerprint spectra.…”

RING NMR dynamics: software for analysis of multiple NMR relaxation experiments

“…These two important attributes mean that NMR can probe dynamics with atomic spatial resolution and with a temporal resolution matched to the biological process in question. This ability to examine different atomic types and different timescales has led to the development of a wide range of NMR experiments, each optimized for a different dynamics phenomenon and different time scale (Sekhar and Kay 2019;Stetz et al 2019;Marušič et al 2019).…”