Time‐resolved NMR studies of RNA folding

Abstract

The application of real‐time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time‐resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long‐range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time‐resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non‐coding RNAs in cells. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 360–383, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

“…30 and 37. Furthermore, other cofactors such as metal ions could also be used in a caged form to trigger structural transitions in biomolecular systems (38). Light-induced initiation of structural transition events has the advantage of providing experimentally reproducible and precisely controlled conditions, such that multiple experiments can be coadded as done in refs.…”

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

“…Nowadays, a range of different aspects of dynamics can be probed routinely by solution-state NMR, such as the amplitude of fast (picosecond-to-nanosecond) internal motion, properties of overall rotational tumbling as well as exchange processes occurring on millisecond time scales, often involving a small number of distinct states [1][2][3][4][5]. In addition to these equilibrium experiments, kinetic off-equilibrium approaches are available to study processes such as slow folding/unfolding and binding [6][7][8].…”

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

“…NMR is a major source of structural and dynamical information on nucleic acids in solution (Latham et al 2005;Fürtig et al 2007;Shajani and Varani 2007;Cruz and Westhof 2009;Rinnenthal et al 2011;Bardaro and Varani 2012;Salmon et al 2014), and is broadly supported by other forms of spectroscopy (Abdelkafi et al 1998;Leulliot et al 1999;Schiemann et al 2003;Qin and Dieckmann 2004;Bokinsky and Zhuang 2005;Zhuang 2005;Solomatin et al 2010). NMR-derived time averaged quantities such as dipolar couplings, chemical shifts, J-couplings, or NOEs can be translated into geometric restraints to refine RNA structures or conformational ensembles.…”

“…NMR-derived time averaged quantities such as dipolar couplings, chemical shifts, J-couplings, or NOEs can be translated into geometric restraints to refine RNA structures or conformational ensembles. In addition, time-dependent NMR measurements such as NMR relaxation (Lipari and Szabo 1981;Boisbouvier et al 2003;Fürtig et al 2007;Shajani and Varani 2007) can be used to derive time-scales and amplitudes for internal motions and overall rigid-body tumbling (Kowalewski and Maler 2006). Such properties depend not only on the internal macromolecular dynamics but most importantly on the hydrodynamic and long range electrostatic interactions with the surrounding ion atmosphere (Kowalewski and Maler 2006;Bagchi 2012), providing a probe for the collective motion of the entire solvated macromolecule.…”