Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

Abstract

An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large‐amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 384–402, 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

Structural determinants for ligand capture by a class II preQ 1 riboswitch

“…Whereas R 1 and R 1 ρ report on ps-ns dynamics, RDCs have an extended timescale resolution and are sensitive to internal motions ranging from ps to ms, providing insight into dynamics occurring on an ns-μs timescale (48)(49)(50)(51)(52)(53)(54). We performed order tensor analysis (55, 56) using the RAMAH program (57) to compute the generalized degree of order (GDO; ϑ) (58) for each helix.…”

“…In the NMR conditions (60 mM KCl, 3 mM CaCl 2 ; pH 6.3), the riboswitch construct used for NMR (WT) has a K D of 75 ± 10 nM, and the full-length riboswitch including P1 (WT+P1) has a slightly weaker K D of 220 ± 30 nM. Deletion of residues 36-49 [ΔP4 (36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)], which include all of P4 and the two flanking C residues, from the NMR construct decreased the binding affinity by 20-fold, to 2,000 ± 300 nM. A similar result (K D = 2,000 nM) was obtained from 2-aminopurine fluorescence measurements on the Spn preQ 1 -II riboswitch with only P4 deleted (equivalent residues 37-48) (40).…”

“…Examination of NMR spectra of ΔP4 (36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49) showed that deletion of P4 stabilizes P3 base pairs; imino proton resonances for the top five of the six base pairs of P3 were seen in the absence of preQ 1 (Fig. S4B), whereas in the WT construct only A55-U14, G54-U15, and G53-C16 base pairs were observed (Fig.…”

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

“…However, recent advances in NMR techniques over the past two years are now providing an unprecedented view into the structural dynamics of RNA [125][126][127]. Particularly powerful is the ability to determine the amplitude and relative directionality of the internal motion of helical domains through residual dipolar coupling measurements [128,129].…”

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

“…Relaxation rate measurement by NMR has the unique ability to provide residue specific information on dynamics in both protein and RNA over a range of different time-scales [358][359][360]. Fast motions on the pico-second (ps) to nano-second (ns) timescales influence spin relaxation through the modulation of various spin interactions and are typically characterized by the measurement of longitudinal (R 1 ), transverse (R 2 ) or rotating frame (R 1 ρ) and nuclear Overhauser effect (NOE) relaxation rates for 15 N and 13 C nuclei.…”