NMR studies of dynamics in RNA and DNA by ¹³C relaxation

Abstract

T he many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins, or other nucleic acids. 1,2 Although structurally more conservative and therefore dynamically less diverse, local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. 3 These statements make a compelling case to study the sequence dependent dynamics in nucleic acids; yet, residue-specific studies of nucleic acid dynamics are relatively few. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention, this spectroscopy being the only way to access information on a residue-by-residue basis. The questions that are being asked are how motion contributes to the affinity and specificity of biological interactions and what trajectories lead to the remarkably large conformational changes that are sometimes observed.RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. Figure 1 summarizes the NMR spectroscopic techniques commonly used to obtain information in each motional regime. Dynamics occurring on time scales that are considered ''fast'' in NMR spectroscopic studies (ps-ns) largely reflects bond librations associated with small amplitude and localized motions.

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].…”

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.…”

Probing complexes with single fluorophores: factors contributing to dispersion of FRET in DNA/RNA duplexes

“…Data about the collective motion of DNA/RNA helical domains arising from structural fluctuations of the duplex (bending and twisting) are almost non-existent in the literature, especially for short duplexes. However, it can be inferred that these motions mainly cover the range from tens of nanosecond to tens of microseconds (Hogan et al 1982;Naimushin et al 2000;Orden and Jung 2008;Porschke 2007;Schwieters and Clore 2007;Shajani and Varani 2007), although motions in the range 20-400 ls have been reported (Kojima et al 2001). Together, these considerations indicate that in most cases, energy transfer captures a transient ''static'' configuration of the duplex, whereas the slow acquisition rate allows the DNA/RNA duplex and associated fluorophores to adopt all possible configurations within the experimental period used for data acquisition.…”