NMR Methods for Studying the Structure and Dynamics of RNA

Latham, Michael P.; Brown, Darin J.; McCallum, Scott A.; Pardi, Arthur

doi:10.1002/cbic.200500123

Cited by 146 publications

(124 citation statements)

References 85 publications

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“…Platforms involving base-base interactions among invariant nucleotides stabilize the core and explain the observed sequence conservation and thus the informational complexity of the aptamer. Now that we have generated initial models of the Class I aptamer structure, future NMR work can be directed toward obtaining direct evidence for the predicted base-base hydrogen bonds, examining the roles of the obligatory metal ions and investigating the dynamics of the structure (Latham et al 2005). …”

Section: Discussionmentioning

confidence: 99%

Solution structure of an informationally complex high-affinity RNA aptamer to GTP

Carothers¹,

Davis²,

Chou³

et al. 2006

RNA

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Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K d = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K d of 6 mM are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81%-85%). However, the GTP aptamer is more informationally complex ($45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base-base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in K d . These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.

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Section: Discussionmentioning

confidence: 99%

Solution structure of an informationally complex high-affinity RNA aptamer to GTP

Carothers¹,

Davis²,

Chou³

et al. 2006

RNA

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“…[26][27][28][29][30][31][32] Here, we provide a brief description of the basic underpinnings of the methodology, with an emphasis on its application to nucleic acids.…”

Section: Residual Dipolar Couplingsmentioning

confidence: 99%

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

et al. 2007

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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

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“…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.…”

Section: Introductionmentioning

confidence: 99%

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

Giambaşu

York

Case

2015

RNA

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RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields ( ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters ( ff10) are closer to experiment than those for the older ones ( ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.

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NMR Methods for Studying the Structure and Dynamics of RNA

Cited by 146 publications

References 85 publications

Solution structure of an informationally complex high-affinity RNA aptamer to GTP

Solution structure of an informationally complex high-affinity RNA aptamer to GTP

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

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

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