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Examining the relationship between RNA function and motion using nuclear magnetic resonance

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Abstract The biological function of proteins and nucleic acids relies on their complex structures, yet dynamics provides an additional layer of functional adaptability. Numerous studies have demonstrated that RNA is only able to perform the multitude of functions for which it is responsible by readily changing its conformation in response to binding of proteins or small molecules. Examination of RNA dynamics is therefore essential to understanding its biological function. Nuclear magnetic resonance (NMR) has emerged as a leading technique for the examination of RNA motion and conformational transitions. It can examine domain motions as well as motion with atomic level resolution over a wide range of time scales. This review examines how NMR spectroscopy can be applied to examine the relationship between function and dynamics in RNA. WIREs RNA 2012, 3:122–132. doi: 10.1002/wrna.108 This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions

Different nuclear magnetic resonance (NMR) techniques cover different motional timescales and, as a result, examine different biological processes.

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An illustration of the folding of the riboswitch based on the UltraSO‐FAST data after (a) 0 s (b) ∼28 s (c) ∼58 s, and (d) ∼120 s. In the final state, the ligand, adenosine, becomes fully locked in place.

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A physical representation of the domain motion experienced by the lower and upper helices of TAR (represented as cylinders) occurring at µs rates.

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A visual representation of the µs conformational exchange motions experienced by residue (a) U23 and (b) U25 of unbound human immunodeficiency virus 1 (HIV‐1) TAR.

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(a) The binding site for the U1A protein, which tumbles at a rate of about 6 ns; (b) when the RNA is elongated as shown, the tumbling time increases to 18 ns, allowing slower motions to be observed.

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This graph shows the calculated order parameter values for the bases (C6 and C8) of (a) Tat11‐TAR (b) Arg‐TAR (c) L22‐TAR, and (d) Unbound TAR, as a function of residue number. Residues in gray are all base pairs making up the two helices, while residues in blue and green belong to the bulge and apical loop, respectively. These results graphically illustrate changes in dynamics that occur in TAR upon binding of various ligands. Residues without order parameter data correspond to sites that could not be analyzed using the model‐free analysis or for which relaxation data were not obtainable, typically due to spectral overlap.

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Browse by Topic

RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry

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