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Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

Abstract

Many recently discovered noncoding RNAs do not fold into a single native conformation but sample many different conformations along their free-energy landscape to carry out their biological function. Here we review solution-state NMR techniques that measure the structural, kinetic and thermodynamic characteristics of RNA motions spanning picosecond to second timescales at atomic resolution, allowing unprecedented insights into the RNA dynamic structure landscape. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.

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Figure 1: NMR spectroscopy techniques and site-specific probes for characterizing motional modes that carry RNA structure along various regions of the dynamic structure landscape.
Figure 2: Characterization of pico- to nanosecond motions using spin relaxation.
Figure 3: Characterizing motions over sub-millisecond timescales using residual dipolar couplings.
Figure 4: Characterizing microsecond to millisecond exchange by relaxation dispersion.
Figure 5: Characterizing conformational transitions occurring at millisecond and longer timescales by ZZ-exchange and time-resolved NMR spectroscopy.
Figure 6: Characterizing base-pair-opening dynamics by imino proton exchange.

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Acknowledgements

We thank members of the Al-Hashimi lab for insightful comments and A. Kurochkin for maintenance of the NMR instruments. We acknowledge collaborations with the groups of C. Fierke (University of Michigan), I. Andricioaei (University of California, Irvine) and C. Brooks (University of Michigan), and the Michigan Economic Development Cooperation and the Michigan Technology Tri-Corridor for the support of the purchase of a 600-MHz spectrometer. This work was supported by the US National Institutes of Health (R01 AI066975 and R01 GM089846) and the US National Science Foundation Career Award (MCB 0644278).

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Correspondence to Hashim M Al-Hashimi.

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H.M.A.-H. is an advisor to and holds an ownership interest in Nymirum, an RNA-based drug-discovery company.

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Bothe, J., Nikolova, E., Eichhorn, C. et al. Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat Methods 8, 919–931 (2011). https://doi.org/10.1038/nmeth.1735

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