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Visualizing transient low-populated structures of RNA

Abstract

The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA transitions towards ‘invisible’ excited states (ESs), which exist in too little abundance (2–13%) and for too short a duration (45–250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix–junction–helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signalling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes.

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Figure 1: Excited-state structure of the HIV-1 TAR apical loop.
Figure 2: Excited-state structure of the ribosomal A-site internal loop.
Figure 3: Two mutually exclusive excited-state structures in HIV-1 stem-loop 1.

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Acknowledgements

E.A.D., K.P. and J.C contributed equally to this work. We thank members of the Al-Hashimi laboratory for input. We acknowledge the Michigan Economic Development Cooperation and the Michigan Technology Tri-Corridor for the support of the purchase of a 600 MHz spectrometer. K.P. is supported by a postdoctoral Fellowship from the Swedish Research Council (VR-K2011-78PK-21662-0-12). This work was supported by the US National Institutes of Health (R01 AI066975) and by a Rackham Graduate Student Research Grant awarded by the University of Michigan.

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Authors

Contributions

H.M.A., E.A.D., K.P. and J.C. conceived the approaches to structurally characterize RNA ES and wrote the paper. E.A.D. and K.P. performed all experiments and data analyses for HIV TAR and SL1m, respectively. J.C. with assistance from A.C.-N. performed all experiments and data analyses for the A-site.

Corresponding author

Correspondence to Hashim M. Al-Hashimi.

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Competing interests

H.M.A. is an advisor to and holds an ownership interest in Nymirum Inc., which is an RNA-based drug discovery company. The research reported in this article was performed by the University of Michigan faculty and students and was funded by an NIH contract to H.M.A.

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Dethoff, E., Petzold, K., Chugh, J. et al. Visualizing transient low-populated structures of RNA. Nature 491, 724–728 (2012). https://doi.org/10.1038/nature11498

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