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Structural basis for high-affinity fluorophore binding and activation by RNA Mango

Nature Chemical Biology volume 13, pages 807–813 (2017)Cite this article

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Abstract

Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA–fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1–Biotin (Kd ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.

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Figure 1: Overall structure of RNA Mango in complex with TO1–Biotin.
Figure 2: Structure of the G-quadruplex core of RNA Mango.
Figure 3: The duplex–quadruplex junction of RNA Mango resembles a GAAA tetraloop.
Figure 4: Structural basis of TO1–Biotin recognition by RNA Mango.
Figure 5: Structure-based analysis of the RNA Mango–TO1–Biotin complex.

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Acknowledgements

We thank the staff at beamlines 5.0.1 and 5.0.2 of the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, and beamline 24-ID-C of the Advanced Photon Source (APS), Argonne National Laboratory, for crystallographic data collection; G. Piszczek (Biophysics Core, US National Heart, Lung and Blood Institute, NHLBI, National Institutes of Health (NIH)) for analytical ultracentrifugation and dynamic light scattering; D. Lee and R. Levine (NHLBI) for mass spectrometry; and S. Bachas, M. Chen, C. Fagan, C. Jones, T. Numata, D. Sen, L. Sjekloca, L. Truong, K. Warner and J. Zhang for discussions. This work was partly conducted at the ALS, on the on the Berkeley Center for Structural Biology beamlines, and at the APS, on the NE-CAT beamlines, which are supported by the NIH. Use of the ALS and APS was supported by the US Department of Energy. P.J.U. was supported by an NSERC (Canada) operating grant. This work was supported in part by the intramural program of the NHLBI, NIH.

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Authors and Affiliations

  1. Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA

    Robert J Trachman III, Natalia A Demeshkina, Matthew W L Lau & Adrian R Ferré-D'Amaré

  2. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British, Columbia, Canada

    Shanker Shyam S Panchapakesan, Sunny C Y Jeng & Peter J Unrau

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Contributions

P.J.U. and A.R.F.-D. conceived the project; M.W.L.L. performed initial crystallization screens; S.C.Y.J. synthesized ligands; R.J.T., N.A.D. and M.W.L.L. carried out preparative biochemistry; R.J.T. performed crystallization, diffraction data collection, structure determination and refinement; R.J.T., N.A.D., S.S.S.P. and S.C.Y.J. performed structure-guided analyses; R.J.T. and A.R.F.-D. prepared the manuscript with input from all authors.

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Correspondence to Adrian R Ferré-D'Amaré.

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Trachman, R., Demeshkina, N., Lau, M. et al. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat Chem Biol 13, 807–813 (2017). https://doi.org/10.1038/nchembio.2392

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