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The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold

Nature Chemical Biology volume 18, pages 191–198 (2022)Cite this article

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Abstract

Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.

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Fig. 1: Overall structure of the Squash fluorescence turn-on aptamer.
Fig. 2: The Squash fluorophore-binding site is assembled from four strands.
Fig. 3: A-minor motifs anchor both ends of the Squash core.
Fig. 4: Structure-guided mutational analysis of Squash.
Fig. 5: Squash recognition of DFHO and DFHBI-1T.
Fig. 6: Comparison of Squash and the adenine riboswitch aptamer domain.

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Data availability

Atomic coordinates and structure factor amplitudes for the Squash–DFHBI-1T (Ir), Squash–DFHBI-1T (native) and Squash–DFHO complex cocrystal structures have been deposited with the Protein Data Bank under accession codes 7KVT, 7KVU and 7KVV, respectively.

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Acknowledgements

We thank the staff of beamlines 5.0.1 of the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, and 24-ID-C and 24-ID-E of the Advanced Photon Source (APS), Argonne National Laboratory for crystallographic data collection; the staff of beamline 12-ID-B of APS for SAXS; G. Piszczeck and of the Biophysics Core of the National Heart, Lung and Blood Institute (NHLBI) for fluorescence and ITC; and M. Banco, N. Demeshkina, C. Jones, T. Numata and R. Trachman for discussions. This research used resources of the APS, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (NIH P30 GM124165). The Pilatus 6M detector on 24-ID-C beam line is funded by an NIH-ORIP HEI grant (S10 RR029205). This work was supported in part by NIH award R35NS111631 (to S.R.J.) and 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, MD, USA

    Lynda Truong, Hamed Kooshapur, Nico Tjandra & Adrian R. Ferré-D’Amaré

  2. Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY, USA

    Sourav Kumar Dey, Xing Li & Samie R. Jaffrey

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  1. Lynda Truong
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Contributions

S.R.J. and A.R.F.D’A. initiated the project. L.T. performed fluorescence, crystallographic, SAXS and ITC experiments. S.K.D. and X.L. performed initial biochemistry and synthesized fluorophores. H.K. and N.T. performed NMR experiments. A.R.F.D’A. and L.T. wrote the manuscript with contributions from all authors.

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Correspondence to Adrian R. Ferré-D’Amaré.

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The authors declare no competing interests.

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Peer review information Nature Chemical Biology thanks Sven Hennig and other anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Electron density maps for structures determined in this study.

a, Density-modified SAD electron density map for the Squash-DFHBI-1T complex contoured at 1.5 σ (blue mesh), superimposed on the final refined model. b, Composite simulated annealing-omit 2|Fo | -|Fc | electron density map for the Squash-DFHO complex contoured at 1.5 σ (blue mesh), superimposed on the final refined model.

Extended Data Fig. 2 Small-angle X-ray scattering analysis of Squash.

a, Experimental scattering profile of Squash-DFHBI-1T and scattering profile back-calculated2 using CRYSOL, from the co-crystal structure (Methods). I and q are the intensity and the scattering vector, respectively. b, Scattering profile of Squash in the presence and absence of excess DFHBI-1T. c, Scattering profile of Squash mutant with disrupted L2-L3 kissing loop interactions (MM) in the presence and absence of excess DFHBI-1T.

Extended Data Fig. 3 Eight tiers comprise the Squash aptamer core.

Ball-and-stick representation of each tier (numbered 1-8 in bold numerals) in the Squash core. Panel with DFHBI-1T and G14 (tier 2) shows A69 and A70 from adjacent tiers for reference. Orange dashed lines denote hydrogen bonds. Secondary structure representation corresponds to that in Fig. 1e.

Extended Data Fig. 4 ThT recognition by Squash.

a, Fluorescence of Squash RNA (0.5 μM) and thioflavin T (ThT; 1.0 μM) measured in the absence or the presence of increasing concentrations of DFHO (Methods). b, DFHO fluorescence measured from the same mixtures.

Extended Data Fig. 5 Cartoon representation of orthogonal views of DFHO-bound Squash.

RNA color scheme as in Fig. 1. Metal ions and water molecules omitted for clarity.

Extended Data Fig. 6 Isothermal titration calorimetry.

Triplicate, baseline-corrected thermograms and fits for Squash titrated with a, DFHBI-1T (means ± s.d., n = 3). ΔH and ΔG are 41.0 ± 20.8 nM and -21.3 ± 2.3 kcal/Mol, respectively. b, Triplicate, baseline-corrected thermograms and fits for Squash titrated with a, DFHBI-1E (means ± s.d., n = 3). ΔH and ΔG are 30.3 ± 16.6 and -19.2 ± 0.8 kcal/Mol, respectively.

Extended Data Fig. 7 Fluorescence of DFHBI-1T and DFHBI-1E bound Squash.

Absorbance spectra (dashed lines) were recorded at 503 nm and 492 nm, and emission spectra (solid lines) at 451 nm and 431 nm, respectively. Green lines, Squash with DFHBI-1T; blue lines, Squash with DFHBI-1E.

Extended Data Fig. 8 The adenine riboswitch core is smaller than that of Squash.

a, Ball-and-stick representations of each of the five tiers (numbered 1-5 in bold numerals) that comprise the adenine riboswitch core (PDB ID:1Y26; ref. 3). Orange dashed lines denote hydrogen bonds. Base pairs in the secondary structure are in Leontis-Westhof symbols4. Compare with Supplementary Fig. 3. b, Structure-based sequence alignment of Squash (sq) and the V. vulnificus add adenine riboswitch aptamer domain (ar). Residue numbers correspond to Squash. Color scheme is that of Fig. 1. Asterisks and periods denote sequence identity and gaps needed to account for Squash being longer, respectively. Junction regions J1/2, J2/3 and J3/1 have no clear structural correspondence and the residues in these regions are not aligned.

Extended Data Fig. 9 Orthogonal ligand selectivity of the adenine riboswitch and Squash.

a, Fluorescence activity of the adenine riboswitch in the presence of excess DFHBI-1T, normalized to Squash fluorescence (means ± s.d., n = 3; Methods). Ordinate is discontinuous to accommodate different scale of the two samples. b, Normalized fluorescence of Squash-DFHBI-1T in the presence of varying excess of adenine.

Extended Data Fig. 10 Comparison of Squash and iSpinach recognition of DFHBI-1T.

a, Cartoon representation of the fluorophore binding site of iSpinach (PDB:7L0Z; ref. 5). Orange dashed lines denote hydrogen bonds. Residue numbers correspond to those of Spinach (ref. 6). b, Fluorescence lifetimes (Methods) of DFHBI-1T bound to Squash and iSpinach (green squares and cyan triangles, respectively; means ± s.d., n = 3). Black circles, instrument response function (IRF).

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Supplementary Tables 1–3, Extended Data Figs. 1–10, Note and refs.

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Truong, L., Kooshapur, H., Dey, S.K. et al. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol 18, 191–198 (2022). https://doi.org/10.1038/s41589-021-00931-2

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