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Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI.

Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M
RNA 23 1788-1795 (2017)
Cited: 34 times
EuropePMC logo PMID: 28939697

Abstract

Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach, comprising five mutations for which the exact role has not yet been deciphered. In this work, we cocrystallized a reengineered version of iSpinach in complex with the DFHBI and solved the X-ray structure of the complex at 2 Å resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach sheds some light on the possible function of the different beneficial mutations carried by iSpinach.

Reviews - 5ob3 mentioned but not cited (2)

  1. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Neubacher S, Hennig S. Angew Chem Int Ed Engl 58 1266-1279 (2019)
  2. Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers. Trachman RJ, Ferré-D'Amaré AR. Q Rev Biophys 52 e8 (2019)

Articles - 5ob3 mentioned but not cited (10)

  1. Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI. Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M. RNA 23 1788-1795 (2017)
  2. Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET. Jeng SCY, Trachman RJ, Weissenboeck F, Truong L, Link KA, Jepsen MDE, Knutson JR, Andersen ES, Ferré-D'Amaré AR, Unrau PJ. RNA 27 433-444 (2021)
  3. An aptasensor using ceria electrodeposited-screen-printed carbon electrode for detection of epithelial sodium channel protein as a hypertension biomarker. Hartati YW, Komala DR, Hendrati D, Gaffar S, Hardianto A, Sofiatin Y, Bahti HH. R Soc Open Sci 8 202040 (2021)
  4. Identification and Characterization of New RNA Tetraloop Sequence Families. Richardson KE, Adams MS, Kirkpatrick CC, Gohara DW, Znosko BM. Biochemistry 58 4809-4820 (2019)
  5. RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair. Sampedro Vallina N, McRae EKS, Hansen BK, Boussebayle A, Andersen ES. Nucleic Acids Res 51 4613-4624 (2023)
  6. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey. Zirbel CL, Auffinger P. Molecules 27 4365 (2022)
  7. Transcription complexes as RNA chaperones. Said N, Wahl MC. Transcription 12 126-155 (2021)
  8. DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. Rekand IH, Brenk R. J Chem Inf Model 61 4068-4081 (2021)
  9. Intricate 3D architecture of a DNA mimic of GFP. Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferré-D'Amaré AR. Nature 618 1078-1084 (2023)
  10. Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach. Muhammad AM, Zari A, Alsubhi NH, Al-Zahrani MH, Alghamdi RA, Labib MM. Molecules 27 4518 (2022)


Reviews citing this publication (3)

  1. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Bouhedda F, Autour A, Ryckelynck M. Int J Mol Sci 19 E44 (2017)
  2. The emerging structural complexity of G-quadruplex RNAs. Banco MT, Ferré-D'Amaré AR. RNA 27 390-402 (2021)
  3. The Functional Meaning of 5'UTR in Protein-Coding Genes. Ryczek N, Łyś A, Makałowska I. Int J Mol Sci 24 2976 (2023)

Articles citing this publication (19)

  1. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Autour A, C Y Jeng S, D Cawte A, Abdolahzadeh A, Galli A, Panchapakesan SSS, Rueda D, Ryckelynck M, Unrau PJ. Nat Commun 9 656 (2018)
  2. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Trachman RJ, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R, Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR. Nat Chem Biol 15 472-479 (2019)
  3. RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds. Geary C, Grossi G, McRae EKS, Rothemund PWK, Andersen ES. Nat Chem 13 549-558 (2021)
  4. A Multicolor Large Stokes Shift Fluorogen-Activating RNA Aptamer with Cationic Chromophores. Steinmetzger C, Palanisamy N, Gore KR, Höbartner C. Chemistry 25 1931-1935 (2019)
  5. Aptamers as quality control tool for production, storage and biosimilarity of the anti-CD20 biopharmaceutical rituximab. Wildner S, Huber S, Regl C, Huber CG, Lohrig U, Gadermaier G. Sci Rep 9 1111 (2019)
  6. Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA. D'Ascenzo L, Vicens Q, Auffinger P. Nucleic Acids Res 46 7989-7997 (2018)
  7. Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair. Trachman RJ, Cojocaru R, Wu D, Piszczek G, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR. Structure 28 776-785.e3 (2020)
  8. DNA G-Quadruplexes Activate Heme for Robust Catalysis of Carbene Transfer Reactions. Ibrahim H, Mulyk P, Sen D. ACS Omega 4 15280-15288 (2019)
  9. Formation of an RNA Quadruplex-Duplex Hybrid in Living Cells between mRNA of the Epidermal Growth Factor Receptor (EGFR) and a G-Rich Antisense Oligoribonucleotide. Gudanis D, Kaniowski D, Kulik K, Baranowski D, Gdaniec Z, Nawrot B. Cells 9 E2375 (2020)
  10. Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine. Mieczkowski M, Steinmetzger C, Bessi I, Lenz AK, Schmiedel A, Holzapfel M, Lambert C, Pena V, Höbartner C. Nat Commun 12 3549 (2021)
  11. Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer. Steinmetzger C, Bessi I, Lenz AK, Höbartner C. Nucleic Acids Res 47 11538-11550 (2019)
  12. Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes. Baulin E, Metelev V, Bogdanov A. Nucleic Acids Res 48 8675-8685 (2020)
  13. RNA sequence and structure control assembly and function of RNA condensates. Poudyal RR, Sieg JP, Portz B, Keating CD, Bevilacqua PC. RNA 27 1589-1601 (2021)
  14. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Truong L, Kooshapur H, Dey SK, Li X, Tjandra N, Jaffrey SR, Ferré-D'Amaré AR. Nat Chem Biol 18 191-198 (2022)
  15. ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes. Farag M, Messaoudi C, Mouawad L. Nucleic Acids Res 51 2087-2107 (2023)
  16. A ribose modification of Spinach aptamer accelerates lead(ii) cation association in vitro. Savage JC, Shinde P, Bächinger HP, Davare MA, Shinde U. Chem Commun (Camb) 55 5882-5885 (2019)
  17. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer. R O'Steen M, M Kolpashchikov D. Sens Actuators Rep 4 100125 (2022)
  18. Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities. Anisuzzaman S, Geraskin IM, Ilgu M, Bendickson L, Kraus GA, Nilsen-Hamilton M. RNA 28 865-877 (2022)
  19. Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling. D'Anna L, Miclot T, Bignon E, Perricone U, Barone G, Monari A, Terenzi A. Chem Sci 14 11332-11339 (2023)


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