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Structure-based investigation of fluorogenic Pepper aptamer.

Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A
Nat Chem Biol 17 1289-1295 (2021)
Related entries: 7eoh, 7eoi, 7eoj, 7eok, 7eol, 7eom, 7eon, 7eoo, 7eop

Cited: 14 times
EuropePMC logo PMID: 34725509

Abstract

Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.

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  2. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. Mi L, Yu Q, Karunanayake Mudiyanselage APKK, Wu R, Sun Z, Zheng R, Ren K, You M. ACS Sens 8 308-316 (2023)
  3. Structural Basis for Fluorescence Activation by Pepper RNA. Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA. ACS Chem Biol 17 1866-1875 (2022)
  4. In Silico discovery of aptamers with an enhanced library design strategy. Chen L, Zhang B, Wu Z, Liu G, Li W, Tang Y. Comput Struct Biotechnol J 21 1005-1013 (2023)
  5. Allosteric aptasensor-initiated target cycling and transcription amplification of light-up RNA aptamer for sensitive detection of protein. Song D, Yuan D, Tan X, Li L, He H, Zhao L, Yang G, Pan S, Dai H, Song X, Zhao Y. Sens Actuators B Chem 371 132526 (2022)
  6. Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells. Jiang L, Xie X, Su N, Zhang D, Chen X, Xu X, Zhang B, Huang K, Yu J, Fang M, Bao B, Zuo F, Yang L, Zhang R, Li H, Huang X, Chen Z, Zeng Q, Liu R, Lin Q, Zhao Y, Ren A, Zhu L, Yang Y. Nat Methods 20 1563-1572 (2023)
  7. Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer. Chen Z, Chen W, Reheman Z, Jiang H, Wu J, Li X. Nucleic Acids Res 51 8322-8336 (2023)
  8. Trumpet is an operating system for simple and robust cell-free biocomputing. Sharon JA, Dasrath C, Fujiwara A, Snyder A, Blank M, O'Brien S, Aufdembrink LM, Engelhart AE, Adamala KP. Nat Commun 14 2257 (2023)
  9. A novel ternary Y-DNA walker amplification strategy designed fluorescence aptasensor based on Au@SiO2@Fe3O4 nanomaterials for ochratoxin A detection. Dong X, Qi S, Qin M, Ding N, Zhang Y, Wang Z. Mikrochim Acta 190 443 (2023)
  10. A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers. Yin P, Ge M, Xie S, Zhang L, Kuang S, Nie Z. Chem Sci 14 14131-14139 (2023)
  11. AptaDB: a comprehensive database integrating aptamer-target interactions. Chen L, Yu Z, Wu Z, Zhou M, Wang Y, Yu X, Li W, Liu G, Tang Y. RNA 30 189-199 (2024)
  12. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X. Nat Commun 15 4206 (2024)


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