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Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells

  • Aruni P. K. K. Karunanayake Mudiyanselage
    Aruni P. K. K. Karunanayake Mudiyanselage
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
  • Qikun Yu
    Qikun Yu
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
    More by Qikun Yu
  • Mark A. Leon-Duque
    Mark A. Leon-Duque
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
  • Bin Zhao
    Bin Zhao
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
    More by Bin Zhao
  • Rigumula Wu
    Rigumula Wu
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
    More by Rigumula Wu
  • , and 
  • Mingxu You*
    Mingxu You
    Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
    *[email protected]
    More by Mingxu You
Cite this: J. Am. Chem. Soc. 2018, 140, 28, 8739–8745
Publication Date (Web):June 26, 2018
https://doi.org/10.1021/jacs.8b03956
Copyright © 2018 American Chemical Society

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    Abstract

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    DNA and RNA nanotechnology has been used for the development of dynamic molecular devices. In particular, programmable enzyme-free nucleic acid circuits, such as catalytic hairpin assembly, have been demonstrated as useful tools for bioanalysis and to scale up system complexity to an extent beyond current cellular genetic circuits. However, the intracellular functions of most synthetic nucleic acid circuits have been hindered by challenges in the biological delivery and degradation. On the other hand, genetically encoded and transcribed RNA circuits emerge as alternative powerful tools for long-term embedded cellular analysis and regulation. Herein, we reported a genetically encoded RNA-based catalytic hairpin assembly circuit for sensitive RNA imaging inside living cells. The split version of Broccoli, a fluorogenic RNA aptamer, was used as the reporter. One target RNA can catalytically trigger the fluorescence from tens-to-hundreds of Broccoli. As a result, target RNAs can be sensitively detected. We have further engineered our circuit to allow easy programming to image various target RNA sequences. This design principle opens the arena for developing a large variety of genetically encoded RNA circuits for cellular applications.

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