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Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif

Author

Listed:
  • Sandip A. Shelke

    (The University of Chicago)

  • Yaming Shao

    (The University of Chicago)

  • Artur Laski

    (The University of Chicago)

  • Deepak Koirala

    (The University of Chicago)

  • Benjamin P. Weissman

    (The University of Chicago)

  • James R. Fuller

    (The University of Chicago)

  • Xiaohong Tan

    (Carnegie Mellon University
    Carnegie Mellon University)

  • Tudor P. Constantin

    (Carnegie Mellon University)

  • Alan S. Waggoner

    (Carnegie Mellon University
    Carnegie Mellon University)

  • Marcel P. Bruchez

    (Carnegie Mellon University
    Carnegie Mellon University
    Carnegie Mellon University)

  • Bruce A. Armitage

    (Carnegie Mellon University
    Carnegie Mellon University)

  • Joseph A. Piccirilli

    (The University of Chicago
    The University of Chicago)

Abstract

The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.

Suggested Citation

  • Sandip A. Shelke & Yaming Shao & Artur Laski & Deepak Koirala & Benjamin P. Weissman & James R. Fuller & Xiaohong Tan & Tudor P. Constantin & Alan S. Waggoner & Marcel P. Bruchez & Bruce A. Armitage &, 2018. "Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06942-3
    DOI: 10.1038/s41467-018-06942-3
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    Cited by:

    1. Yufan Zhang & Zhonghe Xu & Yu Xiao & Haodong Jiang & Xiaobing Zuo & Xing Li & Xianyang Fang, 2024. "Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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