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

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 and Joseph A. Piccirilli ()
Additional contact information
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
Tudor P. Constantin: Carnegie Mellon University
Alan S. Waggoner: Carnegie Mellon University
Marcel P. Bruchez: Carnegie Mellon University
Bruce A. Armitage: Carnegie Mellon University
Joseph A. Piccirilli: The University of Chicago

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-06942-3

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