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.

Details

Title
Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif
Author
Shelke, Sandip A 1 ; Shao, Yaming 1 ; Laski, Artur 1 ; Koirala, Deepak 1 ; Weissman, Benjamin P 2 ; Fuller, James R 1   VIAFID ORCID Logo  ; Tan, Xiaohong 3 ; Constantin, Tudor P 4 ; Waggoner, Alan S 5   VIAFID ORCID Logo  ; Bruchez, Marcel P 6   VIAFID ORCID Logo  ; Armitage, Bruce A 3 ; Piccirilli, Joseph A 7   VIAFID ORCID Logo 

1  Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA 
2  Department of Chemistry, The University of Chicago, Chicago, IL, USA 
3  Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA 
4  Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA 
5  Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA; Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, USA 
6  Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA; Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, USA 
7  Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Department of Chemistry, The University of Chicago, Chicago, IL, USA 
Pages
1-10
Publication year
2018
Publication date
Oct 2018
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-018-06942-3
ProQuest document ID
2127644382
Copyright
© 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.