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

• DOI: 10.1038/s41467-018-06942-3
• Publication Date: 2018-10-25T11:12:02Z
• Authors: 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; Joseph A. Piccirilli
• Keywords: Aptamer; Cyanine

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 two well-resolved emission colors. Using Fab BL3-6 its cognate hairpin as crystallization module, we solved crystal structures both apo OTB-SO 3 bound forms at 2.0 Å 1.8 resolution, respectively. adopts compact, tuning fork-like architecture comprised helix short stem-loops oriented in parallel create ligand binding site through tertiary interactions. fluorophore binds planar conformation claw-like structure formed by purine base-triple, which provides stacking platform for 3, an unpaired nucleotide, partially caps from top. absence G-quartet or base tetrad makes aptamer unique among fluorogenic RNAs with known 3D structure.