SNAP output for PDB entry 6db8 [SNAP web server]

PDB-id

6db8; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA-immune system

Method

X-ray (1.87 Å)

Summary

Structural basis for promiscuous binding and activation of fluorogenic dyes by dir2s RNA aptamer

Reference

Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA (2018): "Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif." Nat Commun, 9, 4542. doi: 10.1038/s41467-018-06942-3.

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-SO_3, 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.