DSSR-PyMOL cartoon-block schematics: PDB entry 8u5k

PDB-id

8u5k; DSSR-derived features in text and JSON formats

Class

RNA

Method

X-ray (2.8 Å)

Summary

Structure of mango ii aptamer bound to t01-6a

Reference

Lu X, Passalacqua LFM, Nodwell M, Kong KYS, Caballero-Garcia G, Dolgosheina EV, Ferre-D'Amare AR, Britton R, Unrau PJ (2024): "Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD." Nucleic Acids Res., 52, 8039-8051. doi: 10.1093/nar/gkae493.

Abstract

Artificial RNA tags that tightly bind fluorogenic ligands have many RNA imaging and RNA-protein biomolecular purification applications. Here, we report and structurally characterize a very small (20-nt) biologically compatible G-quadruplex based aptamer that can be inserted into commonly found GNRA tetraloops. This aptamer binds its fluorogenic ligand with an unprecedented picomolar binding affinity and is very stable against thermal and chemical insults. As the ligand can be modified to include biotin, this RNA tag can also be bound to streptavidin magnetic beads. After washing, tagged RNA can be cleanly eluted by exposing the beads to intense green light, which photobleaches the bound fluorogenic ligand, triggering the release of the bound RNA complex.