Detailed DSSR results for the G-quadruplex: PDB entry 6e82

PDB id

6e82

Class

RNA

Method

X-ray (3.101 Å)

Summary

Crystal structure of the corn aptamer mutant a14u in complex with tht

Reference

Sjekloca L, Ferre-D'Amare AR (2019): "Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence." Cell Chem Biol, 26, 1159. doi: 10.1016/j.chembiol.2019.04.012.

Abstract

Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.

G4 notes

1 G-tetrad

 1 glyco-bond=---- sugar=-333 groove=---- planarity=0.396 type=other  nts=4 GGGG A.G12,A.G15,A.G22,A.G25

 1 type=lateral   helix=#-1 nts=4 GGUG A.G12,A.G13,A.U14,A.G15
 2 type=lateral   helix=#-1 nts=8 GGUCUGAG A.G15,A.G16,A.U17,A.C18,A.U19,A.G20,A.A21,A.G22
 3 type=lateral   helix=#-1 nts=4 GGAG A.G22,A.G23,A.A24,A.G25