Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6e82
Class
RNA
Method
X-ray (3.1 Å)
Summary
Crystal structure of the corn aptamer mutant a14u in complex with tht
Reference
Sjekloca, L., Ferre-D'Amare, A.R.: (2019) "Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence." Cell Chem Biol, 26, 1159-.
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

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 1 G-tetrad [summary · schematics · helices · stems · costacks · homepage]

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

List of 0 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

List of 0 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 3 non-stem G4-loops (including the two closing Gs)

 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