DSSR-derived G-quadruplex features in PDB entry 6e82
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- X-ray (3.1 Å)
- Crystal structure of the corn aptamer mutant a14u in complex with tht
- 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-.
- 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=---- groove=---- planarity=0.396 type=other nts=4 GGGG A.G12,A.G15,A.G22,A.G25
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