DSSR-derived G-quadruplex features in PDB entry 5v3f
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 (1.7 Å)
- Co-crystal structure of the fluorogenic RNA mango
- Trachman, R.J., Demeshkina, N.A., Lau, M.W.L., Panchapakesan, S.S.S., Jeng, S.C.Y., Unrau, P.J., Ferre-D'Amare, A.R.: (2017) "Structural basis for high-affinity fluorophore binding and activation by RNA Mango." Nat. Chem. Biol., 13, 807-813.
- Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'
1 glyco-bond=---- groove=---- planarity=0.339 type=bowl-2 nts=4 GGGG A.G8,A.G13,A.G18,A.G23 2 glyco-bond=---- groove=---- planarity=0.185 type=saddle nts=4 GGGG A.G9,A.G14,A.G19,A.G24 3 glyco-bond=s--- groove=w--n planarity=0.283 type=other nts=4 GGGG A.G10,A.G16,A.G21,A.G26 4 glyco-bond=---- groove=---- planarity=0.349 type=bowl-2 nts=4 GGGG B.G8,B.G13,B.G18,B.G23 5 glyco-bond=---- groove=---- planarity=0.182 type=saddle nts=4 GGGG B.G9,B.G14,B.G19,B.G24 6 glyco-bond=s--- groove=w--n planarity=0.283 type=other nts=4 GGGG B.G10,B.G16,B.G21,B.G26
Helix#1, 6 G-tetrad layers, inter-molecular, with 2 stems
Stem#1, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
Stem#2, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']