DSSR-derived G-quadruplex features in PDB entry 4q9q
- X-ray (2.45 Å)
- Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with fab
- Huang, H., Suslov, N.B., Li, N.S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.: (2014) "A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore." Nat.Chem.Biol., 10, 686-691.
- Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-PD+P), (2+2), UUDD
1 glyco-bond=--s- groove=-wn- planarity=0.232 type=other nts=4 GGGG R.G22,R.G26,R.G61,R.G57 2 glyco-bond=--ss groove=-w-n planarity=0.154 type=planar nts=4 GGGG R.G23,R.G27,R.G59,R.G54
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.
Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.