DSSR-derived G-quadruplex features in PDB entry 2n9q
- Photoswitchable G-quadruplex
- Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P., Slavov, C., Jonker, H.R., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.: (2016) "Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif." Angew.Chem.Int.Ed.Engl., 55, 2738-2742.
- The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+) ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · (2+2), UDUD · coaxial interfaces: mixed
1 glyco-bond=s-s- groove=wnwn planarity=0.081 type=planar nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5 2 glyco-bond=-s-s groove=wnwn planarity=0.152 type=planar nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4 3 glyco-bond=s-s- groove=wnwn planarity=0.072 type=planar nts=4 GGGG C.DG1,C.DG5,D.DG1,D.DG5 4 glyco-bond=-s-s groove=wnwn planarity=0.139 type=planar nts=4 GGGG C.DG2,C.DG4,D.DG2,D.DG4
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, 4 G-tetrad layers, inter-molecular, with 2 stems
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)
Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [mixed]