DSSR-derived G-quadruplex features in PDB entry 2jwq
- G-quadruplex recognition by quinacridines: a sar, NMR and biological study
- Hounsou, C., Guittat, L., Monchaud, D., Jourdan, M., Saettel, N., Mergny, J.L., Teulade-Fichou, M.: (2007) "G-Quadruplex Recognition by Quinacridines: a SAR, NMR, and Biological Study." ChemMedChem, 2, 655-666.
- The synthesis of a novel group of quinacridine-based ligands (MMQs) is described along with an evaluation of their G-quadruplex binding properties. A set of biophysical assays was applied to characterize their interaction with DNA quadruplexes: FRET-melting experiments and equilibrium microdialysis were used to evaluate their quadruplex affinity and their ability to discriminate quadruplexes across a broad panel of DNA structures. All data collected support the proposed model of interaction of these compounds with G-quadruplexes, which is furthermore confirmed by a solution structure determined by 2D NMR experiments. Finally, the activity of the MMQ series against tumor cell growth is reported, and the data support the potential of quadruplex-interactive compounds for use in anticancer approaches.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.380 type=other nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18 2 glyco-bond=---- groove=---- planarity=0.174 type=other nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19 3 glyco-bond=---- groove=---- planarity=0.153 type=planar nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20
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, 3 G-tetrad layers, inter-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.