DSSR-derived G-quadruplex features in PDB entry 5cdb
- X-ray (1.7 Å)
- Structure of the complex of a bimolecular human telomeric DNA with a 13-diphenylalkyl berberine derivative
- Ferraroni, M., Bazzicalupi, C., Papi, F., Fiorillo, G., Guaman-Ortiz, L.M., Nocentini, A., Scovassi, A.I., Lombardi, P., Gratteri, P.: (2016) "Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes." Chem Asian J, 11, 1107-1115.
- The interaction between 13-phenylalkyl and 13-diphenylalkyl berberine derivatives (NAX) and human telomeric DNA G4 structures has been investigated by both spectroscopic and crystallographic methods. NAX042 and NAX053 are the best compounds improving the performance of the natural precursor berberine. This finding is in agreement with the X-ray diffraction result for the NAX053-Tel12 adduct, showing the ligand which interacts via π-stacking, sandwiched at the interface of two symmetry-related quadruplex units, with its benzhydryl group contributing to the overall stability of the adduct by means of additional π-stacking interactions with the DNA residues. The berberine derivatives were also investigated for their cytotoxic activity towards a panel of human cancer cell lines. Compounds NAX042 and NAX053 affect the viability of cancer cell lines in a dose-dependent manner.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.175 type=bowl-2 nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- groove=---- planarity=0.148 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- groove=---- planarity=0.301 type=bowl nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
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.