DSSR-derived G-quadruplex features in PDB entry 3r6r
- X-ray (2.4 Å)
- Structure of the complex of an intramolecular human telomeric DNA with berberine formed in k+ solution
- Bazzicalupi, C., Ferraroni, M., Bilia, A.R., Scheggi, F., Gratteri, P.: (2013) "The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1." Nucleic Acids Res., 41, 632-638.
- The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features all-parallel strands. The overall folding assumed by DNA is the same found in previously reported crystal structures. Similarly to previously reported structures the ligand molecules were found to be stacked onto the external 5' and 3'-end G-tetrads. However, the present crystal structure highlighted for the first time, the presence of two berberine molecules in the two binding sites, directly interacting with each tetrad. As a consequence, our structural data point out a 2:1 ligand to G-tetrad molar ratio, which has never been reported before in a telomeric intramolecular quadruplex structure.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.100 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 2 glyco-bond=---- groove=---- planarity=0.149 type=planar nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=---- groove=---- planarity=0.221 type=bowl nts=4 GGGG A.DG5,A.DG11,A.DG17,A.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, 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.