DSSR-derived G-quadruplex features in PDB entry 3nyp
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- X-ray (1.18 Å)
- A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains
- Campbell, N.H., Smith, D.L., Reszka, A.P., Neidle, S., O'Hagan, D.: (2011) "Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA." Org.Biomol.Chem., 9, 1328-1331.
- Comparative X-ray structure studies reveal that C-F bond incorporation into the peripheral pyrrolidine moieties of the G-quadruplex DNA binding ligand BSU6039 leads to a distinct pyrrolidine ring conformation, relative to the non-fluorinated analogue, and with a different binding mode involving reversal of the pyrrolidinium N(+)-H orientation.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.268 type=bowl nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9 2 glyco-bond=-ss- groove=w-n- planarity=0.179 type=other nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10 3 glyco-bond=s--s groove=w-n- planarity=0.170 type=other nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11 4 glyco-bond=-ss- groove=w-n- planarity=0.211 type=other nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
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 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.