Detailed DSSR results for the G-quadruplex: PDB entry 7z9l
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 7z9l
- Class
- DNA
- Method
- NMR
- Summary
- Phen-dc3 intercalation causes hybrid-to-antiparallel transformation of human telomeric DNA g-quadruplex
- Reference
- Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J (2022): "Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation." Angew.Chem.Int.Ed.Engl., 61, e202207384. doi: 10.1002/anie.202207384.
- Abstract
- Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high resolution. Here we report that Phen-DC3 , one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG)3 to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(+Ln+Lw+Ln), chair(2+2), UDUD
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=s-s- sugar=3--- groove=wnwn planarity=0.227 type=other nts=4 GGGG A.DG3,A.DG23,A.DG15,A.DG11 2 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.227 type=other nts=4 GGGG A.DG4,A.DG22,A.DG16,A.DG10 3 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.176 type=other nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG9
List of 1 G4-helix
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
 |
1 glyco-bond=s-s- sugar=3--- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG23,A.DG15,A.DG11 2 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG22,A.DG16,A.DG10 3 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG9 step#1 mp(<<,backward) area=0.00 rise=6.67 twist=19.2 step#2 mm(<>,outward) area=19.99 rise=3.42 twist=15.2 strand#1 DNA glyco-bond=ss- sugar=3-- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG23,A.DG22,A.DG21 strand#3 DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 strand#4 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG11,A.DG10,A.DG9 |
| 2 stacking diagrams | |
 |
1 glyco-bond=s-s- sugar=3--- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG23,A.DG15,A.DG11 |
 |
2 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG22,A.DG16,A.DG10 |
List of 1 G4-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.
Stem#1, 3 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 3(+Ln+Lw+Ln), chair(2+2)
 |
1 glyco-bond=s-s- sugar=3--- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG23,A.DG15,A.DG11 2 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG22,A.DG16,A.DG10 3 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG9 step#1 mp(<<,backward) area=0.00 rise=6.67 twist=19.2 step#2 mm(<>,outward) area=19.99 rise=3.42 twist=15.2 strand#1 U DNA glyco-bond=ss- sugar=3-- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG23,A.DG22,A.DG21 strand#3 U DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 strand#4 D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG11,A.DG10,A.DG9 loop#1 type=lateral strands=[#1,#4] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=lateral strands=[#4,#3] nts=3 TTA A.DT12,A.DT13,A.DA14 loop#3 type=lateral strands=[#3,#2] nts=3 TTA A.DT18,A.DT19,A.DA20 |