Detailed DSSR results for the G-quadruplex: PDB entry 2jwq
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
- 2jwq
- Class
- DNA
- Method
- NMR
- Summary
- G-quadruplex recognition by quinacridines: a sar, NMR and biological study
- Reference
- Hounsou C, Guittat L, Monchaud D, Jourdan M, Saettel N, Mergny JL, Teulade-Fichou M (2007): "G-Quadruplex Recognition by Quinacridines: a SAR, NMR, and Biological Study." ChemMedChem, 2, 655-666. doi: 10.1002/cmdc.200600286.
- Abstract
- 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
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.380 type=other nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18 2 glyco-bond=---- sugar=---- groove=---- planarity=0.174 type=other nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19 3 glyco-bond=---- sugar=---- groove=---- planarity=0.153 type=planar nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20
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, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20 step#1 pm(>>,forward) area=12.11 rise=3.39 twist=31.6 step#2 pm(>>,forward) area=12.97 rise=3.22 twist=23.9 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG25,D.DG26,D.DG27 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG18,C.DG19,C.DG20 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19 |
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, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20 step#1 pm(>>,forward) area=12.11 rise=3.39 twist=31.6 step#2 pm(>>,forward) area=12.97 rise=3.22 twist=23.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG25,D.DG26,D.DG27 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG18,C.DG19,C.DG20 |