Detailed DSSR results for the G-quadruplex: PDB entry 2ms6
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
- 2ms6
- Class
- DNA
- Method
- NMR
- Summary
- Human telomeric g-quadruplex DNA sequence (ttagggt)4 complexed with flavonoid quercetin
- Reference
- Tawani A, Kumar A (2015): "Structural Insight into the interaction of Flavonoids with Human Telomeric Sequence." Sci Rep, 5, 17574. doi: 10.1038/srep17574.
- Abstract
- Flavonoids are a group of naturally available compounds that are an attractive source for drug discovery. Their potential to act as anti-tumourigenic and anti-proliferative agents has been reported previously but is not yet fully understood. Targeting human telomeric G-quadruplex DNA could be one of the mechanisms by which these flavonoids exert anticancer activity. We have performed detailed biophysical studies for the interaction of four representative flavonoids, Luteolin, Quercetin, Rutin and Genistein, with the human telomeric G-quadruplex sequence tetramolecular d-(T2AG3T) (Tel7). In addition, we used NMR spectroscopy to derive the first model for the complex formed between Quercetin and G-quadruplex sequence. The model showed that Quercetin stabilises the G-quadruplex structure and does not open the G-tetrad. It interacts with the telomeric sequence through π-stacking at two sites: between T1pT2 and between G6pT7. Based on our findings, we suggest that Quercetin could be a potent candidate for targeting the telomere and thus, act as a potent anti-cancer agent.
- 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=0.576 type=bowl nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 2 glyco-bond=---- sugar=---- groove=---- planarity=0.531 type=bowl nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 3 glyco-bond=---- sugar=33-- groove=---- planarity=0.356 type=saddle nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13
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,C.DG18,B.DG11 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 3 glyco-bond=---- sugar=33-- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13 step#1 pm(>>,forward) area=8.75 rise=3.75 twist=26.4 step#2 pm(>>,forward) area=10.27 rise=3.64 twist=29.2 strand#1 DNA glyco-bond=--- sugar=--3 nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=--- sugar=.-3 nts=3 GGG D.DG25,D.DG26,D.DG27 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG18,C.DG19,C.DG20 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 |
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,C.DG18,B.DG11 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 3 glyco-bond=---- sugar=33-- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13 step#1 pm(>>,forward) area=8.75 rise=3.75 twist=26.4 step#2 pm(>>,forward) area=10.27 rise=3.64 twist=29.2 strand#1 U DNA glyco-bond=--- sugar=--3 nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=--- sugar=.-3 nts=3 GGG D.DG25,D.DG26,D.DG27 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG18,C.DG19,C.DG20 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13 |