Summary information [schematics · tetrads · helices · stems · costacks · homepage]

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, 17574-17574.
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 [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.576 type=bowl   nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11
 2 glyco-bond=---- groove=---- planarity=0.531 type=bowl   nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12
 3 glyco-bond=---- groove=---- planarity=0.356 type=saddle nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12
 3  glyco-bond=---- 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=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--- nts=3 GGG D.DG25,D.DG26,D.DG27
  strand#3 DNA glyco-bond=--- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12
step#1 pm(>>,forward) area=8.75 rise=3.75 twist=26.4

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Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13
step#2 pm(>>,forward) area=10.27 rise=3.64 twist=29.2

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12
 3  glyco-bond=---- 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=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=--- nts=3 GGG D.DG25,D.DG26,D.DG27
  strand#3  U DNA glyco-bond=--- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)