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

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, J.L., Teulade-Fichou, M.: (2007) "G-Quadruplex Recognition by Quinacridines: a SAR, NMR, and Biological Study." ChemMedChem, 2, 655-666.
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 [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=0.380 type=other  nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18
 2 glyco-bond=---- groove=---- planarity=0.174 type=other  nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19
 3 glyco-bond=---- groove=---- planarity=0.153 type=planar nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20

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

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG25,B.DG11,C.DG18
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19
step#1 pm(>>,forward) area=12.11 rise=3.39 twist=31.6

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG26,B.DG12,C.DG19
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,D.DG27,B.DG13,C.DG20
step#2 pm(>>,forward) area=12.97 rise=3.22 twist=23.9

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

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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)