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

PDB-id
2n9q
Class
DNA
Method
NMR
Summary
Photoswitchable G-quadruplex
Reference
Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P., Slavov, C., Jonker, H.R., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.: (2016) "Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif." Angew.Chem.Int.Ed.Engl., 55, 2738-2742.
Abstract
The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+)  ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · (2+2), UDUD · coaxial interfaces: mixed

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-s- groove=wnwn planarity=0.081 type=planar nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
 2 glyco-bond=-s-s groove=wnwn planarity=0.152 type=planar nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4
 3 glyco-bond=s-s- groove=wnwn planarity=0.072 type=planar nts=4 GGGG C.DG1,C.DG5,D.DG1,D.DG5
 4 glyco-bond=-s-s groove=wnwn planarity=0.139 type=planar nts=4 GGGG C.DG2,C.DG4,D.DG2,D.DG4

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, 4 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4
 2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1
 4  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG C.DG4,C.DG2,D.DG4,D.DG2
  step#1  mm(<>,outward)  area=10.77 rise=3.54 twist=20.4
  step#2  pp(><,inward)   area=10.36 rise=3.84 twist=-20.5
  step#3  mm(<>,outward)  area=11.81 rise=3.59 twist=18.5
  strand#1 DNA glyco-bond=-s-s nts=4 GGGG A.DG2,A.DG1,C.DG5,C.DG4
  strand#2 DNA glyco-bond=s-s- nts=4 GGGG A.DG4,A.DG5,C.DG1,C.DG2
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG B.DG2,B.DG1,D.DG5,D.DG4
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG4,B.DG5,D.DG1,D.DG2

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3 stacking diagrams
 1  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4
2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
step#1 mm(<>,outward) area=10.77 rise=3.54 twist=20.4

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 2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
3 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1
step#2 pp(><,inward) area=10.36 rise=3.84 twist=-20.5

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 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1
4 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG C.DG4,C.DG2,D.DG4,D.DG2
step#3 mm(<>,outward) area=11.81 rise=3.59 twist=18.5

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List of 2 G4-stems [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, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4
  step#1  mm(<>,outward)  area=10.77 rise=3.54 twist=20.4
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG A.DG5,A.DG4
  strand#3  U DNA glyco-bond=s- nts=2 GG B.DG1,B.DG2
  strand#4  D DNA glyco-bond=-s nts=2 GG B.DG5,B.DG4
  loop#1 type=lateral   strands=[#1,#2] nts=1 ? A.AZW3
  loop#2 type=lateral   strands=[#3,#4] nts=1 ? B.AZW3

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Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG5,D.DG1,D.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG4,D.DG2,D.DG4
  step#1  mm(<>,outward)  area=11.81 rise=3.59 twist=18.5
  strand#1  U DNA glyco-bond=s- nts=2 GG C.DG1,C.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG C.DG5,C.DG4
  strand#3  U DNA glyco-bond=s- nts=2 GG D.DG1,D.DG2
  strand#4  D DNA glyco-bond=-s nts=2 GG D.DG5,D.DG4
  loop#1 type=lateral   strands=[#1,#2] nts=1 ? C.AZW3
  loop#2 type=lateral   strands=[#3,#4] nts=1 ? D.AZW3

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [mixed]

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