DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 2n9q
Class: DNA
Method: NMR
Summary: Photoswitchable g-quadruplex
Reference: Thevarpadam J, Bessi I, Binas O, Goncalves DP, Slavov C, Jonker HR, 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. doi: 10.1002/anie.201510269.
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, UDUD, anti-parallel:chair, 2+2, coaxial interfaces: mixed

Cartoon-block schematics in six views (download the tarball)

List of 4 G-tetrads

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

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, 4 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4 2* glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5 3 glyco-bond=-s-s sugar=3-3- groove=wnwn WC-->Major -- nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1 4 glyco-bond=s-s- sugar=---- 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 sugar=--3- nts=4 GGGG A.DG2,A.DG1,C.DG5,C.DG4 strand#2 DNA glyco-bond=s-s- sugar=-3-- nts=4 GGGG A.DG4,A.DG5,C.DG1,C.DG2 strand#3 DNA glyco-bond=-s-s sugar=--3- nts=4 GGGG B.DG2,B.DG1,D.DG5,D.DG4 strand#4 DNA glyco-bond=s-s- sugar=-3-- nts=4 GGGG B.DG4,B.DG5,D.DG1,D.DG2 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG2,A.DG4,B.DG2,B.DG4 2* glyco-bond=s-s- sugar=-3-3 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 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5 3 glyco-bond=-s-s sugar=3-3- 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 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=-s-s sugar=3-3- groove=wnwn WC-->Major -- nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1 4 glyco-bond=s-s- sugar=---- 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 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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-tetrads, 0 loops, inter-molecular, UDUD, anti-parallel:chair, 2+2

 1  glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5
 2  glyco-bond=-s-s sugar=---- 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- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=3- nts=2 GG A.DG5,A.DG4
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#4  D DNA glyco-bond=-s sugar=3- nts=2 GG B.DG5,B.DG4

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 2 G-tetrads, 0 loops, inter-molecular, UDUD, anti-parallel:chair, 2+2

 1  glyco-bond=s-s- sugar=-3-3 groove=wnwn Major-->WC -- nts=4 GGGG C.DG1,C.DG5,D.DG1,D.DG5
 2  glyco-bond=-s-s sugar=---- 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- sugar=-- nts=2 GG C.DG1,C.DG2
  strand#2  D DNA glyco-bond=-s sugar=3- nts=2 GG C.DG5,C.DG4
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG1,D.DG2
  strand#4  D DNA glyco-bond=-s sugar=3- nts=2 GG D.DG5,D.DG4