Detailed DSSR results for the G-quadruplex: PDB entry 2n9q
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
- 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, (2+2), UDUD, coaxial interfaces: mixed
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=s-s- sugar=-.-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 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-tetrad layers, 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 groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5 3 glyco-bond=-s-s sugar=.-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=--.- nts=4 GGGG A.DG2,A.DG1,C.DG5,C.DG4 strand#2 DNA glyco-bond=s-s- sugar=-.-- 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 |
| 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 groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG5,B.DG1,B.DG5 |
 |
3 glyco-bond=-s-s sugar=.-3- groove=wnwn WC-->Major nts=4 GGGG C.DG5,C.DG1,D.DG5,D.DG1 |
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-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)
 |
1 glyco-bond=s-s- sugar=-.-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=.- 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 loop#1 type=lateral strands=[#1,#2] nts=1 ? A.AZW3 loop#2 type=lateral strands=[#3,#4] nts=1 ? B.AZW3 |
Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)
 |
1 glyco-bond=s-s- sugar=-.-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=.- 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 loop#1 type=lateral strands=[#1,#2] nts=1 ? C.AZW3 loop#2 type=lateral strands=[#3,#4] nts=1 ? D.AZW3 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [mixed]