DSSR-enabled G4 identification/annotation: PDB entry 6qjo
Summary information and primary citation
- PDB-id
- 6qjo
- Class
- DNA
- Method
- X-ray (1.8 Å)
- Summary
- DNA containing both right- and left-handed parallel-stranded g-quadruplexes
- Reference
- Winnerdy FR, Bakalar B, Maity A, Vandana JJ, Mechulam Y, Schmitt E, Phan AT (2019): "NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes." Nucleic Acids Res., 47, 8272-8281. doi: 10.1093/nar/gkz349.
- Abstract
- Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.163 type=other O+ nts=4 GGGG 1:A.DG1,1:A.DG5,1:A.DG10,1:A.DG14 2 glyco-bond=---- sugar=.--- groove=---- planarity=0.156 type=planar O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG11,1:A.DG15 3 glyco-bond=---- sugar=---- groove=---- planarity=0.140 type=planar O+ nts=4 GGGG 1:A.DG17,1:A.DG20,1:A.DG23,1:A.DG26 4 glyco-bond=---- sugar=---- groove=---- planarity=0.239 type=other O+ nts=4 GGGG 1:A.DG19,1:A.DG22,1:A.DG25,1:A.DG28
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, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG11,1:A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG5,1:A.DG10,1:A.DG14 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG26,1:A.DG23,1:A.DG20,1:A.DG17 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG25,1:A.DG22,1:A.DG19,1:A.DG28 step#1 mp(<<,backward) area=10.09 rise=3.26 twist=34.6 step#2 mm(<>,outward) area=28.42 rise=3.36 twist=-10.5 step#3 pm(>>,forward) area=11.11 rise=3.25 twist=-27.0 strand#1 DNA glyco-bond=---- sugar=.--- nts=4 GGGG 1:A.DG2,1:A.DG1,1:A.DG26,1:A.DG25 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG6,1:A.DG5,1:A.DG23,1:A.DG22 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG11,1:A.DG10,1:A.DG20,1:A.DG19 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG15,1:A.DG14,1:A.DG17,1:A.DG28 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG11,1:A.DG15 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG5,1:A.DG10,1:A.DG14 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG26,1:A.DG23,1:A.DG20,1:A.DG17 |
List of 1 G4-stem
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, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG5,1:A.DG10,1:A.DG14 2 glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG6,1:A.DG11,1:A.DG15 step#1 pm(>>,forward) area=10.09 rise=3.26 twist=34.6 strand#1 U DNA glyco-bond=-- sugar=-. nts=2 GG 1:A.DG1,1:A.DG2 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG5,1:A.DG6 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG10,1:A.DG11 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG14,1:A.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 TT 1:A.DT3,1:A.DT4 loop#2 type=propeller strands=[#2,#3] nts=3 TGT 1:A.DT7,1:A.DG8,1:A.DT9 loop#3 type=propeller strands=[#3,#4] nts=2 TT 1:A.DT12,1:A.DT13 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG 1:A.DG17,1:A.DT18,1:A.DG19,1:A.DG20 2* type=V-shaped helix=#1 nts=4 GGTG 1:A.DG25,1:A.DG26,1:A.DT27,1:A.DG28