DSSR-enabled G4 identification/annotation: PDB entry 7o1h
Summary information and primary citation
- PDB-id
- 7o1h
- Class
- DNA
- Method
- NMR
- Summary
- Hybrid-2r quadruplex-duplex with (-p-p-l) topology and 3 syn residues
- Reference
- Mohr S, Jana J, Vianney YM, Weisz K (2021): "Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex." Chemistry, 27, 10437-10447. doi: 10.1002/chem.202101181.
- Abstract
- Canonical G-quadruplexes can adopt a variety of different topologies depending on the arrangement of propeller, lateral, or diagonal loops connecting the four G-columns. A novel intramolecular G-quadruplex structure is derived through inversion of the last G-tract of a three-layered parallel fold, associated with the transition of a single propeller into a lateral loop. The resulting (3+1) hybrid fold features three syn⋅anti⋅anti⋅anti G-tetrads with a 3'-terminal all-syn G-column. Although the ability of forming a duplex stem-loop between G-tracts seems beneficial for a propeller-to-lateral loop rearrangement, unmodified G-rich sequences resist folding into the new (3+1) topology. However, refolding can be driven by the incorporation of syn-favoring guanosine analogues into positions of the fourth G-stretch. The presented hybrid-type G-quadruplex structure as determined by NMR spectroscopy may provide for an additional scaffold in quadruplex-based technologies.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-P-P-Lw)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---s sugar=---. groove=--wn planarity=0.160 type=planar O+ nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.088 type=planar O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.145 type=planar O+ nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
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, 3 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---s sugar=---. groove=--wn WC-->Major O+ nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major O+ nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26 step#1 pm(>>,forward) area=13.57 rise=3.39 twist=26.7 step#2 pm(>>,forward) area=12.00 rise=3.44 twist=28.4 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26 |
| 2 stacking diagrams | |
|
1 glyco-bond=---s sugar=---. groove=--wn WC-->Major O+ nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28 |
|
2 glyco-bond=---s sugar=---- groove=--wn WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27 |
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, 3 G-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 3(-P-P-Lw)
|
1 glyco-bond=---s sugar=---. groove=--wn WC-->Major O+ nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major O+ nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26 step#1 pm(>>,forward) area=13.57 rise=3.39 twist=26.7 step#2 pm(>>,forward) area=12.00 rise=3.44 twist=28.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 D DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11 loop#3 type=lateral strands=[#3,#4] nts=11 ACGCGCAGCGT A.DA15,A.DC16,A.DG17,A.DC18,A.DG19,A.DC20,A.DA21,A.DG22,A.DC23,A.DG24,A.DT25 |