Detailed DSSR results for the G-quadruplex: PDB entry 6zx7
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
- 6zx7
- Class
- DNA
- Method
- NMR
- Summary
- Antiparallel basket-type g-quadruplex DNA structure formed in human bcl-2 promoter
- Reference
- Bielskute S, Plavec J, Podbevsek P (2021): "Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter." Nucleic Acids Res., 49, 2346-2356. doi: 10.1093/nar/gkab057.
- Abstract
- Misregulation of BCL2 expression has been observed with many diseases and is associated with cellular exposure to reactive oxygen species. A region upstream of the P1 promoter in the human BCL2 gene plays a major role in regulating transcription. This G/C-rich region is highly polymorphic and capable of forming G-quadruplex structures. Herein we report that an oxidative event simulated with an 8-oxo-7,8-dihydroguanine (oxoG) substitution within a long G-tract results in a reduction of structural polymorphism. Surprisingly, oxoG within a 25-nt construct boosts thermal stability of the resulting G-quadruplex. This is achieved by distinct hydrogen bonding properties of oxoG, which facilitate formation of an antiparallel basket-type G-quadruplex with a three G-quartet core and a G·oxoG·C base triad. While oxoG has previously been considered detrimental for G-quadruplex formation, its stabilizing effect within a promoter described in this study suggests a potential novel regulatory role of oxidative stress in general and specifically in BCL2 gene transcription.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-LwD+Ln), basket(2+2), UDDU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.176 type=other nts=4 GGGG A.DG2,A.DG10,A.DG24,A.DG17 2 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.288 type=other nts=4 GGGG A.DG3,A.DG9,A.DG23,A.DG18 3 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.366 type=bowl nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG19
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-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG10,A.DG24,A.DG17 2 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG23,A.DG18 3 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG19 step#1 pp(><,inward) area=16.87 rise=3.39 twist=34.8 step#2 mm(<>,outward) area=15.12 rise=3.42 twist=18.1 strand#1 DNA glyco-bond=-s- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=s-s sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8 strand#3 DNA glyco-bond=s-s sugar=--- nts=3 GGG A.DG24,A.DG23,A.DG22 strand#4 DNA glyco-bond=-s- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19 |
| 2 stacking diagrams | |
 |
1 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG10,A.DG24,A.DG17 |
 |
2 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG23,A.DG18 |
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-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 3(-LwD+Ln), basket(2+2)
 |
1 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG10,A.DG24,A.DG17 2 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG23,A.DG18 3 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG19 step#1 pp(><,inward) area=16.87 rise=3.39 twist=34.8 step#2 mm(<>,outward) area=15.12 rise=3.42 twist=18.1 strand#1 U DNA glyco-bond=-s- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=s-s sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8 strand#3 D DNA glyco-bond=s-s sugar=--- nts=3 GGG A.DG24,A.DG23,A.DG22 strand#4 U DNA glyco-bond=-s- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19 loop#1 type=lateral strands=[#1,#2] nts=3 CGC A.DC5,A.DG6,A.DC7 loop#2 type=diagonal strands=[#2,#4] nts=6 AGGAAG A.DA11,A.DG12,A.DG13,A.DA14,A.DA15,A.DG16 loop#3 type=lateral strands=[#4,#3] nts=2 GC A.DG20,A.DC21 |