Detailed DSSR results for the G-quadruplex: PDB entry 7alu
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
- 7alu
- Class
- DNA
- Method
- NMR
- Summary
- NMR structure of a DNA g-quadruplex containing two sp1 binding sites from hiv-1 promoter
- Reference
- De Rache A, Marquevielle J, Bouaziz S, Vialet B, Andreola ML, Mergny JL, Amrane S (2023): "Structure of a DNA G-quadruplex that modulates SP1 binding sites architecture in HIV-1 promoter." J.Mol.Biol., 168359. doi: 10.1016/j.jmb.2023.168359.
- Abstract
- Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacking on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reactivation or viral latency.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-Lm-Ln-P), (3+1), UDUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.208 type=other nts=4 GGGG A.DG2,A.DG20,A.DG16,A.DG12 2 glyco-bond=---- sugar=.--- groove=---- planarity=0.228 type=other nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21 3 glyco-bond=-s-- sugar=3.-- groove=wn-- planarity=0.396 type=bowl nts=4 GGGG A.DG4,A.DG9,A.DG18,A.DG22
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.DG20,A.DG16,A.DG12 2 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG21,A.DG17,A.DG11 3 glyco-bond=---s sugar=3--. groove=--nw Major-->WC nts=4 GGGG A.DG4,A.DG22,A.DG18,A.DG9 step#1 mm(<>,outward) area=11.53 rise=3.39 twist=20.5 step#2 pm(>>,forward) area=15.24 rise=3.49 twist=26.2 strand#1 DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 strand#4 DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG12,A.DG11,A.DG9 |
| 2 stacking diagrams | |
 |
1 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG16,A.DG12 |
 |
2 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG21,A.DG17,A.DG11 |
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, UDUU, hybrid-(mixed), 3(-Lm-Ln-P), (3+1)
 |
1 glyco-bond=--ss sugar=---- groove=-n-w Major-->WC nts=4 GGGG A.DG2,A.DG12,A.DG16,A.DG20 2 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21 3 glyco-bond=-s-- sugar=3.-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG18,A.DG22 step#1 mm(<>,outward) area=11.53 rise=3.39 twist=20.5 step#2 pm(>>,forward) area=15.24 rise=3.49 twist=26.2 strand#1 U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG2,A.DG3,A.DG4 strand#2* D DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG12,A.DG11,A.DG9 bulged-nts=1 T A.DT10 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 strand#4 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22 loop#1 type=lateral strands=[#1,#2] nts=4 AGGT A.DA5,A.DG6,A.DG7,A.DT8 loop#2 type=lateral strands=[#2,#3] nts=3 CCT A.DC13,A.DC14,A.DT15 loop#3 type=propeller strands=[#3,#4] nts=1 C A.DC19 |