Summary information and primary citation

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, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.208 type=other  O- nts=4 GGGG A.DG2,A.DG12,A.DG16,A.DG20
 2 glyco-bond=---- sugar=3--- groove=---- planarity=0.228 type=other  O+ nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21
 3 glyco-bond=-s-- sugar=3.-- groove=wn-- planarity=0.396 type=bowl   O+ 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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG12,A.DG16,A.DG20
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21
 3  glyco-bond=-s-- sugar=3.-- groove=wn-- WC-->Major O+ 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 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG12,A.DG11,A.DG9
  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.DG20,A.DG21,A.DG22

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG12,A.DG16,A.DG20
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21
  step#1  mm(<>,outward)  area=11.53 rise=3.39 twist=20.5

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 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21
 3  glyco-bond=-s-- sugar=3.-- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG18,A.DG22
  step#2  pm(>>,forward)  area=15.24 rise=3.49 twist=26.2

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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, UDUU, hybrid3, WARNING, 3+1, 3(-Lw-Ln-P), WARNING
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG12,A.DG16,A.DG20
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG11,A.DG17,A.DG21
 3  glyco-bond=-s-- sugar=3.-- groove=wn-- WC-->Major O+ 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=s-- sugar=-33 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

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