Summary information and primary citation

PDB-id
8qn2
Class
gene regulation
Method
X-ray (2.51 Å)
Summary
Helical foldamers as selective g-quadruplex ligands
Reference
Koenig A, Laffile V, Largy E, Thore S, Mackereth C, Ferrand Y, Gabelica V (2025): "Helical aromatic oligoamide foldamers as selective G-quadruplex ligands." Nucleic Acids Res. doi: 10.1093/nar/gkaf1365.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.079 type=planar O+ nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.131 type=planar O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.309 type=bowl   O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#1  pm(>>,forward)  area=10.56 rise=3.37 twist=31.2
  step#2  pm(>>,forward)  area=15.86 rise=3.49 twist=24.3
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
  step#1  pm(>>,forward)  area=10.56 rise=3.37 twist=31.2

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#2  pm(>>,forward)  area=15.86 rise=3.49 twist=24.3

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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, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#1  pm(>>,forward)  area=10.56 rise=3.37 twist=31.2
  step#2  pm(>>,forward)  area=15.86 rise=3.49 twist=24.3
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT5,A.DT6
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT10,A.DT11
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT15,A.DT16

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