Summary information and primary citation

PDB-id
9i5s
Class
DNA
Method
NMR
Summary
Solution structure of an intramolecular anti-parallel g-quadruplex with a 5'-end overhang.
Reference
Avendano Avila C, Heddi B (2025): "An antiparallel G-quadruplex structure with a 5'-end overhang forms predominantly at the human telomeric ds-ss DNA junction." Chem.Commun.(Camb.), 61, 17661-17664. doi: 10.1039/d5cc03633j.
Abstract
G-quadruplex structures formed by human telomeric sequences are highly sensitive to subtle sequence variations and local environment. While most structural studies have focused on sequences containing four uninterrupted G-tracts, the structural consequences of splitting a G-tract remain unexplored. Here, we present the NMR solution structure of a human telomeric sequence with the first G-tract split. The structure adopts an antiparallel topology with a disordered GTT segment at the 5'-end. This conformation is preferentially formed at a biologically relevant double-strand/single-strand DNA junction. These findings broaden our understanding of the structural diversity of human telomeric G-quadruplexes.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)

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List of 2 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.096 type=planar N- nts=4 GGGG A.DG5,A.DG12,A.DG24,A.DG18
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.060 type=planar N+ nts=4 GgGG A.DG6,A.BGM11,A.DG23,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, 2 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG5,A.DG12,A.DG24,A.DG18
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GgGG A.DG6,A.BGM11,A.DG23,A.DG19
  step#1  mm(<>,outward)  area=12.15 rise=3.63 twist=20.2
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG5,A.DG6
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 Gg A.DG12,A.BGM11
  strand#3 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG24,A.DG23
  strand#4 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG18,A.DG19

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1 stacking diagram 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG5,A.DG12,A.DG24,A.DG18
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GgGG A.DG6,A.BGM11,A.DG23,A.DG19
  step#1  mm(<>,outward)  area=12.15 rise=3.63 twist=20.2

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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, 2 G-tetrads, 3 loops, INTRA-molecular, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG A.DG5,A.DG12,A.DG24,A.DG18
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GgGG A.DG6,A.BGM11,A.DG23,A.DG19
  step#1  mm(<>,outward)  area=12.15 rise=3.63 twist=20.2
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG5,A.DG6
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 Gg A.DG12,A.BGM11
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG24,A.DG23
  strand#4  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG18,A.DG19
  loop#1 type=lateral   strands=[#1,#2] nts=4 GTTA A.DG7,A.DT8,A.DT9,A.DA10
  loop#2 type=diagonal  strands=[#2,#4] nts=5 GTTAG A.DG13,A.DT14,A.DT15,A.DA16,A.DG17
  loop#3 type=lateral   strands=[#4,#3] nts=3 TTA A.DT20,A.DT21,A.DA22

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