Summary information and primary citation

PDB-id
8jih
Class
DNA
Method
NMR
Summary
Human telomere two-quartet g-quadruplex at ph 5.0
Reference
Galer P, Wang B, Plavec J, Sket P (2023): "Unveiling the structural mechanism of a G-quadruplex pH-Driven switch." Biochimie, 214, 73-82. doi: 10.1016/j.biochi.2023.08.002.
Abstract
The human telomere oligonucleotide, d[TAGGG(TTAGGG)<sub>2</sub>TTAGG] (TAGGG), can adopt two distinct 2-G-quartet G-quadruplex structures at pH 7.0 and 5.0, referred to as the TD and KDH<sub>+</sub> forms, respectively. By using a combination of NMR and computational techniques, we determined high-resolution structures of both forms, which revealed unique loop architectures, base triples, and base pairs that play a crucial role in the pH-driven structural transformation of TAGGG. Our study demonstrated that TAGGG represents a reversible pH-driven switch system where the stability and pH-induced structural transformation of the G-quadruplexes are influenced by the terminal residues and base triples. Gaining insight into the factors that regulate the formation of G-quadruplexes and their pH-sensitive structural equilibrium holds great potential for the rational design of novel DNA based pH-driven switches. These advancements in understanding create exciting opportunities for applications in the field of nanotechnology, specifically in the development of bio-nano-motors.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UUDD, anti-parallel:basket2, 2+2, 2(+LnD-Lw)

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List of 2 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.226 type=other  N+ nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.123 type=planar N- nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9

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=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=22.37 rise=3.44 twist=10.1
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17
  strand#3 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9

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1 stacking diagram 
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=22.37 rise=3.44 twist=10.1

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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, UUDD, anti-parallel:basket2, 2+2, 2(+LnD-Lw)
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC N+ nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major N- nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=22.37 rise=3.44 twist=10.1
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  loop#1 type=lateral   strands=[#1,#4] nts=4 GTTA A.DG5,A.DT6,A.DT7,A.DA8
  loop#2 type=diagonal  strands=[#4,#2] nts=5 GTTAG A.DG11,A.DT12,A.DT13,A.DA14,A.DG15
  loop#3 type=lateral   strands=[#2,#3] nts=3 TTA A.DT18,A.DT19,A.DA20

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