Summary information

PDB id
5lqh
Class
DNA
Method
NMR
Summary
A two-quartet g-quadruplex formed by human telomere in kcl solution at ph 5.0
Reference
Galer P, Wang B, Sket P, Plavec J (2016): "Reversible pH Switch of Two-Quartet G-Quadruplexes Formed by Human Telomere." Angew.Chem.Int.Ed.Engl., 55, 1993-1997. doi: 10.1002/anie.201507569.
Abstract
A four-repeat human telomere DNA sequence without the 3'-end guanine, d[TAGGG(TTAGGG)2 TTAGG] (htel1-ΔG23) has been found to adopt two distinct two G-quartet antiparallel basket-type G-quadruplexes, TD and KDH(+) in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH(+) form is distinctive with unique protonated T18⋅A20(+) ⋅G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G-quadruplexes in general. Specific stacking interactions amongst two G-quartets flanking base triples and base pairs in TD and KDH(+) forms are reflected in 10 K higher thermal stability of KDH(+) . Populations of TD and KDH(+) forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1-ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+LnD-Lw), basket(2+2), UUDD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.211 type=other  nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.154 type=planar 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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=16.59 rise=3.45 twist=16.3
  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 nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=16.59 rise=3.45 twist=16.3

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 2(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
  step#1  mm(<>,outward)  area=16.59 rise=3.45 twist=16.3
  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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