DSSR-derived G-quadruplex features in PDB entry 5lqh
- A two-quartet G-quadruplex formed by human telomere in kcl solution at ph 5.0
- 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.
- 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
1 glyco-bond=ss-- groove=-w-n planarity=0.211 type=other nts=4 GGGG A.DG3,A.DG16,A.DG22,A.DG10 2 glyco-bond=--ss groove=-w-n planarity=0.154 type=planar nts=4 GGGG A.DG4,A.DG17,A.DG21,A.DG9
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
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.