DSSR-derived G-quadruplex features in PDB entry 2gku
- Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures
- Luu, K.N., Phan, A.T., Kuryavyi, V.V., Lacroix, L., Patel, D.J.: (2006) "Structure of the human telomere in k(+) solution: an intramolecular (3 + 1) g-quadruplex scaffold." J.Am.Chem.Soc., 128, 9963-9970.
- We present the intramolecular G-quadruplex structure of human telomeric DNA in physiologically relevant K(+) solution. This G-quadruplex, whose (3 + 1) topology differs from folds reported previously in Na(+) solution and in a K(+)-containing crystal, involves the following: one anti.syn.syn.syn and two syn.anti.anti.anti G-tetrads; one double-chain reversal and two edgewise loops; three G-tracts oriented in one direction and the fourth in the opposite direction. The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-Lw-Ln), hybrid-1(3+1), UUDU
1 glyco-bond=ss-s groove=-wn- planarity=0.161 type=other nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21 2 glyco-bond=--s- groove=-wn- planarity=0.141 type=planar nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- groove=-wn- planarity=0.233 type=bowl nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
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-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.