DSSR-derived G-quadruplex features in PDB entry 2m91
- Structure of d[gggaagggcgcgaagcattcgcgaggtagg] quadruplex-duplex hybrid
- Lim, K.W., Phan, A.T.: (2013) "Structural Basis of DNA Quadruplex-Duplex Junction Formation." Angew.Chem.Int.Ed.Engl.
- Coaxial and orthogonal orientations of the helices (left and right illustration, respectively) in a quadruplex–duplex junction were realized by incorporating a duplex hairpin across the diverse geometries of a quadruplex. The modularity of the approach was validated through the simultaneous attachment of multiple duplex stems onto a G‐quadruplex scaffold to generate a G‐junction.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-LwD+Ln), basket(2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.105 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG30,A.DG25 2 glyco-bond=-ss- groove=w-n- planarity=0.168 type=other nts=4 GGGG A.DG2,A.DG6,A.DG29,A.DG26
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.