DSSR-derived G-quadruplex features in PDB entry 2m93
- Structure of d[ttgggtgggcgcgaagcattcgcggggtgggt] 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
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.119 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG25,A.DG29 2 glyco-bond=---- groove=---- planarity=0.061 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG26,A.DG30 3 glyco-bond=---- groove=---- planarity=0.034 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG27,A.DG31
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.