DSSR-derived G-quadruplex features in PDB entry 2m92
- Structure of d[agggtgggtgctggggcgcgaagcattcgcgagg] 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 · 2(-PX+P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.068 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 2 glyco-bond=---- groove=---- planarity=0.141 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG33,A.DG14 3 glyco-bond=---- groove=---- planarity=0.100 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG34,A.DG15
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.
Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)
List of 2 non-stem G4-loops (including the two closing Gs)
1* type=V-shaped helix=#1 nts=5 GGGTG A.DG6,A.DG7,A.DG8,A.DT9,A.DG10 2 type=lateral helix=#1 nts=4 GCTG A.DG10,A.DC11,A.DT12,A.DG13