DSSR-derived G-quadruplex features in PDB entry 1rau
- Solution structure of an unusually stable RNA tetraplex containing g-and u-quartet structures
- Cheong, C., Moore, P.B.: (1992) "Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures." Biochemistry, 31, 8406-8414.
- A model for the solution structure of an RNA tetraplex, (rUGGGGU)4, has been obtained by two-dimensional NMR spectroscopy and molecular dynamics. The molecule is parallel stranded and Hoogsteen base-paired in 50 mM KCl, and it is so stable that three of its six imino protons have exchange half-lives measured in days at 40 degrees C. The tetraplex is stabilized by base stacking and by the hydrogen bonds in four G quartets and at least one U quartet. This is the first indication of the existence of U-quartet structures of which we are aware.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.105 type=planar nts=4 GGGG A.G2,B.G2,C.G2,D.G2 2 glyco-bond=---- groove=---- planarity=0.056 type=planar nts=4 GGGG A.G3,B.G3,C.G3,D.G3 3 glyco-bond=---- groove=---- planarity=0.063 type=planar nts=4 GGGG A.G4,B.G4,C.G4,D.G4 4 glyco-bond=---- groove=---- planarity=0.078 type=planar nts=4 GGGG A.G5,B.G5,C.G5,D.G5
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, 4 G-tetrad layers, inter-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.