DSSR-derived G-quadruplex features in PDB entry 2ms9
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- Solution structure of a G-quadruplex
- Chung, W.J., Heddi, B., Schmitt, E., Lim, K.W., Mechulam, Y., Phan, A.T.: (2015) "Structure of a left-handed DNA G-quadruplex." Proc.Natl.Acad.Sci.USA
- Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · 2(+P+P+P), parallel(4+0), UUUU · negative twist
1 glyco-bond=s--- groove=w--n planarity=0.467 type=other nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5 2 glyco-bond=---- groove=---- planarity=0.275 type=other nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12 3 glyco-bond=---- groove=---- planarity=0.182 type=other nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24 4 glyco-bond=---- groove=---- planarity=0.466 type=other nts=4 GGGG A.DG17,A.DG20,A.DG23,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, 4 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(+P+P+P), parallel(4+0)
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG A.DG15,A.DT16,A.DG17,A.DG18 2* type=V-shaped helix=#1 nts=4 GGTG A.DG23,A.DG24,A.DT25,A.DG26