DSSR-derived G-quadruplex features in PDB entry 6jce
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- NMR solution and x-ray crystal structures of a DNA containing both right-and left-handed parallel-stranded G-quadruplexes
- Winnerdy, F.R., Bakalar, B., Maity, A., Vandana, J.J., Mechulam, Y., Schmitt, E., Phan, A.T.: (2019) "NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes." Nucleic Acids Res., 47, 8272-8281.
- Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU · negative twist
1 glyco-bond=---- groove=---- planarity=0.049 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14 2 glyco-bond=---- groove=---- planarity=0.113 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15 3 glyco-bond=---- groove=---- planarity=0.162 type=other nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27 4 glyco-bond=---- groove=---- planarity=0.307 type=other nts=4 GGGG A.DG20,A.DG23,A.DG26,A.DG29
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.DG18,A.DT19,A.DG20,A.DG21 2* type=V-shaped helix=#1 nts=4 GGTG A.DG26,A.DG27,A.DT28,A.DG29