DSSR-derived G-quadruplex features in PDB entry 5j6u
- Diy G-quadruplexes: solution structure of d(ggggtttggggttttggggaagggg) in sodium
- Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.: (2018) "Encoding canonical DNA quadruplex structure." Sci Adv, 4, eaat3007-eaat3007.
- The main challenge in DNA quadruplex design is to encode a three-dimensional structure into the primary sequence, despite its multiple, repetitive guanine segments. We identify and detail structural elements describing all 14 feasible canonical quadruplex scaffolds and demonstrate their use in control of design. This work outlines a new roadmap for implementation of targeted design of quadruplexes for material, biotechnological, and therapeutic applications.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · 4(-LwD+Ln), basket(2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.096 type=planar nts=4 GGGG A.DG1,A.DG11,A.DG25,A.DG16 2 glyco-bond=-ss- groove=w-n- planarity=0.120 type=planar nts=4 GGGG A.DG2,A.DG10,A.DG24,A.DG17 3 glyco-bond=s--s groove=w-n- planarity=0.083 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG23,A.DG18 4 glyco-bond=-ss- groove=w-n- planarity=0.075 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG19
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.