DSSR-derived G-quadruplex features in PDB entry 6r9l
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- A quadruplex hybrid structure with lpp loop orientation and 5 syn residues
- Karg, B., Mohr, S., Weisz, K.: (2019) "Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations." Angew.Chem.Int.Ed.Engl., 58, 11068-11071.
- The oligomer d(GCGTG3 TCAG3 TG3 TG3 ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti→syn transitions and tetrad stackings.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+Ln+P+P), hybrid-1R(1+3), UDDD
1 glyco-bond=s--- groove=w--n planarity=0.265 type=other nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13 2 glyco-bond=s--- groove=w--n planarity=0.301 type=other nts=4 GGGG A.DG6,A.DG20,A.DG16,A.DG12 3 glyco-bond=-sss groove=w--n planarity=0.275 type=other nts=4 GggG A.DG7,A.BGM19,A.BGM15,A.DG11
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.