DSSR-derived G-quadruplex features in PDB entry 6f4z
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- 2'f-arag modified quadruplex with flipped g-tract and central tetrad
- Dickerhoff, J., Weisz, K.: (2018) "Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway." Chembiochem, 19, 927-930.
- A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+LnD-Lw), basket(2+2), UUDD
1 glyco-bond=ss-- groove=-w-n planarity=0.276 type=other nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 2 glyco-bond=--ss groove=-w-n planarity=0.202 type=other nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7 3 glyco-bond=--ss groove=-w-n planarity=0.265 type=other nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6