DSSR-derived G-quadruplex features in PDB entry 6ffr
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.
- DNA-RNA hybrid
- DNA-RNA hybrid quadruplex with flipped tetrad
- Haase, L., Dickerhoff, J., Weisz, K.: (2018) "DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies." Chemistry, 24, 15365-15371.
- A DNA G-quadruplex adopting a (3+1)-hybrid structure was substituted at its 5'-tetrad by riboguanosine (rG) analogs. Incorporation of anti-favoring rG at appropriate syn-positions of the 5'-outer tetrad induced conformational rearrangements to yield a quadruplex featuring a 5'-tetrad with reversed polarity. A high-resolution structure of a disubstituted quadruplex variant as well as direct NMR experimental evidence reveals a non-conventional C-H⋅⋅⋅O hydrogen bond in a medium groove between the 2'-OH of an rG residue adopting a C2'-endo sugar pucker and H8 of a 3'-neighboring anti-G residue. In contrast, a C3'-endo sugar conformation for another guanine ribonucleotide prevents formation of a corresponding hydrogen bond but relocates its 2'-OH substituent from the quadruplex narrow groove into a medium groove. Both the formation of favorable CHO hydrogen bridges and unfavorable interactions of the 2'-hydroxyl group in a narrow groove will promote RNA folding into a parallel topology featuring all-anti core residues and four grooves of medium size.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-PD+Lw), U3D(3+1), UUUD
1 glyco-bond=---s groove=--wn planarity=0.243 type=other nts=4 GGGG A.G1,A.DG6,A.G20,A.DG16 2 glyco-bond=---s groove=--wn planarity=0.253 type=other nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15 3 glyco-bond=---s groove=--wn planarity=0.342 type=bowl-2 nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14