DSSR-derived G-quadruplex features in PDB entry 6yep
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.
- Lna modified G-quadruplex with flipped g-tract and central tetrad
- Haase, L., Weisz, K.: (2020) "Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design." Nucleic Acids Res.
- A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2'-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5'-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3'-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.
- 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=0.293 type=bowl nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 2 glyco-bond=--ss groove=-w-n planarity=0.193 type=other nts=4 GgGG A.DG2,A.LCG15,A.DG21,A.DG7 3 glyco-bond=--ss groove=-w-n planarity=0.238 type=other nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6