DSSR-derived G-quadruplex features in PDB entry 6ycv
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-riboguanosine and lna modified hybrid type G-quadruplex with v-loop
- 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 · 2(-LwX+P), UD3(1+3), UDDD
1 glyco-bond=s--- groove=w--n planarity=0.322 type=bowl nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 2 glyco-bond=-ss- groove=w-n- planarity=0.264 type=other nts=4 GGGg A.DG2,A.DG6,A.DG20,A.LCG15 3 glyco-bond=-s-- groove=wn-- planarity=0.252 type=other nts=4 GgGG A.DG8,A.GF2/14,A.DG17,A.DG22
Helix#1, 3 G-tetrad layers, INTRA-molecular, with 1 stem
Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(-LwX+P), UD3(1+3)
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=7 GACACAg A.DG8,A.DA9,A.DC10,A.DA11,A.DC12,A.DA13,A.GF2/14 2 type=V-shaped helix=#1 nts=4 ggGG A.GF2/14,A.LCG15,A.DG16,A.DG17