DSSR-derived G-quadruplex features in PDB entry 6tcg
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 2'-f-arabinoguanosine modified G-quadruplex with v-loop and all-syn g-tract
- Haase, L., Weisz, K.: (2020) "Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions." Chem.Commun.(Camb.), 56, 4539-4542.
- Mixed 2'-F-riboguanosine and 2'-F-arabinoguanosine disubstitutions of a hybrid-type G-quadruplex are found to induce a refolding into two alternative structures with different types of V-loops upon positional exchange of the two G analogs. While conformational preferences of the incorporated G surrogates fail to fully account for the observed rearrangements, additional hydrogen bonds with a fluorine acceptor are suggested to be critical determinants of the two distinct V-loop conformers imposing different tetrad polarities.
- 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=0.273 type=other nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG16 2 glyco-bond=s--- groove=w--n planarity=0.280 type=other nts=4 GGGg A.DG2,A.DG6,A.DG20,A.GFL15 3 glyco-bond=-s-- groove=wn-- planarity=0.208 type=other nts=4 GgGG A.DG8,A.GF2/14,A.DG17,A.DG22
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.
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.GFL15,A.DG16,A.DG17