DSSR-derived G-quadruplex features in PDB entry 6l92
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- A basket type G-quadruplex in wnt DNA promoter
- Wang, Z.F., Li, M.H., Chu, I.T., Winnerdy, F.R., Phan, A.T., Chang, T.C.: (2020) "Cytosine epigenetic modification modulates the formation of an unprecedented G4 structure in the WNT1 promoter." Nucleic Acids Res., 48, 1120-1130.
- Time-resolved imino proton nuclear magnetic resonance spectra of the WT22m sequence d(GGGCCACCGGGCAGTGGGCGGG), derived from the WNT1 promoter region, revealed an intermediate G-quadruplex G4(I) structure during K+-induced conformational transition from an initial hairpin structure to the final G4(II) structure. Moreover, a single-base C-to-T mutation at either position C4 or C7 of WT22m could lock the intermediate G4(I) structure without further conformational change to the final G4(II) structure. Surprisingly, we found that the intermediate G4(I) structure is an atypical G4 structure, which differs from a typical hybrid G4 structure of the final G4(II) structure. Further studies of modified cytosine analogues associated with epigenetic regulation indicated that slight modification on a cytosine could modulate G4 structure. A simplified four-state transition model was introduced to describe such conformational transition and disclose the possible mechanism for G4 structural selection caused by cytosine modification.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+LnD-P), (3+1), UUUD
1 glyco-bond=sss- groove=--wn planarity=0.070 type=planar nts=4 GGGG A.DG1,A.DG16,A.DG20,A.DG11 2 glyco-bond=---s groove=--wn planarity=0.062 type=planar nts=4 GGGG A.DG2,A.DG17,A.DG21,A.DG10 3 glyco-bond=---s groove=--wn planarity=0.080 type=planar nts=4 GGGG A.DG3,A.DG18,A.DG22,A.DG9
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.