DSSR-derived G-quadruplex features in PDB entry 2kbp
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- Solution structure of a G-quadruplex of human telomeric RNA
- Martadinata, H., Phan, A.T.: (2009) "Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution." J.Am.Chem.Soc., 131, 2570-2578.
- Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.234 type=other nts=4 GGGG A.G3,A.G9,B.G15,B.G21 2 glyco-bond=---- groove=---- planarity=0.169 type=other nts=4 GGGG A.G4,A.G10,B.G16,B.G22 3 glyco-bond=---- groove=---- planarity=0.246 type=other nts=4 GGGG A.G5,A.G11,B.G17,B.G23
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, inter-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.