DSSR-derived G-quadruplex features in PDB entry 201d
- Solution structure of the oxytricha telomeric repeat d[g4(t4g4)3] G-tetraplex
- Wang, Y., Patel, D.J.: (1995) "Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex." J.Mol.Biol., 251, 76-94.
- The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intramolecularly into a right-handed G-tetraplex containing four stacked G-tetrads which are connected by two lateral T4 loops and a central diagonal T4 loop. The guanine glycosidic bonds adopt a syn-anti alternation along the full length of the d[G4(T4G4)3] sequence while the orientation around adjacent G-tetrads switches between syn.syn.anti.anti and anti.anti.syn.syn alignments. Four distinct grooves are formed by the parallel (two of medium width) and anti-parallel (one wide and one narrow width) alignment of adjacent G-G-G-G segments in the G-tetraplex. The T4 residues in the diagonal loop are well-defined while the T4 residues in both lateral loops are under-defined and sample multiple conformations. The solution structure of the Na(+)-stabilized Oxytricha d[G4(T4G4)3] G-tetraplex and an earlier solution structure reported from our laboratory on the Na(+)-stabilized human d[AG3(T2AG3)3] G-tetraplex exhibit a common folding topology defined by the same syn/anti distribution of guanine residues along individual strands and around individual G-tetrads, as well as a common central diagonal loop which defines the strand directionalities. The well-resolved proton NMR spectra associated with the d[G4(T4G4)3] G-tetraplex opens the opportunity for studies ranging from cation-dependent characterization of G-tetraplex conformation and hydration to ligand and protein recognition of the distinct grooves associated with this folding topology.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · 4(-LwD+Ln), basket(2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.464 type=bowl nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17 2 glyco-bond=-ss- groove=w-n- planarity=0.250 type=other nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18 3 glyco-bond=s--s groove=w-n- planarity=0.205 type=other nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19 4 glyco-bond=-ss- groove=w-n- planarity=0.290 type=other nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
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, 4 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.