DSSR-derived G-quadruplex features in PDB entry 1evm
- NMR observation of a-tetrad
- Patel, P.K., Koti, A.S., Hosur, R.V.: (1999) "NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad." Nucleic Acids Res., 27, 3836-3843.
- The structure of the telomeric DNA has been a subject of extensive investigation in recent years due to the realization that it has important functional roles to play in vivo and the observations that truncated telomeric sequences exhibit a great variety of 3D structures in aqueous solutions. In this context, we describe here NMR structural studies on two truncated human telomeric DNA sequences, d-AG(3)T and d-TAG(3)T in solutions containing K(+)ions. The G(3)stretches in both the oligonucleotides were seen to form parallel-stranded quadruplexes. However, the AG(3)segment as a whole, had different structural characteristics. The structure of d-AG(3)T revealed the formation of a novel A-tetrad, which was not seen in d-TAG(3)T. The A's in the tetrad had syn glycosidic conformation as opposed to the anti conformation of the G's in the G-tetrads. The A-tetrad stacked well over the adjacent G-tetrad and the twist angle at this step was smaller in d-AG(3)T than in d-TAG(3)T. These observations are expected to be significant from the point of view of structural diversity and recognition in telomeres.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.175 type=bowl-2 nts=4 GGGG M.DG302,P.DG402,O.DG302,N.DG402 2 glyco-bond=---- groove=---- planarity=0.320 type=bowl nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403 3 glyco-bond=---- groove=---- planarity=0.321 type=bowl nts=4 GGGG M.DG304,P.DG404,O.DG304,N.DG404
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.