DSSR-derived G-quadruplex features in PDB entry 2chk
- nucleic acid
- NMR structure of tllllt quadruplex
- Nielsen, J.T., Arar, K., Petersen, M.: (2006) "NMR Solution Structures of Lna (Locked Nucleic Acid) Modified Quadruplexes." Nucleic Acids Res., 34, 2006-.
- We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA sugars. In particular, a distinct change in the sugar-phosphate backbone is observed at the G2pL3 and L2pL3 base steps and sequence dependent changes in the twist between tetrads are also seen. Both the LNA modified quadruplexes have raised thermostability as compared to the DNA quadruplex. The quadruplex-forming capability of d(TGLGLT) is of particular interest as it expands the design flexibility for stable parallel LNA quadruplexes and shows that LNA nucleotides can be mixed with DNA or other modified nucleic acids. As such, LNA-based quadruplexes can be decorated by a variety of chemical modifications. Such LNA quadruplex scaffolds might find applications in the developing field of nanobiotechnology.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.514 type=other nts=4 gggg A.LCG2,B.LCG8,C.LCG14,D.LCG20 2 glyco-bond=---- groove=---- planarity=0.350 type=other nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21 3 glyco-bond=---- groove=---- planarity=0.212 type=other nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22 4 glyco-bond=---- groove=---- planarity=0.164 type=other nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
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, 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.