DSSR-derived G-quadruplex features in PDB entry 1s9l
- NMR solution structure of a parallel lna quadruplex
- Randazzo, A., Esposito, V., Ohlenschlager, O., Ramachandran, R., Mayola, L.: (2004) "NMR solution structure of a parallel LNA quadruplex." Nucleic Acids Res., 32, 3083-3092.
- The solution structure of a locked nucleic acid (LNA) quadruplex, formed by the oligomer d(TGGGT), containing only conformationally restricted LNA residues is reported. NMR and CD spectroscopy, as well as molecular dynamics and mechanic calculations, has been used to characterize the complex. The molecule adopts a parallel stranded conformation with a 4-fold rotational symmetry, showing a right-handed helicity and the guanine residues in an almost planar conformation with three well-defined G-tetrads. The thermal stability of Q-LNA has been found to be comparable with that of [r(UGGGU)]4, while a T(m) increment of 20 degrees C with respect to the corresponding DNA quadruplex structure [d(TGGGT)]4 has been observed. The structural features of the LNA quadruplex reported here may open new perspectives for the biological application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.227 type=other nts=4 gggg A.LCG2,C.LCG12,D.LCG17,B.LCG7 2 glyco-bond=---- groove=---- planarity=0.208 type=other nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8 3 glyco-bond=---- groove=---- planarity=0.191 type=other nts=4 gggg A.LCG4,C.LCG14,D.LCG19,B.LCG9
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.