A solution state NMR study has shown that d(G4T3G4) in the presence of 15NH4+ ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets. The use of heteronuclear NMR enabled us to localize three 15NH4+ ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement.
COBISS.SI-ID: 4051738
1H NMR conformational study in combination with ab initio calculations has been used to analyse fleximer nucleosides with respect to their natural counterparts. Substitution of purine with more flexible heterocyclic system consisting of two rings leads to increase in the population of North conformers and anti rotamers across glycosidic bond. The observed effects were interpreted in terms of anomeric, gauche and steric effects.
COBISS.SI-ID: 3065626
Oligonucleotide d[(G3T4G4)2] has been folded in the presence of 15NH4+ ions into dimeric G-quadruplex with three G-quartets and two T4 loops. We were able to establish two cation binding sites within the interior of d[(G3T4G4)2]. Surprisingly there is no cation movement along the central ion cavity of this G-quadruplex. On the other hand, we have observed exchange of ammonium ions with ions in bulk solution. 15NH4+ ion movement through the outer G-quartet that is spanned by the edge-wise T4 loop is 12-times faster than through the outer G-quartet which is spanned by the diagonal T4 loop.
COBISS.SI-ID: 3727642
We have determined 3D structure of hairpin adopted by 3'-MOE-2',5'-RNA oligonucleotide. This structure represents the first hairpin structure of the hairpin with exclusively 2',5'-phosphodiester bonds described in the literature. Short RNA oligonucleotides are able to effectively silence gene expression, which opens promising therapeutic opportunities in the treatment of cancer, AIDS and hepatitis.
COBISS.SI-ID: 3267866
Dimeric G-quadruplex structure adopted by guanine rich sequence d(G3T4G4) exhibits two cation binding sites. We have demonstrated experimentally the existence of the mixed form of d(G3T4G4)2 containing one K+ and one 15NH4+ ion inside the G-quadruplex core that represents intermediate in the conversion of di-15NH4+ into di-K+ form.
COBISS.SI-ID: 3290394