Solution-state NMR spectroscopy has been utilized to demonstrate that oligonucleotide d(TG4T) in contrast to the commonly excepted notion does not form a single tetrameric G-quadruplex in solution. One of the two coexisting structures exhibits a T-quartet in addition to the four G-quartets. Substitution of T for U at the 5’-end of the parent sequence leads to dimerization of G-quadruplex units. We have established that NH4+ ion movement along the central ion cavity of tetramolecular G-quadruplexes is ca. 10 times faster in comparison to bi- and monomolecular analogues.
COBISS.SI-ID: 4487962
Description of achievement: Analysis of syn and anti orientations of guanine residues along the skeleton of known G-quadruplex structures enabled us to develop a formalism, which can be used to design new G-quadruplex topologies with desired features in a rational way. Prediction of folding with predicted topology has been experimentally verified and confirmed by synthesis of oligonucleotide, whose 3D structure has been determined by NMR in solution.
COBISS.SI-ID: 4320026
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
Thrombin binding aptamer, 15-mer oligonucleotide d[G2T2G2TGTG2T2G2], was folded into the well known antiparallel unimolecular G-quadruplex in the presence of 15NH4+ ions. Solution-state NMR was used to localize ammonium ions between the two G-quartets within the core of the structure. Exchange of ammonium ions between the inner binding site and bulk solution is characterized by the exchange rate constant of 1.0 s-1 at 15 degs C. T4 and T13 form a noncanonical base pair, which greatly affects access of bulk ions into the cation binding site in the G-quadruplex core.
COBISS.SI-ID: 4305690