1.

Design of a G-quadruplex topology though control of orientation across glycosidic bonds.

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

2.

Cation localization and movement within DNA thrombin binding aptamer in solution

The 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 15NH4+ ions between the two G-quartets. Exchange of 15NH4+ 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