Interactions of sodium and potassium ions with oligonucleotides carrying human telomeric sequence and pyrene moieties at both termini Original Research Article

The organization of human telomeric DNA is of intense interest because of its role in aging, cancer research and bioanalytical applications. The Htelom sequence 5′-G3(T2AG3)3-3′ has been use to prepare two pyrene-modified fluorescence probes with three- and six-carbon linkers: Py-Htelom-Py(C3) and Py-Htelom-Py(C6), respectively. Results of the circular dichroism (CD), native PAGE, steady-state fluorescence, and anisotropy measurements of sodium and potassium quadruplex formation by these pyrene-modified conjugates are presented and discussed in order to clarify which conformation facilitates or renders the pyrene/pyrene or G-tetrad/pyrene stacking interaction. The CD spectra and native PAGE images suggested that conjugation of pyrene moieties has negligible effect on the folding properties of Htelom oligonucleotide. CD melting profiles and thermodynamic parameters revealed that both sodium and potassium quadruplexes are stabilized by the anchoring of pyrene tags with potassium ion being more effective than its sodium counterpart. Monomer emission of pyrene dominated in all investigated systems with fluorescence intensity being sensitive to the nature and concentration of cation and this phenomenon was attributed to the quenching processes and to the particular topologies of sodium and potassium quadruplexes. Strong quenching observed in the presence of KCl was attributed to the peculiarity of the potassium hybrid-type quadruplex, which enables effective stacking of pyrene moieties on the exposed guanine tetrads, thus facilitating static or electron transfer quenching. Plausibility of stacking interactions between pyrene and G-tetrad in a hybrid-type potassium quadruplex was further supported by the anisotropy measurements and molecular modeling results.