Biopolymers and cell. 2007; 23 (6): 529 - 537

Spectrophotometrical study of mechanisms of cytidine analogues and ethidium bromide binding with DNA

Ie. L. Iermak, O. B. Kruglova, L. H. Palchykovska, I. V. Alexeeva

To study the mechanisms of cytidine and its biologically active analogues binding to DNA we analyzed the binding of these ligands to the DNA in the presence of well-known intercalator ethidium bromide (EtBr). Thereto, we carried out the detailed spectrophotometric research of EtBr-DNA mixtures absorption in the presence of cytidine and its analogues in the wide range of wavelengths and DNA concentrations. Cytidine derivatives containing azagroup in the cytosine ring (6AZC, AZAfur, and AZAxyl) compete with EtBr for the DNA binding sites. The binding constants and binding site sizes of the ligand-DNA complexes were calculated via absorption spectra optimization programs COMP and DALSMOD. Unmodified in cytosine ring ligands (cytidine and Ara-C) do not compete with EtBr for the DNA binding sites, however they contribute to the change of concentration dependencies of titration curves in the region of low DNA concentrations.

Keywords: cytidine analogues, DNA, models of binding, spectrophotometry, ethidium bromide.