Interactions of chromomycin A₃ and mithramycin with the sequence d(TAGCTAGCTA)₂

Abstract

Anti-cancer antibiotics, chromomycin A₃ (CHR) and mithramycin (MTR) inhibit DNA directed RNA synthesis <i>in vivo </i>by binding reversibly to template DNA in the minor groove with GC base specificity, in the presence of divalent cations like<i> </i>Mg²⁺. Under physiological conditions, (drug)₂ Mg²⁺ complexes formed by the antibiotics are the potential DNA binding<i> </i>ligands. Structures of CHR and MTR differ in their saccharide residues. Scrutiny of the DNA binding properties reveal<i> </i>significant differences in their sequence selectivity, orientation and stoichiometry of binding. Here, we have analyzed<i> </i>binding and thermodynamic parameters for the interaction of the antibiotics with a model oligonucleotide sequence,<i> </i>d(TAGCTAGCTA)₂ to understand the role of sugars. The oligomer contains two potential binding sites (GpC) for the<i> </i>ligands. The study illustrates that the drugs bind differently to the sequence. (MTR)₂Mg²⁺ binds to both sites whereas<i> </i>(CHR)₂Mg²⁺ binds to a single site. UV melting profiles for the decanucleotide saturated with the ligands show that MTR<i> </i>bound oligomer is highly stabilized and melts symmetrically. In contrast, with CHR, loss of symmetry in the oligomer following its association with a single (CHR)₂Mg²⁺ complex molecule leads to a biphasic melting curve. Results have been interpreted in the light of saccharide dependent differences in ligand flexibility between the two antibiotics.