Toxic interaction of thionine to deoxyribonucleic acids: Elucidation of the sequence specificity of binding with polynucleotides

The sequence specificity of the intercalative DNA damage of the phenothiazine dye thionine has been investigated by absorbance, fluorescence, circular dichroism and viscosity studies using four synthetic polynucleotides, poly(dA-dT)·poly(dA-dT), poly(dA)·poly(dT), poly(dG-dC)·poly(dG-dC) and poly(dG)·poly(dC). Strong hypochromic-bathochromic effects in absorbance and quenching in fluorescence were observed that showed strong binding of thionine to these polynucleotides. Scatchard plots revealed non-cooperative binding and analysis by McGhee-von Hippel equation provided the affinity values in the order of 105 M−1. The binding clearly revealed the high preference of thionine to the alternating GC sequences followed by the homo GC sequences. The AT polynucleotides had lower binding affinities but the alternating AT sequences had higher affinity compared to the homo stretches. The results of ferrocyanide quenching studies in fluorescence and viscosity experiments conclusively proved the intercalation of thionine while circular dichroic studies provided evidence for the structural perturbations associated with the sequence specific intercalative binding. The sequence specificity of the intercalative damage of thionine to deoxyribonucleic acid is advanced from this study.