Phenazinium dyes methylene violet 3RAX and indoine blue bind to DNA by intercalation: Evidence from structural and thermodynamic studies

The structural and energetic aspects of the interaction of two important phenazinium dyes methylene violet 3RAX and indoine blue with DNA were studied by spectroscopic and thermochemical techniques. The binding affinity values of both the dyes were of the order of 105 M−1 but methylene violet 3RAX bound to DNA more strongly. Both dyes bound DNA by intercalation but methylene violet 3RAX bound stronger than indoine blue. The DNA binding of both the dyes was exothermic and favoured by a small negative enthalpy and positive entropy contributions. The effect of ionic strength indicated that electrostatic attraction is an important component of the dye–DNA interaction although the major contribution comes from hydrophobic forces. The temperature dependence of enthalpy changes yielded negative heat capacity value which was higher for methylene violet 3RAX compared to indoine blue suggesting higher contribution from hydrophobic forces in the interaction of the former. Enthalpy–entropy compensation phenomenon was observed for the binding of both dyes to DNA.

► The phenazinium dyes methylene violet 3RAX and indoine blue bind to DNA by intercalation.
► Methylene violet binds more strongly than does indoine blue.
► The binding was favoured by negative enthalpy and positive entropy changes.
► Enthalpy–entropy compensation was observed.
►  Hydrophobic forces play major role in the DNA binding of methylene violet and indoine blue.