Energetics of the binding of two known classical DNA intercalating molecules, ethidium and sanguinarine with four sequence specific polynucleotides, poly(dG-dC) poly(dG-dC), poly(dG) poly(dC), poly(dA-dT) poly(dA-dT), and poly(dA) poly(dT) have been compared under identical conditions The binding of both the molecules was characterized by strong stabilization of the polynucleotides against thermal strand separation in optical melting as well as differential scanning calorimetry studies. Isothermal titration calorimetry results revealed that the binding of both sanguinarine and ethidium to poly(dG-dC) poly(dG-dC), poly(dA-dT) poly(dA-dT), and poly(dG) poly(dC) was exothermic and favoured by negative enthalpy changes. On the other hand, the binding of both molecules to poly(dA) poly(dT) was endothermic and entropy driven The binding affinity values obtained from isothermal titration calorimetry data was in close proximity to that derived from thermal melting data. The heat capacity changes obtained from temperature dependence of the enthalpy change gave negative values in the range (-0 4 to 1 25) kJ mol(-1) K-1 for the binding of ethidium and sanguinarine to these polynucleotides The variations in the values indicate important differences in the formation of the complexes New insights into the energetics and specificity aspects of interaction of these molecules to DNA have emerged from these studies (C) 2010 Elsevier Ltd All rights reserved