The recent studies carried out on the binding of small molecule to deoxyribonucleic acids suggested that the intercalation of a tricyclic heteroaromatic molecule, thionine, with natural DNAs provided thermal stabilization to the DNA complex. In the present study, we reported theoretical analysis of thionine binding with natural DNAs of varying base composition by using an amended Zimm and Bragg theory, to explain the melting behaviour and heat capacity of DNAs with and without thionine binding. We used experimental models of Paul et al. for implementing this study (Paul et al., 2010). The sharpness of transition has been examined in terms of half width and sensitivity parameter (Delta H/sigma). The results of theoretical analysis concluded that the various parameters such as heat capacity curve, transition profile, half widths and sharpness of the transition are in good agreement with the experimental measurements for binding of thionine determined through DSC. The theoretical analysis proposed in this study, therefore, may be useful to understand interaction of small molecules with deoxyribonucleic acids. This approach may also be applied to design DNA binding therapeutic molecules and in the process of drug formulation and development. (c) 2012 Published by Elsevier B.V.