ABSTRACT The recent study on binding of small molecules to double stranded DNA suggested that the intercalation of a tricyclic heteroaromatic molecule, thionine, with natural DNA provided thermal stabilization to the complex. In the present study, we reported theoretical analysis of thionine binding with Clostridium perfringenes DNA duplex (CP-DNA) by using an amended Zimm and Bragg theory, to explain the melting behaviour and heat capacity of CP-DNA with and without thionine binding. The experimental models of Paul et al. (2010) have been used for the study. The sharpness of transition has been examined in terms of half width and sensitivity parameter (?H/σ). The results of theoretical approach suggested that the various parameters such as transition profile, sharpness of the transition, heat capacity curve and half widths are in good agreement with the experimental measurements for binding of thionine. Therefore, the proposed theoretical analysis may be useful in order to understand interaction of small molecules to DNA that may be applied in the process of drug development and for designing more potential DNA binding therapeutic molecules.
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