Abstract

Recent analysis on structure and dynamics of nucleic acid suggest that the DNA helix undergoes conformational transition as function of salt and solvent. This flexibility leads folding of DNA either smoothly or its chain direction changes abruptly by the generation of kinks. The steroid diamine binds to DNA through the minor groove at the kink site and stabilized the complex. In the present study, we reported theoretical analysis of steroid diamine, dipyrandium, binding with DNA duplex by using an amended Zimm and Bragg theory, to explain the melting behavior and heat capacity of DNA with and without dipyrandium binding. The experimental models of Marky et al. (1983) were used for the study. The sharpness of transition has been examined in terms of half width and sensitivity parameter (∆H/δ). 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 dipyrandium. This theoretical analysis can be applied in order to understand bimolecular interaction and thus can be applied in the process of drug designing and development.

Key words: Dipyrandium, DNA binding, transition profile, heat capacity, drug design.