Salt Effect on DNA Denaturation

We developed a method to evaluate the influence of salt on the chemical denaturation process of DNA. Our main objective was to reveal the influence of specific physical forces on the process of chemical DNA denaturation in the presence of salts. We used fractional cohesion parameters shown in the modified equations using the cohesive energy density approach to expose these forces. The original cohesive energy density equation does not apply to ionic systems. So we modified this equation and developed a protocol for applying this modified equation to evaluate the influence of a salt. We did this by allocating salt effects to either the water or the denaturant, creating an "effective" cohesion parameter, and then comparing this effective cohesion parameter to the control cohesion parameters without salt. Our theory has been developed for the chemical denaturation of DNA in the presence of salts for low- and medium-denaturation degrees, including but not limited to 50\% denaturation. Specifically, we show the degrees of influence salts have on hydrogen bonding, dispersion, polar forces, proton donor/acceptor ratio, dipole induction, orientation parameter, and electrostatic interaction in the denaturation process of DNA. By analyzing independent experimental data, we show that salt affects electrostatic repulsion forces, with the most significant compensating attractive forces being dispersion forces, suggesting that at constant 50\% denaturation, salt leads to the formation of bubbles between DNA strands. Results also show that salt has the least effect on hydrogen bonding. However, there is an internal change in the electron donor and electron acceptor characteristics of hydrogen bonding shown.