The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA

The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.