Modelling of the binding specificity in the interactions of cationic porphyrins with DNA.

A theoretical investigation is performed of the complexes of a tetracationic porphyrin, tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), with the hexanucleotides d(CGCGCG)2 and d(TATATA)2, considering the possibility of both the intercalative and the groove binding interactions. These computations demonstrate that T4MPyP manifests a significant preference for intercalation in its complex with d(CGCGCG)2 but for non intercalative binding in the minor groove in its complex with d(TATATA)2. Such a dual binding behaviour of T4MPyP as a function of the sequence to which it is attached is fully consistent with available experimental data. It demonstrates that intercalation and groove binding may be viewed as two potential wells on a continuous energy surface. In agreement with experiment, the computations indicate that in the here considered case the deepest well is associated with intercalation.