Consecutive intercalation of a cationic porphyrin dimer between the GC base-pairs: a kinetic study

Abstract

One of the porphyrin moieties of the porphyrin dimer intercalates rapidly between the DNA base-pairs, followed by the slow intercalation of the other. The slow intercalation of the second porphyrin moiety of porphyrin dimer to poly[d(G-C)(2)] was investigated by normal absorption and circular dichroism spectroscopy. The change in absorbance in the Soret band of porphyrin upon association with poly[d(G-C)(2)] can be best elucidated by the combination of the two single exponential curves, suggesting the intercalation occurred via two independent first order reactions. Activation energies of these two first order reactions were calculated to be 0.37 kcal/mol and 3.19 kcal/mol, respectively. The intercalation associated with lower activation energy can be assigned to the intercalation of second porphyrin moiety to 5'CG3' site while that with higher activation energy to 5'GC3' intercalation site. Increasing the flexibility of poly[d(G-C)(2)] by adding Na+ ion resulted in an enhancement of the reaction rate for both steps in an exponential manner.