Porphyrin interactions with nucleic acids

Abstract

The interactions of tetrakis(4-N-methylpyridyl)porphine (H 2TMpyP-4) and its copper(II), nickel(II), zinc(II), cobalt(III), iron(III), and manganese(III) derivatives with several nucleic acids have been investigated. Spectrophotometric titrations of H 2TMpyP-4 and Cu(II)TMpyP-4 with the synthetic polymer poly(dG-dC) could be analyzed by a near-neighbor exclusion model leading to n ≈2 and equilibrium binding constants of 7.7 × 10 5 M −1 and 8.0 × 10 5 M −1, respectively. The other metal derivatives (except for the nickel porphyrin) do not provide sufficiently large color changes with poly(dG-dC) to allow analysis. In contrast, all of these porphyrins interact with poly(dA-dT) and DNA. For those porphyrins investigated the binding profiles are not adequately fit by a near-neighbor exclusion model but have bonding profiles suggesting cooperativity effects are important. Spectral and circular dichroic experiments both suggest base specificity. With calf thymus DNA, the copper(II) and nickel(II) derivatives show primarily prominent negative CD features and large red shifts and hypochromicity of visible absorption bands in the Soret region characteristics of GC specificity (as demonstrated with the synthetic polymer); the other metal derivatives show prominent positive induced visible CD features with small red shifts and hypochromicity of the absorbance bands in the Soret region characteristic of AT specificity. Only the metal-free derivative has a conservative CD spectrum suggestive of distribution among GC and AT sites. Stopped-flow kinetic experiments corroborate the interpretation of the static experiments. Both association and dissociation kinetics involving poly(dA-dT) are too rapid to be seen by the stopped-flow method in all the derivatives. However, the copper(II), nickel(II), and non-metallo derivatives show measurable kinetic profiles in the stopped-flow region with poly(dG-dC). The temperature-jump method was used to investigate the reactions of H 2TMpyP-4 with DNA and poly(dG-dC). Although the former reaction is multiphasic in the former case, a single relaxation process was obtained for the latter system yielding a forward rate constant of 5.7 × 10 5 M −1 s −1 and 1.8 s −1 for the reverse rate constant. Temperature-jump relaxation studies of mixtures of poly(dA-dT) and poly(dG-dC) indicate that the redistribution of H 2TMpyP-4 between AT and GC sites occurs via a mechanism involving dissociation rather than direct tranfer. A comparison of the relaxation times obtained for this system with those obtained for DNA strongly suggests that in the natural system the porphyrin can move from site to site without dissociation into the solvent medium.