Systematic investigation on the central metal ion dependent binding geometry of M-meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to DNA and their efficiency as an acceptor in DNA-mediated energy transfer

Binding geometry to DNA and the efficiency as a donor for energy transfer of various metallo- and nonmetallo-porphyrins were investigated mainly by polarized light spectrscopy and fluorescence measurements. Planar porphyrins including nonmetallo meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP), CuTMPyP, and NiTMPyP produced large red-shift and hypochromism in absorption spectrum and a negative circular dichroism (CD) in the Soret band suggesting that these porphyrins intercalate between DNA base-pairs as expected. In the intercalation pocket, the molecular plane of these porphyrins tilts to a large extent. From a linear dichroism (LD) study, the angle between the two electric transition moments in the Soret band were 16°, 12°, and 11° for TMPyP, NiTMPyP, and CuTMPyP, respectively. On the other hand, porphyrins with axial ligands namely, VOTMPyP, TiOTMPyP, and CoTMPyP, produced a positive CD signal in the Soret band. Hyperchromism and less red-shift were apparent in the absorption spectrum. These observations indicated that the porphyrins with an axial ligand bind outside of the DNA. The angles of both the B_x and B_y transition with respect to the local DNA helix were 39°∼46° for all porphyrins. From these results, the conceivable binding site of porphyrins with axial ligands is suggested to be the minor groove. All porphyrins were able to quench the fluorescence of intercalated ethidium. Strong overlap between emission spectrum of ethidium and the absorption spectrum of porphyrins when they simultaneously bound to DNA was found suggesting the mechanism behind energy transfer is, at least in part, the Förster type resonance energy transfer (FRET). The minimum distance in base pairs between ethidium and porphyrin required to permit the excited ethidium to emit a photon was the longest for CoTMPyP being 17.6 base pairs and was the shortest for CuTMPyP and NiTMPyP at 8.0 base pairs. The variation in the distance was almost proportional to the extent of the spectral overlap, the common area under emission spectrum of ethidium and absorption spectrum of porphyrin, supporting the FRET mechanism, whereas the effect of the orientation factor which was considered by relative binding geometry was limited.