Binding mode of cationic monomer and dimer porphyrin with native and synthetic polynucleotides studied by polarized light spectroscopy.

Binding properties of the tricationic porphyrin monomer with a phenolic substituent at the periphery and the porphyrin dimer conjugated with hydrophilic triethylene glycol were investigated in this study using absorption and polarized spectroscopy, namely, circular dichroism (CD) and linear dichroism (LD). The spectral properties of the porphyrin monomer, when complexed with polynucleotides, were essentially the same as that of the well-known meso-tetrakis(N-methylpyridiniumyl)porphyrin, indicating that the substitution at one peripheral pyridiniumyl ring did not affect the binding mode. When the porphyrin dimer formed a complex with poly[d(G-C)(2)], a negative CD band and a negative LD(r) spectrum were apparent in the Soret absorption region, with its LD(r) magnitude significantly smaller than that in the DNA absorption region. As the complex was stabilized over time, the intensity of the negative CD band and the negative LD(r) increased. These observations indicated that one of the porphyrin moieties of the dimer intercalated initially and than the other one also intercalated consecutively within a few hours. In the porphyrin dimer-poly[d(A-T)(2)] complex case, a bisignate CD was apparent and remained for at least 12 h, indicating that the porphyrins are stacked along the polynucleotide stem even at a very low [porphyrin]/[DNA base] ratio. A wavelength-dependent and time-dependent LD(r) of this complex suggests that the porphyrin molecular plane tilts strongly relative to the polynucleotide helix axis. The spectral properties of the porphyrin dimer-DNA complex are similar to those of the porphyrin dimer-poly[d(G-C)(2)] complex. However, some of the porphyrin moieties were located at the groove, which was evident by some positive characters in the CD and LD(r) spectra at the short wavelength in the Soret band.