Orientation and Linear Dichroism Characteristics of Porphyrin-DNA Complexes

The linear dichroism spectra of complexes of tetrakis(N-methyl-4-pyridinio)porphine (H₂TMpyP) and its zinc(II) derivative (ZnTMpyP) with DNA oriented in a flow gradient have been investigated. The dichroism of H₂TMpyP determined within the Soret band and the Q_yband system is consistent with an intercalative conformation in which the plane of the porphyrin ring system is nearly parallel to the planes of the DNA bases. In the case of ZnTMpyP on the other hand, the porphyrin ring system is inclined at angles of 62-67° with respect to the axis of the DNA helix. The pyridyl groups in both cases are characterized by a low degree of orientation with respect to the axis of the helix. In contrast to H₂TMpyP which does not significantly affect the degree of alignment of the DNA in the flow gradient, the binding of ZnTMpyP causes a significant decrease (about 50% for a base pair/ZnTMpyP ratio of 20) in the intrinsic dichroism at 260 nm due to the oriented DNA bases; the binding of ZnTMpyP to DNA either gives rise to regions of higher flexibility or causes bends or kinks at the binding sites. Increasing the ionic strength has little influence on the linear dichroism of the ZnTMpyP-DNA complexes, but the number of molecules bound at intercalation sites diminishes in the case of the H₂TMpyP-DNA complexes; the accompanying changes in the linear dichroism characteristics suggest that external H₂TMpyP complexes are formed at the expense of intercalation complexes. Taken together, these linear dichroism results are consistent with the intercalative model for H₂TMpyP-DNA and the external binding model for ZnTMpyP-DNA complexes proposed by Fiel et al. [Fiel, R. J., Howard, J. C., & Datta Gupta, N. (1979) Nucleic Acids Res. 6, 3093–3118] and Pasternack et al. [Pasternack, R. F., Gibbs, E. J., & Villafranca, J. J. (1983) Biochemistry 22, 5409–5417].