Z-form DNA specific binding geometry of Zn(II) meso-tetrakis(N-methylpyridinium-4-yl)porphyrin probed by linear dichroism spectroscopy.

Zn(II) meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (ZnTMPyP) produced a unique linear dichroism (LD) spectrum when forming a complex with Z-form poly[d(G-C)(2)]. The spectrum was characterized by a large positive wavelength-dependent LD signal in the Soret absorption region. The magnitudes of LD in both the DNA and Soret band increased as the [porphyrin]/[DNA base] ratio increased and were larger by 20-40 times compared to the negative LD of the ZnTMPyP bound to B-form poly[d(G-C)(2)] and poly[d(A-T)(2)]. The angles calculated from LD were respectively 49° and 42° for B(x) and B(y) transitions of the porphyrin with respect to the local helix axis of Z-form poly[d(G-C)(2)]. The appearance of the unique LD spectrum for the Z-form poly[d(G-C)(2)] complex was accompanied by a bisignate circular dichroism spectrum in the Soret region, whose magnitude was proportional to the square of the porphyrin concentration, suggesting a stacking interaction between Z-form poly[d(G-C)(2)]-bound ZnTMPyP with other bound ZnTMPyP. From these observations, a conceivable binding mode of ZnTMPyP to Z-form poly[d(G-C)(2)] complex was proposed, in which ZnTMPyP binds at the major groove or across the groove. In contrast with Z-form poly[d(G-C)(2)], ZnTMPyP binds to poly[d(A-T)(2)] in a monomeric manner with the angles of 57° and 59° for the two porphyrin's transition moments with respect to the local polynucleotide helix axis. The polarized spectral properties of ZnTMPyP bound to B-form poly[d(G-C)(2)] coincide with the intercalated nonmetallic TMPyP, namely, a negative CD signal in the Soret band and a negative wavelength-dependent reduced LD signal, with a magnitude larger than that in the DNA absorption region in spite of its axial ligands.