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

Abstract

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 By 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 porphyrins 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. © 2012 American Chemical Society.