Binding Geometry of Free Base and Mn(III)meso‐Tetrakis(N‐methylpyridium‐4‐yl)porphyrin to Various Duplex and Triplex DNAs

Abstract

The binding mode of free base and Mn(III)meso‐tetrakis(N‐methylpyridium‐4‐yl)porphyrin (TMPyP and MnTMPyP) to various duplex and triplex synthetic polynucleotides was investigated by polarized light spectroscopy, specifically circular and linear dichroism (CD and LD) spectroscopy. Both TMPyP and MnTMPyP produced a similar positive CD spectrum in the Soret absorption region when bound to poly(dA)·poly(dT) duplex and poly(dA)·[poly(dT)]2 triplex. Considering that the third poly(dT) strand blocks the major groove, this result suggested that both porphyrins bound near the minor groove where the axial ligands of the central Mn(III) ion did not affect the binding mode. In contrast, TMPyP intercalated and MnTMPyP bound the exterior of poly(dG)·poly(dC) and poly(dI)·poly(dC) duplexes, as judged from the negative and positive CD signals, respectively. The CD signals for both intercalated TMPyP and externally bound MnTMPyP were greatly altered when bound to poly(dG)·poly(dC)·poly(dC)+ and poly(dI)·poly(dC)·poly(dC)+ triplexes, indicating that the binding modes of both porphyrins were affected by the presence of the third strand, poly(dC)+, which contrasted with the AT polynucleotides. This observation supported the conclusion that the external binding site of MnTMPyP at the GC and IC duplexes is the major groove. The reduced LD spectrum indicated that the angles of the two electric transition moments of both TMPyP and MnTMPyP in the Soret absorption region were 57° and 65° with respect to the local DNA helix axis when bound to the poly(dA)·[poly(dT)]2 triplex. On the other hand, a strong, wavelength‐dependent reduced LD was observed in the Soret region for both porphyrins when associated with CGC triplex, and the excessive tilt degree prevented any reasonable calculation of the angles.