Effect of the Position and Number of Positive Charges on the Intercalation and Stacking of Porphyrin to Poly[d(G-C)₂], Poly[d(A-T)₂], and Native DNA

Abstract

The effect of the number and position of the positive charges on porphyrin with respect to the mode of binding to poly[d(G-C)2] and poly[d(A-T)2] were investigated by absorption and polarized spectroscopy, including circular and linear dichroism (CD and LD). Meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP), which possesses four positive charges on the periphery pyridinium rings, produces a negative CD and wavelength-independent reduced LD (LDr) spectra in the Soret absorption region when it associates with poly[d(G-C)2]. These spectral characteristics have been considered as diagnostic for intercalation. In contrast, both trans- and cis-bis(N-methylpyridinium-4-yl)diphenylporphyrin (trans- and cis-BMPyP), where the number of positive charges was reduced to two, multisignate CD and strong wavelength-dependence of the LDr spectra were observed, indicating that these porphyrins do not intercalate. Therefore, four positive charges are required for TMPyP intercalation. When associated with poly[d(A-T)2], trans-BMPyP exhibited a positive CD signal at a low [porphyrin]/[nucleobase] ratio with the appearance of a bisignate CD upon increase of the mixing ratio, suggestive of binding at the groove of the double helix at low mixing ratios, and stacking at increasing mixing ratios. Conversely, no monomeric binding was evident in the bis-BMPyP bisignate CD spectrum; hence, only the stacking mode was found for cis-BMPyP, even at the lowest [porphyrin]/[nucleobase] ratio, suggesting the importance of the position of the positive charges in determining monomeric groove binding or stacking. The binding geometries of trans- and cis-BMPyP were similar when associated with poly[d(A-T)2], as determined from the similar LDr spectrum. When associated with DNA, TMPyP exhibited similar spectral properties with that of the TMPyP-poly[d(G-C)2] complex, indicating intercalation of TMPyP between the DNA base pairs. Conversely, CD and LDr characteristics of both trans- and cis-BMPyP-DNA complexes resembled those that complexed with poly[d(A-T)2] at a high [porphyrin]/[DNA] ratio, suggesting that both porphyrins were stacked along the DNA stem.

Energy Transfer from Ethidium to Cationic Porphyrins Mediated by DNA and Synthetic Polynucleotides at Low Binding Densities

“…33, 34 The CD spectrum at these low BMPyP concentrations was extremely weak, as previously reported, 34 and therefore not shown. Polarized spectroscopic study suggested that BMPyP stacked along the stem of the DNA and poly[d(A-T) 2 ] and bound to the outside of poly[d(G-C) 2 ] in a monomeric manner.…”

“…Polarized spectroscopic study suggested that BMPyP stacked along the stem of the DNA and poly[d(A-T) 2 ] and bound to the outside of poly[d(G-C) 2 ] in a monomeric manner. 34 The presence of ethidium did not alter the spectral properties of BMPyP bound to any of the polynucleotides, similar to TMPyP, suggesting that the simultaneous binding of BMPyP and ethidium to DNA and the synthetic polynucleotides did not affect their binding modes.…”

“…The efficiency of the energy transfer from DAPI is far higher than predicted by the "sphere of action model" when meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (hereafter referred to as TMPyP, Figure 1) is used as an acceptor. 28,29 However, fluorescence quenching with cis-bis(N-methylpyridinium-4-yl)porphyrin (hereafter referred BMPyP, Figure 1), which stacks along DNA and poly[d(A-T) 2 ], 33,34 is less efficient than with TMPyP. For both TMPyP and BMPyP, the concentration of DAPI was high enough to saturate the minor groove of the DNA.…”

DNA Mediated Energy Transfer from 4',6-Diamidino-2-phenylindole to tetra- and bis-cationic Porphyrins at Low Binding Densities

“…Differences in the binding geometries of the acceptors, TMPyP and BMPyP, resulted in different relative orientations. The binding modes of TMPyP and BMPyP to DNA and to selected synthetic polynucleotides has been investigated by polarized light spectroscopy, 34,35 with TMPyP found to intercalate between DNA base-pairs and BMPyP stackinf along the DNA stem. Therefore, their transition dipoles would be differently oriented relative to the DAPI.…”

“…34,35 Their different binding modes to DNA allow investigation of the effects of spectral overlap and relative orientation in RET. DAPI was used at a concentration ratio to DNA bases of 0.005, one DAPI molecule per 200 bases.…”