Stacking of meso-Tetrakis(3-N-methylpyridiniumyl)porphyrin on Poly[d(A-T)2]: Importance of the Distance between Porphyrin's Positive Charges

Binding Properties of Various Cationic Porphyrins to DNA in the Molecular Crowding Condition Induced by Poly(ethylene glycol)

The binding modes of various cationic porphyrins to DNA in an aqueous solution and under the molecular crowding condition induced by poly(ethylene glycol) (PEG) were compared by normal absorption, circular dichroism (CD), and linear dichroism (LD) spectroscopy techniques. Large negative CD and LD signals in the Soret absorption regions of the meta- and para-TMPyP [meso-tetrakis (n-N-methylpyridiniumyl) porphyrin (meta, n = 3) and (para, n = 4)] were apparent in the aqueous solution, indicating an intercalative-binding mode, while a positive CD spectrum and a less intense negative LD spectrum for the ortho-TMPyP (n = 2)-complexed DNA suggested a major-groove-binding mode. These binding modes are retained under a molecular crowding condition, suggesting that the PEG cluster cannot access the TMPyPs that are intercalated between the DNA base pairs or that bind at the major groove. The spectral properties of the ortho-, meta-, and para-trans-BMPyP [trans-bis(N-methylpyrodinium-n-yl)diphenyl porphyrin, n = 2,3,4]-bound DNA in an aqueous solution correspond to neither the intercalative-binding nor the groove-binding mode, which is in contrast with the TMPyP cases. The spectral properties under the molecular crowding condition are altered considerably for all of the three trans-BMPyPs compared to those in an aqueous solution, suggesting that the matted PEG cluster is in contact with the cationic trans-BMPyPs, causing a change in the polarity of the porphyrin environment. Consequently, trans-BMPyPs bind to the external side of the DNA.

Length and sequence effect on the B-Z transition of [d(A-T)n]2 oligonucleotide induced by a cationic porphyrin

trans-BMPyP induced the B-Z transition for alternated AT oligonucleotides as it was evident by inversed CD spectrum. The transition occurred simultaneously with appearance of the extensive stacking of porphyrin. Complete B-Z transition required at least 14 base-pairs long. Insertion of one or two GC base pairs prevented the B-Z transition.

Porphyrins bearing quaternary azaaromatic moieties

In this review, porphyrins bearing quaternary azaaromatic moieties are described as follows: firstly those with useful physicochemical properties, then, species showing biological activities and finally, porphyrins bound with fullerenes and with cyclodextrins.

Effect of number and position of positive charges on the stacking of porphyrins along poly[d(A-T)(2)] at high binding densities

At high porphyrin densities, the effects of the number and position of the positive charges of the periphery ring on the stacking of the porphyrin on poly[d(A-T)(2)] was investigated using polarized spectroscopy, including circular and linear dichroism (CD and LD, respectively). The CD spectrum of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin(TMPyP) consisted of two positive bands in the Soret absorption region at low [porphyrin]/[DNA base] ratios (R ratios) and changed to two distinguishable categories of the bisignate CD spectrum with increasing R ratio. These CD spectra were attributed to the monomeric groove binding, and the moderately and extensively stacked TMPyPs. In contrast, trans-bis(N-methylpyridinium-4-yl)porphyrin (trans-BMPyP) dominantly produced a CD spectrum that corresponded to the extensive stacking, except at the lowest R ratio that was used in this work (R = 0.04). However, for cis-bis(N-methylpyridinium-4-yl)porphyrin (cis-BMPyP), the intensity of the apparent bisignate CD signal was too small to assign it to the extensive stacking. Moreover, the shape of the CD spectrum in the DNA absorption region showed that the conformation of poly[d(A-T)(2)] was retained, in contrast to the extensively stacked TMPyP and trans-BMPyP. In the extensively stacked TMPyP- poly[d(A-T)(2)] assembly, the large negative LD signal in the Soret band was observed suggesting that the direction of the molecular planes of TMPyP was close to perpendicular with respect to the orientation axis (flow axis). In contrast, the LD spectrum of the trans-BMPyP-poly[d(A-T)(2)] complex produced positive LD signal in the same wavelength region, suggesting the orientation of the molecular plane was nearly parallel relative to the flow direction. Surprisingly, the LD signal in the DNA absorption region for both of the porphyrins was positive. Therefore, the helix axis of the DNA was near perpendicular relative to the flow direction in the porphyrin-polynucleotide assembly.

Role of environmental factors on the structure and spectroscopic response of 5'-DNA-porphyrin conjugates caused by changes in the porphyrin-porphyrin interactions

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

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

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.

Dispersion of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin on [d(A-T)n]2 oligonucleotides

The binding modes of the free-base meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with [d(AT)n]2 oligonucleotides (where n=3-8, corresponding to 6 to 16 AT base pairs) were studied by circular dichroism (CD). When associated with the shortest oligonucleotide, ([d(AT)3]2), a bisignate CD spectrum was produced in the Soret absorption region at the mixing ratio between 2.0 and 0.25, corresponding to one TMPyP per 0.5 to 4 oligonucleotides. Apparent bisignate CD was attributed to a stacked TMPyP along the DNA. On the other hand, when the oligonucleotide length reaches one helical turn or longer, ([d(AT)n]2, n=6,7,8), TMPyP exhibited a positive CD signal, that corresponds to the monomeric groove binding mode, at the mixing ratio below 1.0 (one TMPyP per oligonucleotide). As the mixing ratio increases, the CD signal was best accounted for by the sum of the stacked and groove-binding TMPyP. At the intermediate oligonucleotide length ([d(AT)n]2, n=4,5), the CD spectrum appeared to be the sum of the stacked and groove binding TMPyP at all mixing ratios. Therefore, it is conclusive that the full dispersion of TMPyP requires at least one helical turn of the AT sequence at a mixing ratio below 1.0. Further increase of the mixing ratio resulted in the stacking of TMPyP even at the long oligonucleotides.