Interactions of water-soluble porphyrins with hexadeoxyribonucleotides: resonance raman, UV-visible and 1H NMR studies

Study on the interaction of new water-soluble porphyrin with DNA

A porphyrin meso-tetrakis{[4-(1-pyridyl)propoxy]phenyl}porphyrin (TPyPP) and its Ni complex (TPyPP(Ni)) have been synthesized and characterized by 1H NMR, UV-vis spectra. The interaction of two porphyrins with calf thymus-DNA (CT-DNA) has been explored by UV-vis, fluorescence and circular dichroic spectroscopy and viscosity measurements. The results suggest that these porphyrins can bind to DNA by the same binding mode. TPyPP outside binds by self-stack with DNA both at low drug load r (=[porphyrin]/[DNA]) and high drug load. Though TPyPP(Ni) has center metal nickel, binding mode with DNA has little difference compared with TPyPP, dominating out-binding mode with different direction along DNA. The binding constants of the TPyPP and TPyPP(Ni) to DNA were 4.65 x 10(5) M(-1) and 3.2 x 10(5) M(-1), respectively. A colored precipitate was found after time in two porphyrin's viscosity measurement. The reasonable interpretation is the porphyrins with alkyl connected N-position of pyridine can strongly interact with the anionic phosphates of DNA and lead to hydrophobic complex.

Copper insertion facilitates water-soluble porphyrin binding to rA.rU and rA.dT base pairs in duplex RNA and RNA.DNA hybrids

The binding of the copper(II) complex of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to double-helical polynucleotides has been studied by optical absorption, circular dichroism (CD), and resonance Raman spectroscopic methods. The target polymers were RNA and RNA.DNA hybrids consisting of rA.rU, rI.rC, rA.dT, and rI.dC base pairs. Relative to the metal-free H(2)TMPyP [Uno, T., Hamasaki, K., Tanigawa, M., and Shimabayashi, S. (1997) Inorg. Chem. 36, 1676-1683], CuTMPyP binds to poly(rA).poly(dT) and poly(rA).poly(rU) with a greatly increased binding constant. The external self-stacking of the porphyrin on the surface of the polymers was evident from the strong conservative-type induced CD signals. The signal intensity correlated almost linearly with the number of stacking sites on the polymer except for poly(rA).poly(dT), which showed extraordinarily strong CD signals. Thus, the bound porphyrin may impose an ordered architecture on the polymer surface, the stacking being facilitated by the more planar nature of the CuTMPyP than the nonmetal counterpart. Resonance Raman spectra of the stacked CuTMPyP were indistinguishable from those of the intercalated one with positive delta(Cbeta-H) and negative delta(Cm-Py) bending shifts, and hence the stacked porphyrins are suggested to adopt a similar structure to that of intercalated ones. Porphyrin flattening by copper insertion opens a new avenue for medical applications of porphyrins, blocking biological events related to RNA and hybrids in malignant cells.

Cationic porphyrins bearing diazolium rings: synthesis and their interaction with calf thymus DNA

Two novel cationic porphyrins bearing five-membered rings at the meso-positions, meso-tetrakis(1,3-dimethylimidazolium-2-yl)porphyrin (H2TDMImP) and meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin (H2TDMPzP), have been synthesized. These two compounds interact with calf thymus DNA (CTDNA) in different binding modes from that of mesotetrakis(N-methylpyridinium-4-yl)porphyrin (H2TMPyP). H2TDMImP outside binds to the minor groove of CTDNA while H2TDMPzP intercalates into CTDNA. These two novel cationic porphyrins strongly bind to CTDNA even at high ionic strength and the binding constant of H2TDMPzP to CTDNA is comparable to that of H2TMPyP. The binding of H2TDMImP to CTDNA is enthalpically driven. The favorable free energy changes in binding of H2TDMPzP to CTDNA come from the large negative enthalpy changes accompanied by small positive entropy changes.

5,10,15,20-Tetrakis(4-N-methylpyridyl)porphyrinato-palladium(II ) as a differentiation probe for sensing binding modes with B-DNA duplexes: electronic MCD and CD spectra

We report our detailed electronic MCD, CD, and optical spectroscopic measurements and analysis of the porphyrin Soret (B(o)) region of four-coordinate 5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrinatopalladium( II), PdP(4), and its bound states with B-DNA duplexes poly(A-T)2, poly(G-C)2, and calf thymus DNA (CT DNA). For system PdP(4)/poly(A-T)2 it was possible to conclude that the porphyrin is bound edge-on in the major groove, specifically at the 5'AT3' site. For this orientation the porphyrin's electric dipole transition moments (edtm), mu(x) (most perturbed direction) and mu(y) (least perturbed direction), have tilt angles alpha approximately 90 degrees and approximately 45 degrees , respectively, relative to the helix axis. It was further concluded from the small shifts of B(o) optical and MCD band intensities and wavelengths and from the net MCD (+) A-term sign retention upon binding that the porphyrin's frontier ppi MOs (1a(1u) 3a(2u) 4eg) are only weakly perturbed by the heterocyclic bases of poly(A-T)2, and therefore that the LUMO (4eg) splitting is less than the |1a(1u)-3a(2u| energy separation, deltaHOMO, that is, deltaLUMO < deltaHOMO for the bound state in PdP(4)/poly(A-T)2. For intercalation systems PdP(4)/ poly(G-C)2 and /CT DNA, with PdP(4) centered in the intercalation "pocket" and having two of its 4-N-methylpyridyls extending into each of the major and minor grooves, the edtms mu(x) and mu(y) were determined to be oriented perpendicular (gamma approximately 0 degrees) and parallel (gamma approximately 90 degrees) to the hydrogen bonds of the base pairs, respectively. Intercalation is characterized by a much stronger binding interaction, viz., the B(o) optical band and net MCD extrema wavelength shifts are relatively large, and the net MCD (+) A-term of PdP(4) is substantially quenched as it becomes the (-) pseudo-A-term of intercalated PdP(4)/poly(G-C)2. This A-term sign reversal informs that the porphyrin MOs are so strongly perturbed by the GC base pairs that deltaLUMO > deltaHOMO, which gives rise to a (-) pseudo-A-term. Also, the findings demonstrate (1) the potential of PdP(4) as a sensitive, discriminating analytical probe of DNA sequences and (2) the diagnostic capability of the composite of five spectra [net MCD, CD, and optical of free and bound PdP(4)] in differentiating the site and sequence selectivity and preferred binding mode of this porphyrin.

A series of meso-tris (N-methyl-pyridiniumyl)-(4-alkylamidophenyl) porphyrins: synthesis, interaction with DNA and antibacterial activity

A series of meso-5,10,15-tris(N-methyl-4-pyridiniumyl)-20-(4-alkylamidophen yl) porphyrins were synthesized by derivatizing the amino group on the phenyl ring with the following hydrophobic groups: -C(O)C7F15, -C(O)CH=CH2, C(O)CH3, -C(O)C7H15, and -C(O)C15H31. The cationic tris-pyridiumyl porphyrin core serves as a DNA binding motif and a photosensitizer to photomodify DNA molecules. The changes of the UV-Vis absorption spectra during the titration of these porphyrins with calf thymus DNA revealed a large bathochromic shift (up to 14 nm) and a hypochromicity (up to 55%) of the porphyrins Soret bands, usually considered as proof of porphyrin intercalation into DNA. Association constants (K) calculated according to the McGhee and von Hippel model, were in the range of 10(6)-10(7) M(-1). An increase in hydrophobicity of the substituents at the 20-meso-position produced higher binding affinity. These porphyrins caused photomodification of the supercoiled plasmid DNA when a green laser beam at 532 nm was applied. Those with higher surface activity acted more efficiently as DNA photomodifiers. The porphyrin with a perfluorinated alkyl chain (-COC7F15) at the meso-20-position inhibited the growth of gram-positive bacteria (S. aureus, or S. epidermidis). Other porphyrins exhibited moderate activity against both gram-negative and gram-positive organisms.

Binding of meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin to Double Helical RNA and DNA.RNA Hybrids

The binding properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (H(2)TMPyP) to RNA and DNA.RNA hybrid duplexes were studied by absorption and circular dichroism (CD) spectra. The duplexes studied were poly(rA).poly(rU), poly(rA).poly(dT), poly(rI).poly(rC), poly(rI).poly(dC), poly(rG).poly(rC), and poly(rG).poly(dC). The hypochromicity (about 40%) and the bathochromic shift (about 15 nm) of the porphyrin Soret absorption band upon binding were quite similar among the duplexes examined. The large bathochromic shift and hypochromicity suggested a significant perturbation in the porphyrin pi electrons upon binding. H(2)TMPyP was found to bind in a single step to poly(rI).poly(rC), poly(rG).poly(rC), and poly(rG).poly(dC) and in a multistep manner to poly(rA).poly(rU), poly(rA).poly(dT), and poly(rI).poly(dC). The induced CD spectra in the visible range suggested that the porphyrin preferred to bind to the RNA duplexes with self-stacking along the polymer surface and to the hybrids with intercalation, at least at higher duplex load. This implied a distinct conformational difference between the RNA duplexes and DNA.RNA hybrids, and a drug molecule is able to recognize the difference. The number of binding sites per base pairs (n), however, was very different among the RNA duplexes examined. We also found that the intensity of the bisignate-induced CD bands is proportional to the n value. This suggested that the transition moments on the neighboring porphyrins are interacting considerably with each other to produce intense induced CD peaks.

H NMR and electronic absorption spectroscopy of paramagnetic water-soluble meso-tetraarylsubstituted cationic and anionic metalloporphyrins

The ionization, mu-oxo-dimerization and axial ligation equilibria of free bases, iron(III) and manganese(III) derivatives of meso-tetrakis(p-sulfonatophenyl)porphyrin (TPPS4) and meso-tetrakis(4-N-methyl-pyridiniumyl)porphyrin (TMPyP) in aqueous solution are studied by 1H NMR and electronic absorption spectroscopy. At physiological pH, Fe(III) complexes of TMPyP and TPPS4 exist predominantly as dimers and may undergo transition to low spin species upon binding to biomolecules, whereas Mn(III) complexes are essentially monomeric. Dicyano and bis-imidazole complexes of FeTMPyP and FeTPPS4 are low spin monomer adducts in the pH range 2.0 to 11.2. No low spin dimeric complexes were found. The low spin monocyano and high spin mono-imidazole complexes of FeTMPyP are formed in acidic and alkaline media, respectively. T1-relaxation enhancement of water protons at 200 MHz induced by FeTPPS4 falls dramatically in the sequence high spin >> dimeric > low spin form.

Base pair selectivity in the binding of copper (II) tetrakis (4-N-methylpyridyl)porphine to polynucleotides under closely packed conditions

The base pair selectivity of the intercalative binding of the copper porphyrin, copper (II) tetrakis(4-N-methylpyridyl)porphine (Cu(II)TMpyP-4), to DNA has been investigated using a variety of DNA types and the synthetic polynucleotides poly(dG-dC)2 and poly(dA-dT)2. The studies utilize electron paramagnetic resonance of concentrated gels which are thought to mimic the closely packed state of nuclear DNA. The results indicate that intercalation of this porphyrin is preferred for sites containing two adjacent G-C base pairs, irrespective of sequence.

Fluorescence formation during photodynamic therapy in the nucleus of cells incubated with cationic and anionic water-soluble photosensitizers

The variations of fluorescence during light exposure of the cationic sensitizers methylene blue (MB) and meso-tetra(4N-methylpyridyl)porphyrin (T4MPyP) as well as the anionic meso-tetra(4-sulphonatophenyl)porphyrin (TPPS4) were measured at different intracellular sites using video-intensified microscopy in combination with microspectrofluorometry. Before light exposure the sensitizers were localized in distinct parts of the cytoplasm, especially in fluorescent organelles. During irradiation a drastic fluorescence formation and increase in the cytoplasm and nucleus, which was most pronounced in the nucleoli, could be observed for the cationic sensitizers as well as TPPS4. In the case of MB the increase in fluorescence was concomitant with a spectral shift in the emission spectra. For TPPS4 and T4MPyP the formation of a second species with a Soret band shifted towards longer wavelengths was observed and correlated with the fluorescence increase in the nucleoli. Cell deformations also took place.