DNA-binding studies of Cu(T4), a bulky cationic porphyrin

Carbazole appended trans-dicationic pyridinium porphyrin finds supremacy in DNA binding/photocleavage over a non-carbazolyl analogue

A carbazolyl appended trans-pyridyl porphyrin (1) was synthesized and its dicationic form 2 was obtained by methylation of the pyridyl group. Copper and zinc complexes of porphyrin 2 (Cu(II), 3; Zn(II), 4) were isolated and characterized by various modern spectroscopic techniques. The DNA binding properties of 2, 3, and 4 have been explored against calf thymus-DNA (CT-DNA). DNA binding was quantized using the intrinsic binding constant (K_b) that was calculated by UV-visible absorption spectroscopy, and the value K_b = 1.6 × 10⁶ M^-1 for compound 2 reveals a better interaction of 2 towards CT-DNA than those of 3 (3.1 × 10⁵ M^-1) and 4 (3.4 × 10⁵ M^-1), which follows the order 2 > 4 > 3. The fluorescence quenching efficiency and ethidium bromide quenching assay also indicated a good binding affinity of all the compounds towards CT-DNA. Furthermore, the spectroscopic data suggest that the possible mode of interaction is intercalation. The docking studies were in accordance with the experimental results. Notably, DNA cleavage studies reveal that 2 shows better damage than 3 and 4 which is in accordance with the binding affinity order 2 > 4 > 3. The observed quantum yield (2: 0.65, 3: 0.33, and 4: 0.97) and no change in DNA cleavage in the presence of NaN₃ reveal the involvement of singlet oxygen. The singlet excited state lifetimes were in the range of 6.3-1.2 ns. Furthermore, these porphyrins can be investigated as interesting photosensitizers in photodynamic therapy and photochemotherapy.

DNA binding of Pd(TC3), a conformable cationic porphyrin with a long-lived triplet state

The goal of this work has been to synthesize and investigate Pd(TC3), an intercalating porphyrin that has conformable substituents capable of groove binding to B-form DNA. (TC3 denotes the doubly deprotonated form of 5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)prop-1-yl]porphyrin.) Palladium(ii) is an apt choice for the central metal ion because it remains strictly four-coordinate and provides for a luminescent triplet excited state with a long lifetime. The DNA hosts are hairpin-forming sequences programmed to differ in base composition. Luminescence, absorbance, and circular dichroism results are consistent with the idea that congruent structural reorganization takes place at the host and ligand during uptake. Photoexcitation of DNA-bound Pd(TC3) generates a comparatively modest steady state concentration of singlet oxygen, due to a relatively slow reaction with molecular oxygen in solution. The sheer size of the substituent groups disfavors quenching, but groove-binding interactions compound the problem by inhibiting mobility. The results show how ligand design affects adduct structure as well as function.

Drop-Coating Deposition Raman (DCDR) Spectroscopy as a Tool for Membrane Interaction Studies: Liposome-Porphyrin Complex

Drop-coating deposition Raman (DCDR) spectroscopy is based on the measurement of a sample that has been preconcentrated by being dried on a special hydrophobic plate. In addition to its higher sensitivity, the advantage of DCDR over the conventional Raman spectroscopy is the small sample volume needed, the lack of interference from solvents, and the capability of segregating any impurities present and separating components in more complex samples. In this study, DCDR spectroscopy was employed to investigate the complex of the cationic copper(II) 5,10,15,20-tetrakis(1-methyl-4-pyridyl) porphyrin (CuTMPyP) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes. Drop-coating deposition Raman spectra were treated using factor analysis (FA), which led to the following conclusions: (i) the distribution of CuTMPyP in the complex is not homogenous, (ii) the DCDR technique segregates complexed and noncomplexed parts of the sample, (iii) the spectral changes caused by the drying process and by the interaction of CuTMPyP with the DPPC liposomes can be distinguished, and (iv) the porphyrin molecules interacting with DPPC affect both the order-disorder properties of the lipid chains and the lipid head.

Synthesis, characterization and biomolecule-binding properties of novel tetra-platinum(ii)-thiopyridylporphyrins

New tetra-platinum(ii)-thiopyridylporphyrin complexes and their DNA binding studies.

Primary photoprocesses in cationic 5,10,15,20-meso-tetrakis(4-N-methylpyridiniumyl)porphyrin and its transition metal complexes bound with nucleic acids

Photophysical properties of meso-tetrakis(4-N-methylpyridiniumyl)porphyrin ( TMpyP 4) and its metallocomplexes M (II) TMpy P4 ( M = Zn , Cu , Ni , Co ) bound to natural DNA and synthetic poly-, oligo- and mononucleotides are considered with a primary emphasis placed upon intermolecular interaction of the photoexcited porphyrins with the nearest environment. Quenching of the fluorescent S 1 (but not triplet T 1) state due to guanine to porphyrin electron transfer is observed for TMpyP 4 intercalated between GC base pairs of the double-strand helixes, whereas in the case of TMpyP 4 complexed with guanosine monophosphate (GMP) both S 1 and T 1 states of the porphyrin are quenched. Furthermore, a dependence of the efficiency of TMpyP 4 triplet state quenching by the dissolved molecular oxygen from air on the porphyrin localization enables one to readily distinguish porphyrin groove binding mode from intercalation. Excited states of the TMpyP 4 complexes with transition metals, in spite of their very short lifetimes, also interact with nucleic acid components by means of an axial ligand binding/release to/from the metal. A possible structure of the five-coordinate excited complex (“exciplex”) formed in case of CuTMpyP 4 groove binding to some single- and double-strand polynucleotides is discussed.

Kinetics of porphyrin adsorption and DNA-assisted desorption at the silica-water interface

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) has been used to study in situ the kinetics of the adsorption of 5,10,15,20-tetrakis(4-N-methylpyridiniumyl)porphyrin (TMPyP) from pH 7.4 phosphate buffer solution (PBS) to the silica-water interface and the interaction of calf thymus DNA (CT-DNA) with the resulting TMPyP-functionalized surface. TMPyP was delivered to the silica surface using an impinging jet technique to allow relatively fast surface kinetics to be accessed. Adsorption was first-order in TMPyP, and the initial adsorption rate constant at the bare surface was found to be k = (4.1 +/- 0.6) x 10(-2) cm s(-1). A deceleration in the adsorption kinetics was observed at longer times that could be described semiquantitatively using an Elovich-type kinetic expression. The limiting value of the absorbance corresponded approximately to monolayer coverage (6.2 x 10(13) molecules cm(-2)). Exposure of the TMPyP-modified silica surface to CT-DNA, achieved by flowing CT-DNA solution over the functionalized surface, resulted in efficient desorption of the TMPyP. The desorption process was driven by the interaction of TMPyP with CT-DNA, which UV-vis spectroscopy indicated involved intercalative binding. The desorption kinetics were also simulated using complementary finite element modeling of convection-diffusion coupled to a surface process.

Steric effects direct the binding of porphyrins to tetramolecular quadruplex DNA

The binding motifs of copper(II) porphyrins with G quadruplex DNA structures vary markedly depending on the steric demands of the ligand and the host structure.

Synthesis of novel diselenide-linked porphyrin dimers under phase-transfer catalysis condition and their interactions with DNA

Novel diselenide-linked porphyrin dimers were synthesized under phase-transfer catalysis conditions. The targeted compounds were characterized by (1)H-NMR, high-resolution mass spectrometry, UV/VIS and fluorescence spectroscopies, redox-potential measurements, and elemental analysis. The interaction of the title compounds with DNA was studied using UV/VIS, fluorescence, and circular dichroism (CD) spectroscopies. The relative rates of singlet-oxygen production from the diselenide-linked porphyrin dimers upon photoirradiation were also measured.

Pyrophosphate-bridged complexes with picomolar toxicity

Recently, we have observed the emergence of a new series of pyrophosphate-bridged coordination complexes. Such complexes have been prepared by overcoming the ready hydrolysis of the pyrophosphate moiety. To date, no exploration has been conducted on the cytotoxicity of such complexes. Three pyrophosphate-bridged complexes, namely {[Ni(phen)(2)](2)(mu-P(2)O(7))}.27H(2)O, {[Cu(phen)(H(2)O)](2)(mu-P(2)O(7))}.8H(2)O and {[Co(phen)(2)](2)(mu-P(2)O(7))}.6MeOH, (where phen is 1,10'-phenanthroline) were chosen for their comparative structural similarities and suitable aqueous solubility. Cytotoxicity studies in the adriamycin-resistant ovarian cancer cell line A2780/AD demonstrated highly significant efficacy, with values as low as 160pM for the cobalt complex at 72h. The underlying mechanism for such exceptional toxicity is investigated focusing on DNA interactions, topoisomerase I enzyme inhibition and oxidative stress (followed by intracellular glutathione levels). The role of hydrolysis in uptake and toxicity is also explored (followed by electronic absorption spectroscopy, (31)P NMR, and confocal microscopy) and the complexes are compared to cisplatin controls. Overall a clear picture of the extraordinary toxicity emerged. The results demonstrate a new class of prodrugs with significant potential for future development for the treatment of drug-resistant cancer cell lines.

Novel ebselen–porphyrin conjugates: Synthesis and nucleic acid interaction study

Novel porphyrins bearing ebselen (2-phenyl-1,2-benzisoselenazol-3[2H]-one) moiety were synthesized and characterized. Their interactions with herring sperm DNA were studied by means of UV-visible, fluorescence, circular dichroism spectroscopy, and gel electrophoresis.

DNA binding studies of a new dicationic porphyrin. Insights into interligand interactions

Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.

Interaction of an Fe derivative of TMAP (Fe(TMAP)OAc) with DNA in comparison with free-base TMAP

We investigated the interaction of meso-tetrakis (N-para-methylanilium) porphyrin (TMAP) in its free base and Fe(II) form (Fe(TMAP)OAc) as a new derivative, with high molecular weight DNA at different ionic strengths, using various spectroscopic methods and microcalorimetry. The data obtained by spectrophotometery, circular dichroism (CD), fluorescence quenching and resonance light scattering (RLS) have demonstrated that TMAP association with DNA is via outside binding with self-stacking manner, which is accompanied with the "end-on" type complex formation in low ionic strength. However, in the case of Fe(TMAP)OAc, predominant mode of interaction is groove binding and after increasing in DNA concentration, unstable stacking-type aggregates are formed. In addition, isothermal titration calorimetric measurements have indicated the exothermic process of porphyrins binding to DNA, but the exothermisity in metal derivative of porphyrin is less than the free base. It confirmed the formation of a more organized aggregate of TMAP on DNA surface. Interactions of both porphyrins with DNA show high sensitivity to ionic strength. By addition of salt, the downfield CD signal of TMAP aggregates is shifted to a higher wavelength, which indicates some changes in the aggregates position. In the case of Fe(TMAP)OAc, addition of salt leads to changes in the mode of binding from groove binding to outside binding with self-stacking, which is accompanied with major changes in CD spectra, possibly indicating the formation of "face-on" type complex.

Origin of the bathochromically shifted optical spectra of meso-tetrathien-2'- and 3'-ylporphyrins as compared to meso-tetraphenylporphyrin

The UV-Vis and fluorescence spectra of free base and diprotonated meso-tetrathien-2'-ylporphyrins are, when compared to the spectra of meso-tetra-phenyl- or even -thien-3'-ylporphyrins, characterized by surprisingly large red-shifts. A comparison of the optical spectra and the computed rotational barriers for these meso-aryl-substituted porphyrins and a detailed conformational analysis of the single crystal X-ray structure of a diprotonated meso-tetrathien-2'-ylporphyrin suggest that the origin of the altered electronic properties of meso-tetrathien-2'-ylporphyrins are mainly due to the contribution of conformations in which the thienyl groups adopt idealized co-planar arrangements with the porphyrin ring. These conformations allow an efficient extension of the porphyrinic pi-system through conjugation. We synthesized a meso-tetrathien-2'-ylporphyrin with methyl groups in the o-position, thus preventing the formation of conformers with co-planar thienyl groups and a corresponding thien-2'-ylporphyrin with methyl substituents in a distal position that possesses the same steric requirements for thienyl group rotation as the parent compound, to conclusively deduce the influence of the conformers on the electronic structure. A MNDO-PSDCI computation of their optical spectra further supports our key hypothesis. DFT computations of the total energies of the hypothetical diprotonated thien-2'-ylporphyrin conformer with perpendicular thienyl groups and the conformer containing near-co-planar thienyl groups quantify the resonance stabilization energy. Our results support and complement recent photophysical and theoretical studies by Gupta and Ravikanth and Friedlein et al. on thien-2'-yl-substituted core-modified porphyrins and [meso-tetra(5'-bromothien-2'-yl)porphyrinato]Zn(ii), respectively.

The DNA-Porphyrin Interactions Studied by Vibrational and Electronic Circular Dichroism Spectroscopy

The interactions of three different porphyrins, without axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP), with axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Fe(III) pentachloride (Fe(III)TMPyP), and with bulky meso substituents - 5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)-porphyrin tetrachloride (TMAP), with calf thymus DNA were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy, and by IR and UV-VIS absorption spectroscopy. It has been shown that Cu(II)TMPyP prefers the intercalative binding mode with DNA in the GC-rich regions and the intercalative sites are saturated at the c(DNA)/c(Cu(II)TMPyP) ratio ~3:1, where c(DNA) and c(Cu(II)TMPyP) are total molar concentrations of nucleic acid in base pairs and porphyrin, respectively. Fe(III)TMPyP does not intercalate between the GC base pairs but binds to DNA in the minor groove. At higher c(DNA)/c(TMAP) ratios, TMAP interacts with DNA in the minor groove, but at lower ratios in the major groove and by the external binding mode accompanied by self-stacking of porphyrins along the phosphate backbone. VCD spectroscopy reliably discriminates the binding modes and specifies the conformational changes of the DNA matrices. It has been also shown that VCD spectroscopy is an effective tool for the conformational studies of DNA-porphyrin complexes. New spectroscopic "markers" in VCD spectra have been found for the specific DNA-porphyrin interactions.

Synthesis of beta-substituted cationic porphyrins and their interactions with DNA

The beta-substituted cationic porphyrins (7, 8 and 10) have been synthesized and their interactions with plasmid DNA investigated. We found that substituents at the beta-position of porphyrins (7 and 8) have apparently affected their interactions with DNA compared with non-beta-substituted porphyrins (10).

Synthesis of novel types of copper-bipyridyl porphyrins and characterization of their interactions and reactivity with DNA

The inherent ability to interact with DNA makes cationic metallo-porphyrins attractive targets as antitumor drugs. Many studies describe their interaction with DNA and the mechanism by which they induce DNA cleavage. Since porphyrins can be used as anchors for chemically reactive groups, it is possible to modify them to generate a family of compounds with specific functions. In the present work, we used chemical groups such as copper-bipyridinium (Cu-bpy), which hydrolyze phosphodiester bonds, and a porphyrin core to synthesize two novel Cu(2)-bpy-porphyrins. Their interactions with DNA have been characterized using classic spectroscopic methods, and their oxidative and hydrolytic reactivity toward supercoiled plasmid DNA has been studied in vitro. Our results show that Cu(2)-bpy-porphyrins interact with DNA via external association and intercalation and that their ability to cleave DNA and the mechanisms depends on the experimental conditions.

Peripheral substituents of di(pyridiumyl)porphyrins affected on their interactions with DNA

meso- and beta-Substituted di(pyridiumyl)porphyrins 3, 4, and 7 have been synthesized and their interactions with DNA have been investigated. meso-Substituted porphyrins showed the stronger effect on DNA than that of beta-substituted porphyrin. Cytotoxicity of compound 3 (IC(50)) to THP-1 tumor cell was up to 0.11 nM.

Photophysics and photochemistry of water-soluble, sitting-atop bis-thallium(i) 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin

In aqueous solutions, thallium(I) ions and 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin form a kinetically labile metalloporphyrin of 2 : 1 composition (Tl(2)P(4-)). The formation constant of this sitting-atop (SAT) complex is relatively low (beta2/[H+]2= 3.55 x 10(3) M(-2) at pH = 7), due to the large size and rather small charge of Tl+. As a consequence of the considerably weak metal-ligand interaction in this system, the 1 : 1 species does not appear in detectable concentration. Both the absorption and the emission properties of the Tl(2)P(4-) complex are characteristic for the typical SAT metalloporphyrins. Compared to the corresponding values of the free-base porphyrin, the diminished fluorescence quantum efficiency (Qfl= 0.0131 vs. 0.056) of Tl(2)P(4-) can be accounted for by the heavy-atom effect, while the larger Stokes shift (442 vs. 282 cm(-1)) indicates a stronger distortion of the ligand plane. Both Soret- and Q-band irradiations of the Tl(2)P(4-) complex lead to the degradation of the porphyrin with quantum yields of magnitude 3 x 10(-4). The primary photochemical step in this process is ligand-to-metal charge transfer reaction, which is unusual for normal (coplanar) metalloporphyrins. In the case of SAT complexes, the kinetic lability facilitates the separation of the primary redox products, followed by an irreversible ring-opening of the oxidized porphyrin. Photoinduced electron ejection as a considerable step in the degradation mechanism could be ruled out.

Preparation, electrochemical and spectral properties of N-methylated pyridylethynyl porphyrins

A new series of electron-deficient porphyrins were prepared by attaching one or two N-methylated 2-, 3- or 4-pyridylethynyl groups to the 10,20-meso positions of (5,15-biphenylporphinato)zinc(II). Electrochemical studies showed significant changes in the reduction potentials of these porphyrins, and N-methyl-2-pyridylethyne is the strongest electron-withdrawing substituent in the series. UV-visible spectra demonstrated largely red-shifted absorptions, and N-methyl-4-pyridylethyne has the greatest impact to the porphyrin absorptions. Electrochemical, UV-visible and EPR results concluded that porphyrins Zn2 and Zn6 reversibly undergo two one-electron porphyrin-ring reductions to their anion radicals then dianions. The first reductions of porphyrins Zn1, Zn3, Zn4 and Zn5 were irreversible one-electron transfer processes. The instability of these reduction products was suggested to result from the eletrophilic attacks at the substituents.

New Dicationic Porphyrin Ligands Suited for Intercalation into B-Form DNA

This paper describes the synthesis and characterization of a new series of sterically nondemanding, dicationic porphyrins that exhibit novel DNA-binding interactions. Cationic porphyrins continue to be the focus of a great deal of effort because of the promise they have for use in photodynamic, antiviral, and anticancer therapies. The systems explored here include 5,15-di(N-methylpyridinium-4-yl)porphyrin (H2D4), 5,15-di(N-methylpyridinium-3-yl)porphyrin (H2D3), and 5,15-di(N-methylpyridinium-2-yl)porphyrin (H2D2), as well as Zn(D4) and Zn(D3), the zinc(II)-containing derivatives of H2D4 and H2D3, respectively. Viscometry studies, in conjunction with various spectroscopic techniques, reveal the nature of the adducts formed with DNA. Irrespective of the base composition, H2D4 and H2D3 bind to DNA by intercalation. The zinc derivatives Zn(D4) and Zn(D3) are also intercalators; however, the binding constants are smaller because uptake requires the loss of an axial ligand. The decisive roles that steric factors and structural rigidity play in shaping the adducts with DNA become clear. Sequences that contain mainly adenine-thymine base pairs easily depart from the canonical B-form DNA structure and generally accommodate bulky porphyrins in external binding sites. However, with the H2D3 and H2D4 systems, the steric requirements are so minimal that intercalation becomes the preferred mode of binding, even in [poly(dA-dT)]2. The intercalated form of the H2D2 isomer is less stable, probably because of frontal strain associated with the (N-methyl)pyridinium-2-yl groups. A qualitative energy-level diagram is useful for assessing the forces that influence binding and could guide the design of new porphyrin ligands.