Binding mode of porphyrins to poly[d(A-T)2] and poly[d(G-C)2]

Features of the interaction of 5-[4'-(6″-aminopurin-2″-yl)phenyl]-10,15,20-tri(N-methylpyridin-3'-yl)-porphyrin with nucleic acids

Directed synthesis of novel water-soluble asymmetric porphyrins containing in a molecule three cationic fragments and residues of adenine (PorAD) was performed, using metal-complex catalysis method. The interaction of the synthesized porphyrin with the oligonucleotides poly[d(AT)2] and poly[d(GC)2] and double-stranded deoxyribonucleic acid of the calf thymus (ctDNA) was studied by means of spectral and hydrodynamic methods. It was established that PorAD intercalated not only into GC-enriched regions, but also into AT regions. It was revealed that a distinctive feature of PorAD complexes with nucleic acids was a weak shielding from water molecules, and it implies significant disturbances in the conformation of the nucleic acid; the disturbances being especially pronounced for poly[d(AT)2].

Development of viscometric methods for studying the interaction of various porphyrins with DNA. Part IV: Meso-tetra-(4N-allylpyridyl) porphyrin and its Cu-, Co- and Zn-containing derivatives

The influence of water soluble cationic meso-tetra-(4N-allylpyridyl) porphyrin (H2TAlPyP4) and its metal complexes with Cu, Co and Zn on hydrodynamic and spectral behavior of DNA solutions has been studied by viscometry, CD and UV-vis spectroscopy methods. The results were compared with the results of previously conducted similar studies on meso-tetra-(3N-allylpyridyl) porphyrin (H2TAllPyP3). It has been shown that the change in position of peripheral radicals on the pyridylic ring has absolutely no effect on the rules of interaction of investigated porphyrins with DNA in the case of outside binders CoTAllPyP4 and ZnTAllPyP4. Planar porphyrin H2TAllPyP4 interacts with DNA predominantly by the intercalation mode at low relative concentrations of [Formula: see text] ([Formula: see text] [Porphyrin]/[DNA]) and by external binding mode at high values of [Formula: see text]. CuTAllPyP4 shows unusual behavior by interacting with DNA via a non-classical (partial) intercalation binding mode. It was shown that H[Formula: see text]TAllPyP3 and its metal complexes bind to DNA much more intensely than H2TAllPyP4 and its metal complexes.

Sequence selective photoinduced electron transfer of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to various DNAs (calf thymus DNA (Ct-DNA), poly[d(G-C)2], and poly[d(A-T)2]) have been investigated using circular dichroism and linear dichroism measurements. Based on the polarization spectroscopic results, it can be shown that the pyrenyl and porphryin planes are skewed to a large extent for PyTMPyP in an aqueous environment and in the binding site of poly[d(G-C)2]. In this complex, a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties occurs. On the other hand, PET was not observed in the PyTMPyP-poly[d(A-T)2] complex, whereas the fluorescence intensity of TMPyP was enhanced. The molecular planes of the pyrene and porphyrin moieties are almost parallel in the poly[d(A-T)2] and Ct-DNA adducts. Moreover, the generation of 1O2 species occurs only for the PyTMPyP-Ct-DNA and PyTMPyP-poly[d(A-T)2] complexes. We discuss the photophysical properties of PyTMPyP which are attributed to the binding patterns and the sequence of DNA bases.

Copper-metformin ternary complexes: Thermal, photochemosensitivity and molecular docking studies

The copper(II) complexes [Cu(Cl)₂(met)(o-phen)] (1), [Cu(Cl)₂(met)(en)] (2) and [Cu(Cl)₂(met)(opda)] (3) (met = metformin, o-phen = ortho-phenanthroline, en = ethylenediamine, opda = ortho-phenylenediamine) were synthesized and characterized by LC-MS, elemental analysis, molar conductance, thermal analysis, infrared spectra, magnetic moment, electronic spectra and XRD studies. The metal center was found in an octahedral geometry. The activation thermodynamic properties were calculated using Coats-Redfern method. Thermal decomposition processes of complexes 1, 2, 3 are non-spontaneous, i.e., the complexes are thermally stable. The positive value of Gibbs free energy of decomposition (ΔG^⁎) for the Cu(II) complexes is non-spontaneous processes. UV-Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV-Vis spectrum with DNA. The binding constants K_b from UV-Vis absorption studies were 4.6 × 10⁵, 1.48 × 10⁵, 2.09 × 10⁵ M^-1 for 1, 2, 3 respectively and Stern-Volmer quenching constants (K_sq) from fluorescence studies were 0.636, 0.293, 0.487 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT-DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decreases in the order of 1 > 3 > 2. The complexes were docked in to B-DNA sequence, 5'(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3' retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.

Relationship between the photoinduced electron transfer and binding modes of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to DNA and its photophysical properties have been investigated using various spectroscopic techniques. The circular dichroism (CD) spectrum of PyTMpyP bound to DNA (PyTMpyP-DNA) showed one negative and two positive bands in the Soret region. The CD signal in the pyrene absorption region was positive. The shape of the CD spectrum does not support an intercalative binding mode of TMpyP, which would typically afford a negative CD band in the absence of the pyrene moiety. Linear dichroism (LD) experiments revealed a very small signal in the Soret region, which also challenges the intercalation of TMpyP into DNA. Upon excitation of the pyrene moiety, the emission intensity of porphyrin in aqueous solution was quenched due to a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties. On the other hand, the emission of porphyrin was markedly enhanced upon binding to DNA, as the PET process from the excited pyrene moiety to TMpyP was suppressed when bound to DNA. The PET process occurs in the timescale of 65 ps, and could be detected by femtosecond transient absorption spectroscopic methods. Two fluorescence decay times were observed for PyTMpyP in aqueous solution (0.78 and 4.8 ns). Both decay times increased upon binding to DNA owing to environment and/or conformational changes in PyTMpyP. The driving force (ΔG) of the PET process was evaluated under conditions of minor and major groove binding. The PET process and photophysical properties of the PyTMpyP dyad were concluded to be influenced by the binding mode.

Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA

Although the transition from B-DNA to the A-form is essential for many biological concerns, the properties of this transition have not been resolved. The B to A equilibrium can be analyzed conveniently because of the significant changes in circular dichroism (CD) and absorption spectrum. CD and linear dichroism (LD) methods were used to examine the binding of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) and its derivatives, Co-TMPyP, with B- and A-calf thymus DNA. B- to A-transitions occurred when the physiological buffer was replaced with a water-ethanol mixture (∼80 v/v %), and the fluorescence emission spectra of TMPyP bound to DNA showed a different pattern under ethanol-water conditions and water alone. The featureless broad emission bands of TMPyP were split into two peaks near at 658 and 715 nm in the presence of DNA under an aqueous solution. In the case of an ethanol-water system, however, the emission bands are split in two peaks near at 648 and 708 nm and 656 and 715 nm with and without DNA, respectively. This may be due to a change in the solution polarity. On the basis of the CD and LD data, TMPyP interacts with B-DNA via intercalation at a low ratio under a low ionic strength, 1 mM sodium phosphate. On the other hand, the interaction with A-DNA (80 v/v % ethanol-water system) occurs in a nonintercalating manner. This difference might be because the structural conformations, such as the groove of A-DNA, are not as deep as in B-DNA and the bases are much more tilted. In the case of Co-TMPyP, porphyrin binds preferably via an outside self-stacking mode with B- and A-DNA.

Chiral Selective Stacking of a Cationic Porphyrin along Z-Form Poly[d(A-T)2]

In this study, the binding mode of porphyrin-free single-stranded poly[d(AT)] and trans-BMPyP was observed in the Z-form trans-BMPyP-poly[d(A-T)₂] complex induced by extensive stacking depending on the temperature and concentration through circular dichroism (CD). The Z-form trans-BMPyP-poly[d(A-T)₂] complex (R = 0.30) retained the Z-form DNA structure at a low temperature (20 °C) by the trans-BMPyP molecules. When the temperature was increased to 60 °C, the DNA was almost unfolded as a single-stranded poly[d(AT)], but the extensive stacking binding mode of trans-BMPyP was maintained and the shape of the porphyrin Soret band was symmetrically changed in comparison with the shape of the Z-form DNA. However, when the temperature was raised to 80 °C, the extensive stacking binding mode of trans-BMPyP was also unfolded almost completely. The binding mode of the trans-BMPyP-single-stranded poly[d(AT)] complex was very similar to the already known binding mode of porphyrins and a double-stranded DNA. The binding mode was dependent on the concentration ratio ([porphyrin]/[DNA]): a monomeric binding mode at a concentration ratio of 0.04, a moderate groove binding mode at a concentration ratio between 0.08 and 0.16, and extensive stacking at a concentration ratio between 0.20 and 0.30. The same result was obtained when the temperature of the Z-form DNA (R = 0.30) was increased to 60 °C. However, those binding modes were not found in cis-BMPyP, which was because, in the extensive stacking of trans-BMPyP along the DNA skeleton, the distance between the two positive methylpyridine ions at the trans site and thymine, one of the DNA bases, is decreased, creating a much more hydrophobic environment. In addition, the poly AT sequences found from the CD spectra for the binding of trans-BMPyP-poly[d(A-T)₂] and trans-BMPyP-poly[d(AT)] (R = 0.30) showed that both of them underwent effective extensive stacking and that the chirality of extensive stacking was dependent on the form of DNA.

DNA-Accelerated Catalysis of Carbene-Transfer Reactions by a DNA/Cationic Iron Porphyrin Hybrid

A novel DNA-based hybrid catalyst comprised of salmon testes DNA and an iron(III) complex of a cationic meso-tetrakis(N-alkylpyridyl)porphyrin was developed. When the N-methyl substituents were placed at the ortho position with respect to the porphyrin ring, high reactivity in catalytic carbene-transfer reactions was observed under mild conditions, as demonstrated in the catalytic enantioselective cyclopropanation of styrene derivatives with ethyl diazoacetate (EDA) as the carbene precursor. A remarkable feature of this catalytic system is the large DNA-induced rate acceleration observed in this reaction and the related dimerization of EDA. It is proposed that high effective molarity of all components of the reaction in or near the DNA is one of the key contributors to this unique reactivity. This study demonstrates that the concept of DNA-based asymmetric catalysis can be expanded into the realm of organometallic chemistry.

Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT)15 and oligo(dG.dC)15

Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed.

Selective binding and reverse transcription inhibition of single-strand poly(A) RNA by metal TMPyP complexes

Ni-, Cu-, and Zn-TMPyP are capable of binding to single-strand poly(A) RNA with high preference and affinity and inhibiting the reverse transcription of RNA by both M-MuLV and HIV-1 reverse transcriptase. With 10 nM azidothymidine, the IC50 value of M-TMPyP could be lowered to 10(-1) μM order.

Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA

We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.

Shedding light on the interactions of guanine quadruplexes with tricationic metalloporphyrins

G-quadruplex DNA presents a potential target for the design and development of novel anticancer drugs. The porphyrin TMPyP4 was early reported to be a suitable motif for G-quadruplex DNA interaction. We inserted various metal ions such as Zn(II), Cu(II), Co(III) in the center of the aromatic core of tricationic TMPyP4-like porphyrin and examined their interactions with an antiparallel G-quadruplex DNA by a combination of spectroscopy and Job plot methods. Porphyrin metallation allowed the conclusion that the presence of one axial ligand perpendicular to the aromatic plane did not hamper π-π stacking interactions between quadruplex and the aromatic parts of porphyrin on the other face while porphyrin with two axial ligands was unable to undergo such interaction due to geometrical factors. Free base porphyrin and porphyrin without axial ligands are able to stabilize the quadruplex structure to a greater extent than the other metal complexes and thus may be potential anti-cancer drugs.

Porphyrin self-assembly as template for RNA?

The self-assembly of chiral porphyrin molecules HpD (hematoporphyrin IX derivative) has been shown to form helical fibers in low salt aqueous conditions. The spectroscopic (UV and circular dichroism (CD)), thermodynamic (Tm, differential scanning calorimetry (DSC)) and microscopic (light and scanning force microscopy (SFM)) examinations of the HpD properties were performed individually and in the presence of nucleic acid double strands (15–60 °C, 0–50 mM NaCl ). The asymmetric HpD molecules themselves at room temperature show sharp positive or negative CD signals, which increase enormously with HpD concentration. The data show strong evidence for the external self-stacking interaction of HpD , pure and in the presence of polynucleotides. At low salt concentration (<40 mM NaCl , pH 7) the spectra change completely by increasing the temperature. At 35 to 40 °C RNA-similar spectra of the pure HpD self-assemblies (without nucleic acids) occur. At higher temperatures the aggregates become unstable and break off. At room temperature the helical structure of the fibers could be visualized by SFM investigations. Molecular modeling analysis offers dynamic arrangements of the self-assemblies from stacks to spiral-like superstructures with increasing temperature. Hydrogen bonding, electron transferring and electrostatic interactions determine the shape of the proposed highly flexible arrangements. Moreover, the interrelation between the HpD stacks and the helix of the polynucleotides was studied. The calculated low transition energies indicate the importance of these structures as a crossing link. All data are discussed in favor of a hypothetical evolutionary matrix role in porphyrin self-assembly for RNA.

Oligopyrenotides: chiral nanoscale templates for chromophore assembly

Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).

Specific visible spectral changes induced by guanine binding to cytosine-derivatized porphyrin

The interaction of the free nucleic acid bases adenine, cytosine, and thymidine with meso-tri(4-sulfonatophenyl) meso 4-phenyl porphyrin cytosine amide (TPSC) trisodium salt at pH 5.9, 7.4, and 9.3 results is a decrease in the absorbance of the Soret (B-band) at 413 nm of TPSC. A decrease in Soret band absorbance is observed with guanine below pH 8; at higher pH values a new absorbance band at 424 nm is observed. The appearance of the band is consistent with hydrogen bonding between the cytosine-functionalized porphyrin and guanine and the resulting perturbation of the electron orbitals of the porphyrin.

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.

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.

A novel and sensitive method for recognition and indirect determination of Al(III) in biological fluid based on the quenching of resonance Rayleigh scattering intensities of "Al(III)-EV-DNA" complexing system

A novel method for recognition and indirect determination of Al(III) by using biological molecules has been established based on the quenching of RRS intensity. In the weak acidic medium, the reaction of ethyl violet (EV) and DNA would result in great enhancement of RRS intensity. However, the presence of Al(III) would lead to the decrease of the RRS intensity owing to the competition coordination of Al with DNA. The decreased intensity of RRS is directly proportional to the concentration of Al(III) in the range of (0.1-2.5)x10(-6) and (0.30-4.5)x10(-5)M, respectively. The method has high sensitivity and its detection limit (3sigma) is 3.6x10(-8)M. The characteristics of RRS spectra of the system, the optimum conditions of the reaction, and the reaction mechanism have been investigated. The method can recognize Al(III) selectively owing to its strong binding to the phosphate backbone of DNA, and has been applied to the determination of Al(III) concentration in synthetic biological samples with satisfactory results. Therefore, the proposed method is promising as an effective means for selective recognition and sensitive determination in situ of Al(III). Furthermore, this study would contribute to further understanding of the biological significance of Al neurotoxicity.

Spectroscopic studies of DNA binding modes of cation-substituted anthrapyrazoles derived from emodin

The DNA binding properties of three cation-substituted anthrapyrazole derivatives of emodin with calf thymus DNA were characterized by spectroscopic methods and the specific binding modes were elucidated. At low drug and high DNA concentrations, compound 1 with a mono-cationic amino side chain exhibited an intercalative binding mode, 2 with a much longer and more flexible di-cationic side chain exhibited an external binding mode, and 3 with a rigid di-cationic side chain exhibited both intercalative and external binding modes. The DNA binding mode of compounds was altered after structural modification. The molecular structure-DNA binding relationships found from this study may be useful for the design of anthrapyrazole derivatives with desired binding characteristics.

Binding, electrochemical activation, and cleavage of DNA by cobalt(II) tetrakis-N-methylpyridyl porphyrin and its beta-pyrrole brominated derivative

The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-beta-octabromoporphyrin, (Br(8)TMPyP)Co, was investigated by UV-visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 10(5)-10(6) M(-1). These values were higher for the more electron-deficient (Br(8)TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of polynucleotides by (TMPyP)Co and (Br(8)TMPyP)Co in the presence of oxygen preferentially at the A-T base pair region. Gel electrophoresis experiments further supported the cleavage of nucleic acids. The results indicate that the beta-pyrrole brominated porphyrin, (Br(8)TMPyP)Co, binds strongly and cleaves nucleic acids efficiently as compared with (TMPyP)Co. This electrolytic procedure offers a unique tool in biotechnology for cleaving double-stranded DNA with specificity at the A-T regions.

Quantitative analysis of DNA-porphyrin interactions

The binding of manganese(III)-tetra(4-N-methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA-dT)2, poly(dI-dC)2, and poly(dG-dC)2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD spectra, which changed greatly depending on the porphyrin to DNA base-pair molar ratio (r), were normalized with respect to DNA concentration and deconvoluted. Three independent component binding modes (named mode 1, 2, and 3 in the order of increasing r values) were identified, which successfully simulated the observed CD spectra with negligibly small residuals for a wide range of r values. In the case of poly(dA-dT)2, poly (dI-dC)2, and CT DNA, all the three modes appeared, whereas in the case of poly(dG-dC)2 DNA, only modes 1 and 3 appeared in the r range studied. The r dependence of each binding mode, i.e., its relative affinity toward DNA, has been revealed by this analysis. Mode 1, which appeared as a single binding mode at very low r values (r < or = ca. 0.05), was inhibited by the addition of methyl green, a drug that preferentially binds to the major groove of poly (dA-dT)2 DNA. Berenil, a known minor groove binder to poly(dA-dT)2 or poly(dI-dC)2 DNA, inhibited modes 2 and 3. From these inhibition experiments as well as comparison of the component spectra for DNAs of different sequence, a binding site on DNA was proposed for each component binding mode. The number of DNA base pairs covered by a single molecule of porphyrin was estimated.

Binding and photocleavage of cationic porphyrin–phenylpiperazine hybrids to DNA

The binding properties of cationic porphyrin-phenylpiperazine hybrids to calf thymus (CT) DNA were investigated by using absorption, fluorescence and circular dichroism (CD) spectra, and the apparent affinity binding constants (K(app)) of the porphyrins for CT DNA were determined by using a competition method with ethidium bromide (EB). Intercalation of porphyrin into CT DNA occurred when two phenylpiperazines were introduced at cis position onto the periphery of cationic porphyrin. The photocleavages of pBR322 plasmid DNA by the porphyrins were consistent with the values of K(app). With [porphyrin]/[DNA base pairs] ratio increased, the binding mode tended to be outside binding, and the cleavage abilities of the porphyrins varied. In the presence of sodium azide, a quencher of 1O2, the cleavage of DNA by the porphyrin of intercalation was less inhibited.

[Ru(phen)2DPPZ]2+ is in contact with DNA bases when it forms a luminescent complex with single-stranded oligonucleotides

The luminescence intensity of the Delta- and Lambda-enantiomer of [Ru(phen)2DPPZ]2+ ([Ru(phenanthroline)2 dipyrido[3,2-a:2',3'-c]phenazine]2+) complex enhanced upon binding to double stranded DNA, which has been known as "light switch effect". The enhancement of the luminescence required the intercalation of the large ligand between DNA base pairs. In this study, we report the enhancement in the luminescence intensity when the metal complexes bind to single stranded oligonucleotides, indicating that the "light switch effect" does not require intercalation of the large DPPZ ligand. Oligonucleotides may provide a hydrophobic cavity for the [Ru(phen)2DPPZ]2+ complex to prevent the quenching by the water molecule. In the cavity, the metal complex is in contact with DNA bases as is evidenced by the observation that the excited energy of the DNA bases transfer to the bound metal complex. However, the contact of the metal complex with DNA bases is different from the stacking of DPPZ in the intercalation pocket. In addition to the normal two luminescence lifetimes, a short lifetime in the range of 1-2 ns was found for both the delta- and lambda-enantiomer of [Ru(phen)2DPPZ]2+ when complexed with single stranded oligonucleotides, which may be assigned to the metal complex that is outside of the cavity, interacting with phosphate groups of DNA.

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.

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.

Stabilization of guanine quadruplex DNA by the binding of porphyrins with cationic side arms

Many aromatic ligands, including tetra-(N-methyl-4-pyridyl)porphyrin (TMPyP4), have been reported to bind and stabilize quadruplex structure of telomeric DNA. We synthesized novel quadruplex-interacting porphyrins with cationic pyridinium and trimethylammonium arms at para- or meta-position of all phenyl groups of tetratolyl porphyrin. An antiparallel quadruplex structure was found to be stabilized more greatly by the meta-isomers than by the para-isomers and well-studied TMPyP4, as revealed by the increase in melting temperature of the quadruplex. One mole equivalent of the isomers was sufficient to stabilize the quadruplex. From the results of absorption, induced circular dichroism, and fluorescence resonance energy transfer spectroscopic methods, the unique site for the porphyrin binding is suggested to be the external guanine tetrad or groove of the quadruplex. The cationic side arms played a key role in the stabilization of the quadruplex structure.

Binding mode of cationic monomer and dimer porphyrin with native and synthetic polynucleotides studied by polarized light spectroscopy

Binding properties of the tricationic porphyrin monomer with a phenolic substituent at the periphery and the porphyrin dimer conjugated with hydrophilic triethylene glycol were investigated in this study using absorption and polarized spectroscopy, namely, circular dichroism (CD) and linear dichroism (LD). The spectral properties of the porphyrin monomer, when complexed with polynucleotides, were essentially the same as that of the well-known meso-tetrakis(N-methylpyridiniumyl)porphyrin, indicating that the substitution at one peripheral pyridiniumyl ring did not affect the binding mode. When the porphyrin dimer formed a complex with poly[d(G-C)(2)], a negative CD band and a negative LD(r) spectrum were apparent in the Soret absorption region, with its LD(r) magnitude significantly smaller than that in the DNA absorption region. As the complex was stabilized over time, the intensity of the negative CD band and the negative LD(r) increased. These observations indicated that one of the porphyrin moieties of the dimer intercalated initially and than the other one also intercalated consecutively within a few hours. In the porphyrin dimer-poly[d(A-T)(2)] complex case, a bisignate CD was apparent and remained for at least 12 h, indicating that the porphyrins are stacked along the polynucleotide stem even at a very low [porphyrin]/[DNA base] ratio. A wavelength-dependent and time-dependent LD(r) of this complex suggests that the porphyrin molecular plane tilts strongly relative to the polynucleotide helix axis. The spectral properties of the porphyrin dimer-DNA complex are similar to those of the porphyrin dimer-poly[d(G-C)(2)] complex. However, some of the porphyrin moieties were located at the groove, which was evident by some positive characters in the CD and LD(r) spectra at the short wavelength in the Soret band.

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.

Binding of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to AT oligomers: effect of chain length and the location of the porphyrin stacking

Circular dichroism (CD) spectra of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) that are associated with various duplex and triplex AT oligomers were investigated in this study. A strong positive CD was apparent for both the TMPyP complexed with duplex d[(A-T)(12)](2), d(A)(12).d(T)(12) and triplex d(A)(12).d[(T)(12)](2) at a low mixing ratio. As the mixing ratio increased, bisignate excitonic CD was produced for TMPyP complexed with duplexes, whereas the positive CD signal remained the same for the TMPyP-d(A)(12).d[(T)(12)](2) complex. This difference in the CD spectrum in the presence of duplex and triplex oligomers indicates that the moderate stacking of TMPyP occurs at the major groove of the duplex and the monomeric binding occurs in (or near) the minor groove. When TMPyP forms a complex with duplex d[(A-T)(6)](2) only excitonic CD was observed, even at a very low mixing ratio. Therefore, at least seven or more basepairs are required for TMPyP to exhibit a monomeric CD spectrum. After close analysis of the CD spectrum, the TMPyP-poly[d(A-T)(2)] complex could be explained by a combination of the CD spectrum of the monomeric, moderately stacked, and extensively stacked TMPyP.