Metalloporphyrin mediated DNA cleavage by a low concentration of HaeIII restriction enzyme

Interactions of Co(II)- and Zn(II)porphyrin of 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin with DNA in Aqueous Solution and Their Antimicrobial Activities

Antibiotics are frequently used to treat, prevent, or control bacterial infections, but in recent years, infections resistant to all known classes of conventional antibiotics have significantly grown. The development of novel, nontoxic, and nonincursive antimicrobial methods that work more quickly and efficiently than the present antibiotics is required to combat this growing public health issue. Here, Co(II) and Zn(II) derivatives of tetrakis(1-methylpyridinium-4yl)porphyrin [H2TMPyP]4+ as a tetra(ρ-toluenesulfonate) were synthesized and purified to investigate their interactions with DNA (pH 7.40, 25 °C) using UV-vis, fluorescence techniques, and antimicrobial activity. UV-vis results showed that [H2TMPyP]4+ had a high hypochromicity (∼64%) and a substantial bathochromic shift (Δλ, 14 nm), while [Co(II)TMPyP]4+ and [Zn(II)TMPyP]4+ showed little hypochromicity (∼37%) and a small bathochromic shift (Δλ, 3-6 nm). Results reveal that [H2TMPyP]4+ interacts with DNA via intercalation, while Co(II)- and [Zn(II)TMPyP]4+ interact with DNA via outside self-stacking. Fluorescence results also confirmed the interaction of [H2TMPyP]4+ and the metalloporphyrins with DNA. Results of the antimicrobial activity assay revealed that the metalloporphyrins showed inhibitory effects on Gram-positive and Gram-negative bacteria and fungi, but that neither the counterions nor [H2TMPyP]4+ exhibited any inhibitory effects. Mechanism of antimicrobial activities of metalloporphyrins are discussed.

Kinetics and mechanism of formation of nickel(II)porphyrin and its interaction with DNA in aqueous medium

Kinetics between 5,10,15,20-tetrakis(N-methylpyridium-4-yl)porphyrin and Ni²⁺ species were investigated in aqueous solution at 25 ±1 °C in I = 0.10 M (NaNO₃). Speciation of Ni²⁺ was done in I = 0.10 M (NaNO₃) for knowing distribution of Ni²⁺ species with solution pH. Experimental data were compared with speciation diagram constructed from the values of hydrolysis constants of Ni²⁺ ion. Speciation data showed that hexaaquanickel(II) ions took place in hydrolysis reactions through formation of [Ni(OH₂)_6-n(OH)_n]^2-n species with solution pH. According to speciation of Ni²⁺ and pH dependent rate constants, rate expression can be written as: d[Ni(TMPyP)⁴⁺]/dt = (k₁[Ni²⁺_(aq)] + k₂[Ni(OH)⁺_(aq)] + k₃[Ni(OH)₂^o_(aq)] + k₄[Ni(OH)₃^-_(aq)])[H₂TMPyP⁴⁺], where k₁, k₂, k₃ and k₄ were found to be k₁ = (0.62 ± 0.22) × 10^-2; k₂ = (3.60 ± 0.40) × 10^-2; k₃ = (2.09 ± 0.52) × 10^-2, k₄ = (0.53 ± 0.04) × 10^-2 M^-1s^-1 at 25 ±1 °C, respectively. Formation of hydrogen bonding between [Ni(H₂O)₅(OH)]⁺ and [H₂TMPyP]⁴⁺ causes enhanced reactivity. Rate of formation of [Ni(II)TMPyP]⁴⁺ complex was to be 3.99 × 10^-2 M^-1s^-1 in I = 0.10 M, NaNO₃ (25 ± 1 °C). UV-Vis and fluorescence data suggested that [Ni(II)TMPyP]⁴⁺ and [H₂(TMPyP)]⁴⁺ interact with DNA via outside binding with self-stacking and intercalation, respectively.

SYNOPSIS

Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases

The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.

Ground and excited state interactions of metalloporphyrin PtTMPyP4 with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2

The ground- and excited-state interactions of Pt(ii) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2 have been investigated using UV/visible, circular dichroism, and steady-state and time-resolved emission spectroscopy. PtTMPyP4 intercalates into [poly(dG-dC)]2 with K∼ 10(6) M(-1). When bound to [poly(dG-dC)]2 in aerated solution there is a six-fold emission enhancement with 18 nm red-shift in emission maximum. Emission lifetimes are biexponential. In the presence of [poly(dA-dT)]2 at least two distinct groove-binding modes are observed, depending on the binding ratio. In [poly(dA-dT)]2 the emission intensity increases by a maximum factor of 17 with no shift in the emission spectrum. Three exponentials were required for lifetime fitting. The lower extent of emission enhancement in the presence of [poly(dG-dC)]2 suggests that a slow electron transfer may take place to guanine, which is significantly less efficient than that previously observed for PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP). The results are compared to those previously recorded with free base H2TMPyP4.

A three-layer ONIOM model for the outside binding of cationic porphyrins and nucleotide pair DNA

In this work we investigated the outside binding mode between a cationic porphyrin and a nucleotide pair of DNA, adenine-thymine and guanine-cytosine, in a supramolecular assembly. We used two structural models (semi-extended, extended) that differ in the size of porphyrin, two kinds of theoretical methods: a three layer ONIOM (B3LYP/6-31G(d)/PM3/UFF), and DFT B3LYP/6-31G(d,p), and three cationic porphyrins. ONIOM method was first tested on the semi-extended model that was calculated in four environments: gas phase, solution phase using an explicit solvent model (H(2)O), in the presence of a sodium cation (Na(+)) and in both (H(2)O + Na(+)). From interaction energy results, we found that the affinity of the cationic substituent by the adenine nucleotide is favored upon the thymine nucleotide. The extended model that considers the whole porphyrin was applied in the gas phase to the four nucleotides. All the cationic porphyrins showed affinity by the nucleotides in the order adenine > guanine > thymine > cytosine. The interaction energy values for outside binding showed a strong porphyrin-nucleotide interaction (≈-90 kcal mol(-1)), that slightly varies between the nucleotides suggesting that this kind of cationic porphyrin has a little selectivity for some of them. We also found that the effect of the nature of the cationic substituent (chain length) in the porphyrin on the outside binding is small (≈2-13 kcal mol(-1)). Coherence between the results showed that ONIOM is a useful tool to get a reasonable molecular geometry to be used as a starting point in calculations of density functional theory.

Water-soluble ionic benzoporphyrins

Novel ionic water-soluble tetrabenzoporphyrins have been successfully synthesized via a cascade reaction based on the Heck reaction. The UV-Vis spectra of these porphyrins displayed red-shifted and broadened Soret bands, and significantly enhanced Q bands. These porphyrins are highly water soluble.

Interactions of tetracationic mercury(II), cadmium(II) and lead(II) porphyrins with DNA and their effects on DNA cleavage

The effects of tetrakis(1-methylpyridinium-4-yl)porphyrinatomercury(II) [ Hg ( TMPyP )]4+(6) along with [ Pb ( TMPyP )]4+(7), [ Cd ( TMPyP )]4+(8), and [ H2( TMPyP )]4+(1) (free base porphyrin) on DNA cleavage by Haemophilus aegyptius (HaeIII) have been studied using gel electrophoresis, UV-vis absorption spectroscopy, and circular dichroism (CD) spectroscopy. The gel electrophoresis results indicate that in the absence of 6, HaeIII restriction enzyme could not cleave plasmid DNA at a low concentration of 0.2 units μl-1after 1 h incubation at 37 °C. However, DNA cleavage occurred in the presence of 6 at the concentrations of 1.0 × 10-6and 1.0 × 10-7M and 0.2 units μl-1of HaeIII under the same conditions. In addition, acceleration of DNA cleavage occurred at a higher concentration of HaeIII (0.4 units μl-1) in the presence of a wider concentration range of 6 from 1.0 × 10-5to 1.0 × 10-7M . 8, 7, and 1 could not enhance DNA cleavage in the presence of HaeIII (0.2 units μl-1). However, when the concentration of HaeIII was increased to 0.4 units μl-1, only 8 inhibited DNA cleavage by HaeIII at higher concentrations (1.0 × 10-5-10-6M ) whereas 6, 7, and 1 did not. The UV-vis and CD spectroscopic results indicate that these porphyrins interact differently with DNA based on their binding modes. 6 enhanced DNA cleavage due to the synergistic effect of the Hg2+ions and the free base porphyrin 1 that dissociated from the mercury(II) porphyrin complex upon binding to DNA which resulted in the enhanced transformation of the DNA conformation from the original B-form to a Z-like conformation, while 8 inhibited HaeIII activity at higher concentrations and 7 and 1 neither enhanced nor inhibited DNA cleavage. A mechanism for this phenomenon is suggested.

DNA binding and photocleavage specificities of a group of tricationic metalloporphyrins

The interactions of 5,10,15-tris(1-methylpyridinium-4-yl)-20-(4-hydroxyphenyl)porphyrinatozinc(II) Zn[TMPyHP](3+) (2) along with Cu[TMPyHP](3+) (3), Co[TMPyHP](4+) (4), Mn[TMPyHP](4+) (5) and the free base porphyrin H(2)[TMPyHP](3+) (1) with duplex DNA have been studied by using a combination of absorption, fluorescence titration, surface-enhanced Raman spectroscopy (SERS), induced circular dichroism (ICD) spectroscopy, thermal DNA denaturation, viscosity measurements as well as gel electrophoresis experiment. Their binding modes and intrinsic binding constants (K(b)) to calf DNA (CT DNA) were comparatively studied and were found significantly influenced by different metals coordinated with the porphyrin plane. Except 3, which has four-coordination structure at the metal, all the metal derivatives showed non-intercalative DNA-binding mode and lower K(b) than the free base porphyrin 1, most probably due to the steric hindrance results from the axial ligands of the inserted metals which are five or six-coordination structures. Meanwhile, the insertion of metals into cationic porphyrin greatly removed the self-aggregation of the metal-free porphyrins, and thus fully enhanced the singlet oxygen ((1)O(2)) productivities in the DNA photocleavage experiments. Therefore, these metalloporphyrins have comparable DNA cleavage ability with the free base porphyrin.

Enhanced conformational changes in DNA in the presence of mercury(II), cadmium(II) and lead(II) porphyrins

The interactions of the metalloporphyrins of tetrakis (1-methylpyridinium-4yl)porphyrin ([M(TMPyP)](4+)) where M=Hg(II), Cd(II) and Pb(II)) with pBluescript II plasmid DNA have been studied by the measurement of circular dichroism (CD), UV-visible and fluorescence spectra at 0.1 M NaNO(3), pH 7.5 and 25 degrees C. The CD spectra of the DNA changed quite significantly, with the conformational changes in the presence of the metalloporphyrins being much more enhanced compared to that of their free metal ion counterparts. The conformational changes in DNA upon binding to the Hg(II) porphyrin and Hg(II) were, however, different from those of the Cd(II) porphyrin, Pb(II) porphyrin, Pb(II), Cd(II) and H(2)(TMPyP)(4+). In the concentration range of 0-2.30 x 10(-5) M of DNA, the absorption spectra of H(2)(TMPyP)(4+) showed substantial hypochromicity at 423 nm and a red shift of Deltalambda=16 nm in the presence of DNA whereas the Hg(II)-, Pb(II)- and Cd(II) porphyrins showed blue shifts of absorption maximum wavelengths of Deltalambda=-17 nm, Deltalambda=-35 nm and Deltalambda=-4.5 nm, respectively. Furthermore, the shifted absorption maximum wavelengths/nm of the porphyrins in excess amount of DNA were comparable; 438, 439, 440 and 440 for H(2)(TMPyP)(4+), Hg(II)-, Pb(II)- and Cd(II) porphyrins, respectively. The changes in absorption spectra for Hg(II)-, Pb(II)- and Cd(II) porphyrins revealed that these metalloporphyrins dissociated upon binding to DNA which was confirmed by CD as well as fluorescence spectra. The CD results, UV-Vis and fluorescence data indicate that the metalloporphyrins interact differently with DNA based on their binding modes. And the enhanced changes in conformation of DNA in the presence of the metalloporphyrins are due to the synergistic effects of the simultaneous binding of the metal ions and the free base porphyrin to DNA compared to their free metal ion counterparts: [M(TMPyP)](4+)+DNA+2H(+) right harpoon over left harpoon [M(II)(DNA)H(2)(TMPyP)(4+)]. The detailed equilibrium reactions have been described along with suggestions of possible applications in the medical and biological fields.

Toxic effects of mercury(II), cadmium(II) and lead(II) porphyrins on Trypanosoma brucei brucei growth

The effects of free mercury(II), cadmium(II) and lead(II) ions and their metalloporphyrin-derivatives on Trypanosoma brucei brucei growth in culture were studied. All experiments were conducted in the dark. IC(50) values on growth obtained in 24-h time-course experiments were 1.5 x 10(-7), 2.4 x 10(-6), 4.4 x 10(-6) and 2.6 x 10(-5) M for mercury(II) porphyrin, cadmium(II) porphyrin, lead(II) porphyrin and free base porphyrin, respectively. While the IC50 values for Hg2+, Cd2+ and Pb2+ were 3.6 x 10(-6), 1.5 x 10(-5) and 1.6 x 10(-5) M, respectively. These results clearly indicate that the toxicity of the metalloporphyrin complexes of mercury(II), cadmium(II) and lead(II) to T. b. brucei parasites was much higher compared to their free metal ions and free base porphyrin at low concentrations. It was also observed after 8 h incubation that the metalloporphyrins were effective in inhibiting the division of the parasites at concentrations >1.25 x 10(-7) M for mercury(II) porphyrin, concentrations >1.2 x 10(-6) M for cadmium(II) and lead(II) porphyrins and at concentrations >3.6 x 10(-6) M for Hg2+ ion. These observations were not detected in samples treated with the free metal ions and the free base porphyrin at the same concentrations. Interestingly, trypanosomes treated with metalloporphyrin complexes displayed different morphological features from those cells treated with free base porphyrin or metal ions. The chemotherapeutic potential of the metalloporphyrins of H2TMPyP for treatment of African trypanosomiasis is discussed.