DNA binding behaviors and cleavage properties of a Ru(II) polypyridyl complex

A novel complex, [Ru(phen)₂pzip]²⁺1 (phen = 1,10-phenanthroline; pzip = 2-(pyrazine-2-yl)imidazo-[4,5-f][1,10]phenanthroline]), has been synthesized and characterized by elemental analysis, ES-MS, ¹H NMR. The DNA-binding behaviors of this complex were studied by spectroscopic methods and viscosity measurements. The results indicate that the complex can bind to CT-DNA in an intercalative mode. When irradiated at 365 nm, complex 1 can promote the cleavage of plasmid pBR322DNA. Furthermore, Zn²⁺ can trigger the DNA cleavage of complex 1 without irradiation. The mechanism studies revealed that the DNA cleavage by complex 1 in the presence of Zn²⁺ is likely to proceed via a hydrolytic cleavage process.     

Synthesis of a novel linear polymer of a macrocyclic polyamine copper (II) complex and its interaction with plasmid DNA

The novel linear polymer of a macrocyclic polyamine copper (II) complex, which has many cyclen groups linked by epichlorohydrin, has been synthesized as a DNA cleavage agent. The structure of the polymer 3 was identified by 1HNMR and IR and its molecular weight was measured by GPC. The result of agarose gel electrophoresis assay showed that Cu-(II) complex 4 could act as a powerful catalyst for the cleavage of plasmid DNA under physiological conditions.     

DNA cleavage promoted by trigonal-bipyramidal zinc(II) and copper(II) complexes formed by asymmetric tripodal tetradendate 2-[bis(2-aminoethyl)amino]ethanol

Asymmetric trigonal-bipyramidal Zn(II) complex 1 formed by 2-[bis(2-aminoethyl)amino]ethanol (L) was found to be able to promote the cleavage of supercoiled plasmid DNA pBR322 to the nicked and linear DNA via a hydrolytic manner but only in neutral Tris-HCl buffer, no cleavage was observed in HEPES or NaH₂PO₄/Na₂HPO₄ buffer. However, the copper complex 2 of L, possessing the similar coordination geometry, can only promote DNA cleavage via an oxidative mechanism in the presence of ascorbic acid. ESI-MS study implies that complex 1 exist mainly as [Zn(L)]²⁺/[Zn(L-H)]⁺ in neutral Tris-HCl buffer. Moreover, there is no discriminable species for complex 1 in HEPES or NaH₂PO₄/Na₂HPO₄ buffer. A phosphate activation mechanism via phosphate coordinating to Zn(II) center of [Zn(L)]²⁺/[Zn(L-H)]⁺ to form the stable trigonal-bipyramidal structure is proposed for the hydrolytic cleavage promote by complex 1. For complex 2, the abundance of [Cu(L)Cl]⁺ is higher than that of [Cu(L)]²⁺/[Cu(L-H)]⁺ in Tris-HCl buffer. The lower phosphate binding/activating ability of Cu(II) in complex 2 may be the origin for its incapability to promote the hydrolytic DNA cleavage. However, the readily accessible redox potential of Cu(II) makes complex 2 promote the oxidative DNA cleavage. Although the DNA cleavage promoted by complex 1 has no specificity, trigonal-bipyramidal Zn(II) complexes formed by asymmetric tripodal polyamine with ethoxyl pendent should be a novel potential model for practical artificial nuclease.     

One-pot synthesis of a new 2-substituted 1,2,3-triazole 1-oxide derivative from dipyridyl ketone and isonitrosoacetophenone hydrazone: Nickel(II) complex,DNA binding and cleavage properties

An efficient and simple one-pot synthesis of a new 1,2,3-triazole-1-oxide via reaction between isonitrosoacetophenone hydrazone and dipyridyl ketone in the EtOH/AcOH at room temperature has been developed smoothly in high yield. The reaction proceeds via metal salt free, in-situ formation of asymmetric azine followed by cyclization to provide 1,2,3-triazole 1-oxide compound. It has been structurally characterized. The 1:1 ratio reaction of the 1,2,3-triazole 1-oxide ligand with nickel(II) chloride gives the mononuclear complex [Ni(L)(DMF)Cl₂], hexa-coordinated within an octahedral geometry. Characterization of the 1,2,3-triazole compound and its Ni(II) complex with FTIR, ¹H and ¹³C NMR, UV–vis and elemental analysis also confirms the proposed structures of the compounds. The interactions of the compounds with Calf thymus DNA (CT-DNA) have been investigated by UV–visible spectra and viscosity measurements. The results suggested that both ligand and Ni(II) complex bind to DNA in electrostatic interaction and/or groove binding, also with a slight partial intercalation in the case of ligand. DNA cleavage experiments have been also investigated by agarose gel electrophoresis in the presence and absence of an oxidative agent (H₂O₂). Both 1,2,3-triazole 1-oxide ligand and its nickel(II) complex show nuclease activity in the presence of hydrogen peroxide. DNA binding and cleavage affinities of the 1,2,3-triazole 1-oxide ligand is stronger than that of the Ni(II) complex.     

Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs

In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV–Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (K_b = 1.4 × 10⁴ M^?1) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 ?4.8 × 10⁴ M^?1. CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.     

Metal complexes of naphthoquinone based ligand: synthesis,characterization, protein binding,DNA binding/cleavage and cytotoxicity studies

Protein binding, DNA binding/cleavage and in vitro cytotoxicity studies of 2-((3-(dimethylamino)propyl)amino)naphthalene-1,4-dione (L) and its four coordinated M(II) complexes [M(II) = Co(II), Cu(II), Ni(II) and Zn(II)] have been investigated using various spectral techniques. The structure of the ligand was confirmed by spectral and single crystal XRD studies. The geometry of the complexes has been established using analytical and spectral investigations. These complexes show good binding tendency to bovine serum albumin (BSA) exhibiting high binding constant values (10⁵ M^?1) when compared to free ligand. Fluorescence titration studies reveal that these compounds bind strongly with CT-DNA through intercalative mode (K_app 10⁵ M^?1) and follow the order: Cu(II) > Zn(II) > Ni(II) > Co(II) > L. Molecular docking study substantiate the strength and mode of binding of these compounds with DNA. All the complexes efficiently cleaved pUC18-DNA via hydroxyl radical mechanism and the Cu(II) complex degraded the DNA completely by converting supercoiled form to linear form. The complexes demonstrate a comparable in vitro cytotoxic activity against two human cancer cell lines (MCF-7 and A-549), which is comparable with that of cisplatin. AO/EB and DAPI staining studies suggest apoptotic mode of cell death, in these cancer cells, with the compounds under investigation.     

Copper- and Arene-Catalyzed Cleavage of DNA

DNA was found to be cleaved by arenes and copper(II) salts in neutral solutions. The efficiency of this reaction is comparable with the DNA cleavage by such systems as Cu(II)–phenanthroline and Cu(II)–ascorbic acid in efficiency, but, unlike them, it does not require the presence of an exogenous reducing agent or hydrogen peroxide. The Cu²⁺–arene system does not cleave DNA under anaerobic conditions. Catalase, sodium azide as well as bathocuproine, a specific chelator of Cu(I), completely inhibit the reaction. Our results suggest that Cu(I) ions, superoxide radical and singlet oxygen participate in this reaction. It was shown by EPR and spin traps that the reaction proceeds with the formation of alkoxyl radicals capable of inducing breaks in DNA molecules. An efficient cleavage of DNA in the Cu(II)–o-bromobenzoic acid system requires the generation of radicals under the conditions of formation of a specific copper–DNA–o-bromobenzoic acid complex, in which copper ions are likely to be coordinated with oxygen atoms of the DNA phosphate groups.     

Study on Interaction of DNA from Calf Thymus with 1,10-phenanthrolinehexyldithiocarbamatopalladium(II) nitrate as Potential Antitumor Agent

Abstract

A novel palladium(II) complex has been synthesized with hexyldithiocarbamate (Hex-dtc) and 1,10-phenanthroline (phen) by the reaction of [Pd(phen)(H₂O)₂](NO₃)₂ with sodium salt of hexyldithiocarbamate and a complex of type [Pd(Hex-dtc) (phen)]NO₃ has been obtained. The complex has been characterized by elemental analysis, molar conductance, ¹H NMR, IR and electronic spectroscopic studies. The dithiocarbamate ligand acts in bidentate fashion. This water-soluble complex was screened against chronic myelogenous leukemia cell line, K562, for cytotoxic effects and showed significant antitumor activity much lower than that of cisplatin. The interaction of this complex with calf thymus DNA (ctDNA) was extensively investigated by a variety of spectroscopic techniques. Absorbance titration experiments imply the interaction of 4 Pd(II) complex molecules per 1000 nucleotides on DNA with positive cooperativity in the binding process and the complex denature the DNA at very low concentration (～14.3 μM). Fluorescence titration spectra and fluorescence Scatchard plots suggest that the Pd(II) complex intercalate in DNA. The gel chromatograms obtained from Sephadex G-25 column experiments showed that the binding of metal complex with DNA is so strong that it does not readily break. Furthermore, some thermodynamic and binding parameters found in the process of UV-Visible studies are described. They may provide specificity of the compound with ctDNA.     

Correlation of enzyme-induced cleavage sites on negatively superhelical DNA between prokaryotic topoisomerase I and S1 nuclease

Negatively superhelical pNS1 DNA with a molecular weight of 2.55 MDa (4 kbp) was found to contain 13 specific, unbasepaired sites that are sensitive to a single-strand-specific S₁ nuclease cleavage. The S₁-cleavage occurred once at these sites. In the absence of added Mg²⁺, the topoisomerase I purified from Haemophilus gallinarum formed a complex with the superhelical pNS1 DNA which has a hidden strand cleavage. Extensive proteinase K digestion of the complex led to cleavage of the DNA chain. Then the proteinase K-cleaved product was digested with S₁, which can cut the opposite strand at the preexisting strand cleavage to generate unit-length linear DNA. Restriction endonuclease analysis of the linear DNA shows that the topoisomerase-induced cleavage occurred once at ten specific sites on the DNA. The topoisomerase caused mainly single-strand cleavage at these sites, but infrequently also caused double-strand cleavage at the same sites. Of interest is the fact that these sites considerably coincide with the S₁-cleavable, unbasepaired sites.     

Elucidation of the DNA-interacting properties and anticancer activity of a Ni(II)-coordinated mithramycin dimer complex

Mithramycin (Mith) forms a drug-metal complex with a 2:1 stoichiometry by chelation with a Ni(II) ion, which was determined using circular dichroism spectroscopy. Mith exhibits an increased affinity (~55 fold) for Ni(II) in the presence of DNA compared to the absence of DNA, suggesting that DNA acts as an effective template to facilitate chelation. Also, we characterized the DNA-acting properties of a Ni(II) derivative of Mith. Kinetic analysis using surface plasmon resonance and UV melting studies revealed that Ni^II(Mith)₂ binds to duplex DNA with a higher affinity compared to Mg^II(Mith)₂. The thermodynamic parameters revealed a higher free energy of formation for duplex DNA in the presence of Ni^II(Mith)₂ compared to duplex DNA in the presence of Mg^II(Mith)₂. The results of a DNA-break assay indicated that Ni^II(Mith)₂ is capable of promoting one-strand cleavage of plasmid DNA in the presence of hydrogen peroxide; the DNA cleavage rate of Ni^II(Mith)₂ was calculated to be 4.1 × 10^?4 s^?1. In cell-based experiments, Ni^II(Mith)₂ exhibited a more efficient reduction of c-myc and increased cytotoxicity compared to Mith alone because of its increased DNA-binding and cleavage activity. The evidence obtained in this study suggests that the biological effects of Ni^II(Mith)₂ require further investigation in the future.     

Dinuclear macrocyclic polyamine zinc(II) complexes linked with flexible spacers: synthesis, characterization, and DNA cleavage

Dinuclear macrocyclic polyamine zinc(II) complexes, which have two cyclen groups linked by flexible spacers, have been synthesized as DNA cleavage agents. The structures of these new dinuclear complexes are consistent with the data obtained from elemental analysis, MS and ¹H NMR spectroscopy. The catalytic activity of these dinuclear complexes on DNA cleavage was studied. The results showed that the dinuclear zinc(II) complexes can catalyze the cleavage of supercoiled DNA (pUC 19 plasmid DNA) (Form I) under physiological conditions to produce selectively nicked DNA (Form II).     

Metal-based ethanolamine-derived compounds: a note on their synthesis,characterization and bioactivity

Abstract

Metal-based ethanolamines, (L¹)–(L⁴) coordinated with Co(II), Cu(II), Ni(II) and Zn(II) metals in 1:2 (metal:ligand) molar ratio to produce new compounds have been reported. These compounds were screened for their bactericidal/fungicidal activity against a number of bacterial (Escherichia coli, Shigella flexneri, Pseudomonas aeruginosa, Salmonella typhi, Staphylococcus aureus and Bacillus subtilis) and fungal strains (Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata) alongside against a shrimp species known as Artemia salina. The screening results indicated that metal complexes have significantly higher activity than uncomplexed ligands against one or more bacterial/fungal species due to chelation. The ligand (L⁴) displayed good bacterial and fungal activity as compared to other ligands. The antibacterial results revealed that the Zn(II) complex (16) of (L⁴) was found to be the most active complex and Co(II) complex (14) of the same ligand (L⁴), demonstrated the highest antifungal activity.     

Mechanism of bleomycin action: in vitro studies

The cytotoxic activity of bleomucin results from DNA cleavage, which is also accomplished $\text{in vitro}$ by reaction mixtures containing Fe(II), drug and O₂. Bleomycin forms a complex with Fe(II) and O₂ in the presence or absence of DNA. The species attacking DNA forms rapidly from this complex. The nature of the attacking species and of the primary lesion(s) to DNA are not yet known, but two major insults to DNA have been characterized. They are the release of free bases from their glycosidic linkages and, at other residues, the cleavage of the polymer backbone at the deoxyribose C3-C4 bond.     

DNA-binding and photocleavage studies of [Ru(phen)2(NMIP)]

A novel ligand 2′-(2″-nitro-3″,4″-methylenedioxyphenyl)imidazo[4′,5′-f][1,10]-phenanthroline (NMIP) and its complex [Ru(phen)₂(NMIP)]²⁺ have been synthesized and characterized by mass spectroscopy, ¹H NMR and cyclic voltammetry. Binding of the complex with calf thymus DNA (CT DNA) has been investigated by spectroscopic methods, viscosity and electrophoresis measurements. The experimental results indicate that [Ru(phen)₂(NMIP)]²⁺ binds to DNA via partial intercalative mode and the individual enantiomers of it bind to DNA in different rates. [Ru(phen)₂(NMIP)]²⁺ has also been found to promote cleavage of plasmid pBR 322 DNA from the supercoiled Form I to the open circular Form II upon irradiation.     

Metal-directed synthesis of a chiral acyclic pentaamine and pendant-arm macrocyclic hexaamine derived from an amino acid

l-3-Phenylpropane-1,2-diamine (dapp) was prepared by a three-step synthesis based on l-phenylalanine and characterized, including determination of stability constants with M²⁺ ions (Ni, Cu, Zn, Cd). The reaction of L-3-phenylpropane-1,2-diamine as the [Cu(dapp)₂]²⁺ complex ion with formaldehyde and nitroethane in basic solution yields the acyclic (5-methyl-5-nitro-1,9-diphenyl-3,7-diazanonane-1,9-diamine)copper(II) complex ion, [Cu(1)]²⁺, as the major product. In addition, small amounts of the macrocyclic complex ion (2,10-diphenyl-6,13-dimethyl-6,13-dinitro-1,4,8,11-tetraazacyclotetradecane)copper(II), [Cu(2)]²⁺, form. Reduction of the [Cu(1)]²⁺ ion with zinc in aqueous acid yields the acyclic polyamine 5-methyl-1,9-diphenyl-3,7-diazanonane-1,5,9-triamine (3), an analogue of the previously reported pentaamine 5-methyl-3,7-diazanonane-1,5,9-triamine. Using the bis(l-3-phenylpropane-1,2-diamine)palladium(II) as precursor and an excess of other reagents, the macrocyclization reaction to produce [Pd(2)]²⁺ proved more successful. Reduction and recomplexation to copper(II) allowed isolation of the 2,9-dibenzyl-6,13-diammonio-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane)copper(II) ion, [Cu(4H₂²⁺)]⁴⁺. The acyclic complex [Cu(1)]²⁺ promotes the hydrolytic cleavage of plasmid DNA modestly; a mechanism to support this observation is presented.     

Synthesis, crystal structure, nuclease and in vitro antitumor activities of a new mononuclear copper(II) complex containing a tripodal N3O ligand

We present here the synthesis, crystal structure, electrochemical behavior, spectroscopic properties (FT-IR, UV-Vis and EPR), nuclease and in vitro antitumor activities against human myeloid leukemia cell line of the mononuclear copper complex [Cu(HPClNOL)(Cl)]Cl · MeOH (1). The reaction of the tetradentate ligand HPClNOL [1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol] and 1 equiv. of [Cu(OH₂)₆](Cl)₂, in methanol, resulted in 1, which crystallizes as blue monoclinic crystals. The complex is pentacoordinated with a distorted square-pyramidal geometry. The activity of complex 1 toward plasmid DNA and THP-1 carcinogenic cells was investigated. Complex 1 promotes the cleavage of supercoiled DNA (pBlueScript KS⁺ DNA) to nicked circular and linear DNA forms. In addition to the three typical KS⁺ DNA forms, the cleavage resulted in a fourth band, which was visualized above of the nicked circular form. The results reveal that the cleavage mechanism is radical-independent. Furthermore, complex 1 is able to promote cell death of THP-1 cells by apoptosis, as confirmed by fluorescent microscopy, cell morphology and DNA degradation.     

Synthesis and DNA‐Cleavage Activities of Dinuclear Copper(II) Complexes of Urea‐Bridged Macrocyclic Polyamines

Two dinuclear macrocyclic polyamine copper(II) (Cu^II) complexes, which have two cyclen units linked by urea, were synthesized as DNA‐cleavage agents. The structures of these new dinuclear complexes were identified by HR‐ESI‐MS and IR analyses. The catalytic activities of DNA cleavage of these dinuclear Cu^II complexes were subsequently studied. The results show that 6a was the better catalyst in the DNA‐cleavage process than 6b . The effects of reaction time and concentration of complexes were also investigated. The results indicate, that the Cu^II complexes could catalyze the cleavage of supercoiled DNA (pUC 19 plasmid DNA; Form I) under physiological conditions to produce selectively nicked DNA (Form II; no Form III was produced) with high yields (nearly 100%) in short time in the absence of reductant or oxidant.     

Kinetics and DFT studies on the reaction of copper(II) complexes and H2O2

Copper(II) complexes supported by bulky tridentate ligands L1^H (N,N-bis(2-quinolylmethyl)-2-phenylethylamine) and L1^Ph (N,N-bis(2-quinolylmethyl)-2,2-diphenylethylamine) have been prepared and their crystal structures as well as some physicochemical properties have been explored. Each complex exhibits a square pyramidal structure containing a coordinated solvent molecule at an equatorial position and a weakly coordinated counter anion (or water) at an axial position. The copper(II) complexes reacted readily with H₂O₂ at a low temperature to give mononuclear hydroperoxo copper(II) complexes. Kinetics and DFT studies have suggested that, in the initial stage of the reaction, deprotonated hydrogen peroxide attacks the cupric ion, presumably at the axial position, to give a hydroperoxo copper(II) complex retaining the coordinated solvent molecule (H ^R ·S). H ^R ·S then loses the solvent to give a tetragonal copper(II)-hydroperoxo complex (H ^R ), in which the –OOH group may occupy an equatorial position. The copper(II)–hydroperoxo complex H ^R exhibits a relatively high O–O bond stretching vibration at 900 cm⁻¹ compared to other previously reported examples.Electronic Supplementary Material Supplementary material is available for this article at     

Enantiomeric Specificity of Biologically Significant Cu(II) and Zn(II) Chromone Complexes Towards DNA

Novel chiral Schiff base ligands (R)/(S)‐2‐amino‐3‐(((1‐hydroxypropan‐2‐yl)imino)methyl)‐4H‐chromen‐4‐one (L₁ and L₂) derived from 2‐amino‐3‐formylchromone and (R/S)‐2‐amino‐1‐propanol and their Cu(II)/Zn(II) complexes ( R1 , S1 , R2 , and S2 ) were synthesized. The complexes were characterized by elemental analysis, infrared (IR), hydrogen (¹H) and carbon (¹³C) nuclear magnetic resonance (NMR), electrospray ionization‐mass spectra (ESI‐MS), and molar conductance measurements. The DNA binding studies of the complexes with calf thymus were carried out by employing different biophysical methods and molecular docking studies that revealed that complexes R1 and S1 prefers the guanine–cytosine‐rich region, whereas R2 and S2 prefers the adenine–thymine residues in the major groove of DNA. The relative trend in K_b values followed the order R1 S1 R2 S2 . This observation together with the findings of circular dichroic and fluorescence studies revealed maximal potential of (R)‐enantiomeric form of complexes to bind DNA. Furthermore, the absorption studies with mononucleotides were also monitored to examine the base‐specific interactions of the complexes that revealed a higher propensity of Cu(II) complexes for guanosine‐5′‐monophosphate disodium salt, whereas Zn(II) complexes preferentially bind to thymidine‐5′‐monophosphate disodium salt. The cleavage activity of R1 and R2 with pBR322 plasmid DNA was examined by gel electrophoresis that revealed that they are good DNA cleavage agents; nevertheless, R1 proved to show better DNA cleavage ability. Topoisomerase II inhibitory activity of complex R1 revealed that the complex inhibits topoisomerase II catalytic activity at a very low concentration (25 μM). Furthermore, in vitro antitumor activity of complexes R1 and S1 were screened against human carcinoma cell lines of different histological origin. Chirality 24:977–986, 2012. © 2012 Wiley Periodicals, Inc.     

Multispectroscopic studies on the interaction of a copper(ii) complex of ibuprofen drug with calf thymus DNA

The interaction of copper(II)–ibuprofenato complex with calf thymus DNA (ct-DNA) has been explored following, UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, and circular dichroism spectroscopy. In spectrophotometric studies of ct-DNA it was found that [Cu(ibp)₂]₂ can form a complex with double-helical DNA. The association constant of [Cu(ibp)₂]₂ with DNA from UV-Vis study was found to be 6.19 × 10⁴ L mol^?1. The values of K_f from fluorescence measurement clearly underscore the high affinity of [Cu(ibp)₂]₂ to DNA. The experimental results showed that the conformational changes in DNA helix induced by [Cu(ibp)₂]₂ are the reason for the fluorescence quenching of the DNA-Hoechst system. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of [Cu(ibp)₂]₂ represented a significant increase of MB intensity as to release MB from MB-DNA system. The results of circular dichroism (CD) suggested that copper(II)–ibuprofenato complex can change the conformation of DNA. In addition, the results of viscosity measurements suggest that copper(II)–ibuprofenato complex may bind with non-classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that [Cu(ibp)₂]₂ interacts with DNA by partial intercalation mode which contains intercalation and groove properties.