Sequence-specific cleavage of double-stranded DNA caused by X-ray ionization of the platinum atom in the Pt-bis-netropsin--DNA complex.

An analog of the antibiotic netropsin containing two netropsin-like fragments linked covalently via a platinum atom has been synthesized. DNase I and hydroxyl radical footprinting studies have shown that this compound binds at selective sites on a DNA restriction fragment with a known nucleotide sequence. After X-ray irradiation of Pt-bis-netropsin--DNA complexes a platinum-mediated cleavage of DNA is observed at specific DNA sites. This enables one to determine the location of the synthetic ligand on the DNA with a precision of about one nucleotide. The cleavage activity seems to be related to the emission of Auger electrons from the platinum atom that cause rupture of the deoxyribose residues on the two DNA strands near the position of the platinum atom in the complex.     

DNA cleavage and binding selectivity of a heterodinuclear Pt–Cu(3-Clip-Phen) complex

The synthesis and nuclease activity of a new bifunctional heterodinuclear platinum–copper complex are reported. The design of this ditopic coordination compound is based on the specific mode of action of each component, namely, cisplatin and Cu(3-Clip-Phen), where 3-Clip-Phen is 1-(1,10-phenanthrolin-3-yloxy)-3-(1,10-phenanthrolin-8-yloxy)propan-2-amine. Cisplatin is not only able to direct the Cu(3-Clip-Phen) part to the GG or AG site, but also acts as a kinetically inert DNA anchor. The nuclease activity of this complex has been investigated on supercoiled DNA. The dinuclear compound is not only more active than Cu(3-Clip-Phen), but is also capable of inducing direct double-strand breaks. The sequence selectivity of the mononuclear platinum complex has been investigated by primer extension experiments, which reveal that its interaction with DNA occurs at the same sites as for cisplatin. The Taq polymerase recognizes the resulting DNA damage as different from that for unmodified cisplatin. The sequence-selective cleavage has been investigated by high-resolution gel electrophoresis on a 36-bp DNA fragment. Sequence-selective cleavages are observed in the close proximity of the platinum sites for the strand exhibiting the preferential platinum binding sites. The platinum moiety also coordinates to the other DNA strand, most likely leading only to mono guanine or adenine adducts. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparison of DNA complexation with antitumor therapeutic cis-DDP and binuclear bivalent platinum compound containing pyrazine

Conformational properties of DNA molecule upon its complexation with binuclear compounds of bivalent platinum in the cis configuration containing pyrazine ligand were studied by circular dichroism, viscometry, and dynamic birefringence. Comparison with active antitumor therapeutic cis-diamminedichloroplatinum (cis-DDP) was made. Experimental data indicates that interaction of these compounds with DNA results in the formation of coordination bond of platinum with nitrogen bases. The structure of the complex depends on the ratio of platinum and DNA concentrations in initial solution. The study of DNA protonation in complex with the binuclear coordination compound showed that the binding of platinum with DNA bases occurs at the N7 atom of guanine. It was observed a competition between the studied compound and cis-DDP for binding site on DNA. The macromolecule binds stronger to the binuclear platinum compound as compared with cis-DDP.     

Oxidative DNA cleavage induced by an iron(III) flavonoid complex: synthesis, crystal structure and characterization of chlorobis(flavonolato)(methanol) iron(III) complex

A flavonol iron(III) complex, [Fe(flavonolato)(2)Cl(MeOH)], has been prepared. The compound has been characterized by X-ray crystallography, spectroscopy, magnetism and electronic paramagnetic resonance (EPR) at X- and Q-band. The geometrical environment around the metal is best described as rhombic distorted octahedral. This distortion has also been inferred from the magnetic measurements and from the EPR spectra at different temperatures, E/D(rhombicity parameter) approximately 0.06. The DNA cleavage activity of the iron(III) complex with and without ascorbate/hydrogen peroxide is reported. Mechanisms of the oxidative cleavage have been proposed when DNA strand scission is performed both with and without ascorbate/hydrogen peroxide activation.     

Comparison of DNA Complexation with Antitumor Agent cis-DDP and Binuclear Bivalent Platinum Compound Containing Pyrazine

Conformational properties of DNA molecule upon its complexation with binuclear compounds of bivalent platinum in the cis configuration containing pyrazine ligand were studied by circular dichroism, viscometry, and dynamic birefringence. Comparison with an active antitumor agent cis-diamminedichloroplatinum (cis-DDP) was made. Experimental data indicate that interaction of these compounds with DNA results in the formation of a coordination bond of platinum with nucleic bases. The structure of the complex depends on the ratio of platinum and DNA concentrations in the initial solution. The study of DNA protonation in complex with the binuclear coordination compound showed that the binding of platinum with DNA bases involves the N7 atom of guanine. Competition was observed between the studied compound and cis-DDP for the binding site on DNA. The macromolecule binds stronger with the binuclear platinum compound than with cis-DDP.     

DNA cleavage reaction induced by dimeric copper(II) complexes of N-substituted thiazole sulfonamides

A new dinuclear copper(II) complex has been synthesised and structurally characterised: [Cu2(tz-ben)4] (Htz-ben = N-thiazol-2-yl-benzenesulfonamide). Its crystal structure, magnetic properties and electronic paramagnetic resonance (EPR) spectra were studied in detail. In the compound the metal centres are bridged by four non-linear triatomic NCN groups. The coordination geometry of the copper ions in the dinuclear entity is distorted square pyramidal (4+1). Two thiazole N and two sulfonamido N atoms occupy the equatorial positions and one sulfonamido O atom is in the axial position. Magnetic susceptibility data show a strong antiferromagnetic coupling, -2J = 114.1 cm(-1). The EPR spectra of a polycrystalline sample of compound has been obtained at the X- and Q-band frequencies at different temperatures. Above 20K the spectra are characteristic of S = 1 species with a zero field splitting parameter D = 0.4 cm(-1). The EPR parameters are discussed in terms of the known binuclear structures. The chemical nuclease ability of the title complex and that of the related [Cu2(tz-tol)4] compound (Htz-tol = N-thiazol-2-yl-toluenesulfonamide) is reported. The participation of hydroxyl radicals and a singlet oxygen-like entity in the DNA cleavage reaction has been deduced from the assays with radical oxygen scavengers.     

Assessment of DNA binding of platinum-radiosensitizer complexes by inhibition of restriction enzymes

A simple and rapid method has been used to compare the binding of platinum complexes to DNA, in a relatively qualitative manner. A compound bound at or near the restriction site inhibits enzymatic cleavage of DNA; inhibition of BamHI and EcoRI activity by complexes was assessed in this study using linearized pSV2-gpt plasmid. Our particular interest was in DNA binding by complexes of platinum (Pt) with known organic radiosensitizers (RS), to determine whether the Pt was able to target the RS to the DNA. Although the Pt-RS complexes investigated themselves have moderate radiosensitizing ability (like the inorganic complexes, cis- or trans-diamminedichloroplatinum(II), c- or t-DDP) none of the Pt-RS inhibit to the same extent as c- or t-DDP. However, there appears to be some correlation between enhanced radiosensitization by Pt-RS over Pt(RS)2, with the degree of Pt binding (as assessed by our assay). Our results using isolated DNA suggest that not all complexes bind well (e.g. Pt with two RS ligands), but that in certain cases (e.g. Pt with only one RS), it is possible to target the drug to the DNA. An ammine or amine ligand may be required in order to target a radiosensitizer to DNA using platinum.     

Cellular pharmacology of cis and trans pairs of platinum complexes in cisplatin-sensitive and -resistant human ovarian carcinoma cells

The cellular pharmacology of two pairs of cis and trans platinum complexes has been studied in three human ovarian carcinoma cell lines, a parental relatively cisplatin-sensitive line (CH1), a subline possessing acquired cisplatin resistance (3-fold; CH1cisR) and an intrinsically cisplatin resistant line (13-fold; SKOV-3). Growth inhibition studies showed that both JM335 [trans ammine (cyclohexylaminedichloro dihydroxo) platinum(IV)] and its platinum(II) dichloro homolog JM334 were relatively less cross-resistant against both acquired and intrinsic cisplatin resistant cells. In contrast, resistance circumvention was not apparent in these cell lines with their cis isomeric counterparts (JM149 for JM335 and JM118 for JM334). The trans compound JM335 was more potent than its cis isomer against all three cell lines. There was no clear correlation between intracellular accumulation following 2 h exposure to each compound and resulting DNA platination or growth inhibition. The selective activity of the trans platinum complexes against the SKOV-3 cell line correlated with a deficiency in the repair of adducts within a fragment of the N-ras gene induced by trans compounds whereas adducts induced by the cis counterparts, and cisplatin, were repaired. The CH 1 parental line appeared repair deficient at the gene-specific level to adducts induced by both cis (including cisplatin) and trans compounds. Resistance in CH1cisR was associated with a lack of gene-specific repair of lesions formed by JM118 and JM149. All four compounds induced apoptosis in all three cell lines, as measured by fluorescent microscopy and field inverted gel electrophoresis, although the kinetics of apoptosis was markedly faster for the trans versus cis compounds. In summary, the trans platinum complexes JM335 and JM334 possess unique cellular properties compared to their cis counterparts particularly with respect to gene specific repair of DNA adducts and the rate of induction of apoptosis.     

Cytotoxicity studies of [PtCl2(H2bim)] (H2bim = 2,2′-biimidazole): Study of its interaction with a small protein PCI (potato carboxypeptidase inhibitor)

The effect of the platinum compound [PtCl₂(H₂bim)] (H₂bim = 2,2′-biimidazole) on the plasmid DNA conformation was previously studied by electrophoresis in agarose gel and on calf thymus DNA by circular dichroism spectroscopy. The effect of this compound on pBR322 plasmid DNA has now been visualized by atomic force microscopy, which shows that the complex modifies the DNA in the same way as cisplatin does. The cytotoxic activity of [PtCl₂(H₂bim)] in HeLa-229, HL-60, A2780 and A2780cisR cell lines has also been evaluated. Likewise, the interaction of [PtCl₂(H₂bim)] with the small protein potato carboxypeptidase inhibitor (PCI) and a PCI mutant in which glycine 39 was substituted by methionine has been followed by HPLC/mass spectrometry. The interaction with the mutant protein PCI showed the formation of monofunctional adducts that ultimately gave bifunctional adducts. PCI mutant protein could be a good carrier of this platinum compound to the tumour cells in which the antiproliferative behaviour was demonstrated.     

A circular dichroism study of DNA.platinum complexes. Differentiation between monofunctional, cis-bidentate and trans-bidentate platinum fixation on a series of DNAs

The circular dichroism (CD) spectra of a series of DNA . platinum complexes are presented. The following platinum compounds, [Pt(dien)Cl]Cl, cis-Pt(NH3)2Cl2, cis-Pt(en)Cl2, trans-Pt-(NH3)2Cl2, K[Pt(NH3)Cl3] and K2[PtCl4] were complexed with the DNA extracted from bacteria Micrococcus lysodeikticus (72% dG + dC), Escherichia coli (50% dG + dC), Clostridium perfringens (32% dG + dC) and salmon sperm (41% dG + dC). Strong differences were found between the different DNA . Pt complexes. Three types of spectra clearly demonstrate the different platinum binding modes on DNA. In the first type, the platinum compound, i.e. [Pt(dien)Cl]Cl, is fixed to DNA with only one bond (monofunctional complex formation) and no significant change of the CD positive band of DNA is found. The main feature of the second type is a continuous intensity decrease of the positive band as observed for trans-Pt(NH3)2Cl2 (trans-bidentate complex formation). The third type concerns the cis-bidentate platinum fixation obtained with cis-Pt(NH3)2Cl2, cis-Pt(en)Cl2, K[Pt(NH3)Cl3] and K2[PtCl4]. The CD spectra are in this case characterized by an increase in the positive Cotton effect which is dG + dC-dependent up to an rb value around 0.10 (where rb = number of platinum atoms bound per nucleotide), followed by a decrease until DNA saturation with platinum is reached. A linear decrease in the amplitude of the negative band is detected in all the complexes except in the case of the monofunctional DNA . Pt complexes. For the cis-bidentate and trans-bidentate platinum fixation, a continuous bathochromic shift occurs.     

1,4-Benzoquinone is a topoisomerase II poison

Benzene is a human carcinogen that induces hematopoietic malignancies. It is believed that benzene does not initiate leukemias directly, but rather generates DNA damage through a series of phenolic metabolites, especially 1,4-benzoquinone. The cellular consequences of 1,4-benzoquinone are consistent with those of topoisomerase II-targeted drugs. Therefore, it has been proposed that the compound initiates specific leukemias by acting as a topoisomerase II poison. This hypothesis, however, has not been supported by in vitro studies. While 1,4-benzoquinone has been shown to inhibit topoisomerase II catalysis, increases in enzyme-mediated DNA cleavage have not been reported. Because of the potential involvement of topoisomerase II in benzene-induced leukemias, we re-examined the effects of the compound on DNA cleavage mediated by human topoisomerase IIalpha. In contrast to previous reports, we found that 1,4-benzoquinone was a strong topoisomerase II poison and was more potent in vitro than the anticancer drug etoposide. DNA cleavage enhancement probably was unseen in previous studies due to the presence of reducing agents in reaction buffers and the incubation of 1,4-benzoquinone with the enzyme prior to the addition of DNA. 1,4-Benzoquinone increased topoisomerase II-mediated DNA cleavage primarily by enhancing the forward rate of scission. In vitro, the compound induced cleavage at DNA sites proximal to a defined leukemic chromosomal breakpoint and displayed a sequence specificity that differed from that of etoposide. Finally, 1,4-benzoquinone stimulated DNA cleavage by topoisomerase IIalpha in cultured human cells. The present findings are consistent with the hypothesis that topoisomerase IIalpha plays a role in the initiation of specific leukemias induced by benzene and its metabolites.     

A new trinuclear complex of platinum and iron efficiently promotes cleavage of plasmid DNA.

The compound [[Pt(trpy)]2Arg-EDTA]+ is synthesized in five steps, purified, and characterized by 1H, 13C, and 195Pt NMR spectroscopy, mass spectrometry, UV-vis spectrophotometry, and elemental analysis. The binuclear [[(Pt(trpy)]2Arg]3+ moiety binds to double-stranded DNA, and the chelating EDTA moiety holds metal cations. In the presence of ferrous ions and the reductant dithiothreitol, the new compound cleaves DNA. It cleaves a single strand in the pBR322 plasmid nearly as efficiently as methidiumrpropyl-EDTA (MPE), and it cleaves a restriction fragment of the XP10 plasmid nonselectively and more efficiently than [Fe(EDTA)]2-. The mechanism of cleavage was studied in control experiments involving different transition-metal ions, superoxide dismutase, catalase, glucose oxidase with glucose, metal-sequestering agents, and deaeration. These experiments indicate that adventitious iron and copper ions, superoxide anion, and hydrogen peroxide are not involved and that dioxygen is required. The cleavage apparently is done by hydroxyl radicals generated in the vicinity of the DNA molecule. The reagent [[Pt(trypy)]2Arg-EDTA]+ differs from methidiumpropyl-EDTA in not containing an intercalator. This difference in binding modes between the binuclear platinum(II) complex and the planar heterocycle may cause useful differences between the two reagents in cleavage of nucleic acids.     

Single-strand and double-strand cleavage at half-modified and fully modified recognition sites for the restriction nucleases Sau3a and Taqi

The influence of cytosine methylation on the cleavage of DNA by the restriction nucleases Sau3A and TaqI has been investigated. Bovine satellite DNA fragments containing a GATCGA sequence, i.e. a Sau3A site overlapping with a TaqI site have been used in this study. The methylation of these fragments has been determined by sequence analysis. It has been found that a TaqI site (TCGA) methylated at cytosine in both DNA strands is still sensitive to double-strand cleavage. A Sau3A site (GATC), however, is rendered resistant to double-strand cleavage by methylation of a single cytosine. Fragments containing the "half-modified" Sau3A site are nicked in the unmethylated DNA strand. It has been shown by sequence analysis of nicked DNA that the single-strand break occurs at the same position which is cleaved in unmodified DNA.     

Sequence-dependent conformational changes in DNA induced by polynuclear platinum complexes

In this work, the B-->Z transition of poly(dG-dC).poly(dG-dC) and the B-->A transition of poly(dG).poly(dC) and of calf thymus (CT) DNA fragments modified by antitumor bifunctional polynuclear platinum complexes were investigated by circular dichroism (CD). The transition from the B- to Z-form of DNA was inducible with all three compounds studied, as indicated by an inversion of the B-form spectra. The B-->A transition in poly(dG).poly(dC) was induced easily by platinum complex binding alone, while the B-->A transition in CT DNA was induced by ethanol but inhibited by coordination of all polynuclear platinum compounds used here. It was shown that the compound [?cis-PtCl(NH3)2?2 mu-?H2N(CH2)6NH2?] (NO3)2 (1,1/c,c) was most effective at inhibiting the B-->A transition in CT DNA, and [?trans-PtCl(NH3)2?2 mu-?trans-Pt(NH3)2(H2N(CH2)6NH2)2?] (NO3)4 (1,0,1/t,t,t) was least effective, while the effectiveness of [?trans-PtCl(NH3)2?2 mu-?H2N(CH2)6NH2?] (NO3)2 (1,1/t,t) fell between the two. This corresponded to the relative amounts of interstrand crosslinks in double-stranded DNA caused by each compound.     

Measurement of the sequence specificity of covalent DNA modification by antineoplastic agents using Taq DNA polymerase.

A polymerase stop assay has been developed to determine the DNA nucleotide sequence specificity of covalent modification by antineoplastic agents using the thermostable DNA polymerase from Thermus aquaticus and synthetic labelled primers. The products of linear amplification are run on sequencing gels to reveal the sites of covalent drug binding. The method has been studied in detail for a number of agents including nitrogen mustards, platinum analogues and mitomycin C, and the sequence specificities obtained accord with those obtained by other procedures. The assay is advantageous in that it is not limited to a single type of DNA lesion (as in the piperidine cleavage assay for guanine-N7 alkylation), does not require a strand breakage step, and is more sensitive than other primer extension procedures which have only one cycle of polymerization. In particular the method has considerable potential for examining the sequence selectivity of damage and repair in single copy gene sequences in genomic DNA from cells.     

Cytotoxic acridinylthiourea and its platinum conjugate produce enzyme-mediated DNA strand breaks

The reactions of plasmid DNA modified with the novel acridinylthiourea, 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea (1), and the corresponding intercalator-tethered platinum complex (2) with human type I and type II topoisomerases have been studied. Assays were based on evaluating DNA cleavage products resulting from incubations of drug-modified DNA in cell-free systems. 2 produces double-strand breaks in the presence of topo II while 1 proved to be a dual topo I/topo II poison.     

Synthesis,characterization and DNA binding studies of platinum(II) complexes with benzimidazole derivative ligands

The aim of this study was to synthesize and evaluate plasmid DNA interaction of new platinum(II) complexes with some 2-substituted benzimidazole derivatives as carrier ligands which may have potent anticancer activity and low toxicity. Twelve benzimidazole derivatives carrying indole, 2-/or 3-/or 4-methoxyphenyl, 4-methylphenyl, 3,4-dimethoxyphenyl, 3,4,5-trimethoxyphenyl, 4-methoxybenzyl, 3,4,5-trimethoxybenzyl, 3,4,5-trimethoxystyryl, 3,4,5-trimethoxybenzylthio or dimethylamino ethyl groups in their position 2 and twelve platinum(II) complexes with these carrier ligands were synthesized. The chemical structure of the platinum complexes have been characterized by their elemental analysis and FIR, ¹H NMR and mass spectra and their ¹H NMR and FIR spectra were interpreted by comparison with those of the ligands. The interaction of all the ligands and their complexes with plasmid DNA and their restriction endonuclease reactions by BamHI and HindIII enzymes were studied by agarose gel electrophoresis. It was determined that complex 1 [dichloro-di(2-(1H-indole-3-yl)benzimidazole)platinum(II)·2H₂O] has stronger interaction than carboplatin and complex 10 [dichloro-di(2-(3,4,5-trimethoxystyryl)benzimidazole)platinum(II)·2H₂O] has stronger interaction than both carboplatin and cisplatin with plasmid DNA.     

Cleavage by restriction enzymes of DNA modified with the antitumour drug cis-diamminedichloroplatinum(II).

The effect of binding of an antitumour drug cis-diamminedichloroplatinum(II) (cis-[Pt(NH3)2Cl2]) to DNA on cutting effectiveness of BamHI, EcoRI, and SalI restriction endonucleases was quantitatively determined. The platinum complex inhibits the cleavage of plasmid pHC624 DNA linearized by BglI restrictase. From the present results we conclude that the yield of restriction endonuclease cleavage is also lowered if the platinum complex is bound outside the recognition DNA sequence of these enzymes. We propose that the origin of platinum adducts on DNA outside the recognition sequence can decrease the yield of restriction enzyme cleavage via inducing a conformational perturbation in the recognition DNA sequence of these enzymes and also via inhibition of the linear diffusion of these enzymes on DNA.     

DNA interaction and antiproliferative behavior of the water soluble platinum supramolecular squares [(en)Pt(N-N)]4(NO3)8 (en=ethylenediamine, N-N=4,4'-bipyridine or 1,4-bis(4-pyridyl)tetrafluorobenzene)

The interaction with DNA of two water soluble platinum supramolecular squares [(en)Pt(N-N)]4(NO3)8 (en=ethylenediamine, N-N=1,4-bis(4-pyridyl)tetrafluorobenzene, compound 1, N-N=4,4'-bipyridine, compound 2) has been studied by circular dichroism, electrophoretic mobility and atomic force microscopy. the two complexes drastically modify the second and tertiary structures of DNA, but compound 2 does it strongly due probably to its smaller size by comparison with compound 1 and its more suitable structural features for intercalation between base pairs. The two supramolecular squares were assayed against the HL-60 tumor cell line for 24 and 72 h. The IC50 values for 24 h are smaller than that of cisplatin for this time, however for 72 h the IC50 have higher values being the corresponding to compound 2 comparable to that of cisplatin. Apoptotic assays were also carried out for the compounds 1 and 2 against the tumor cell line.     

A novel naturally occurring tripyrrole with potential nuclease and anti-tumour properties

The DNA targeting and membrane damaging activities of a novel tripyrrole 1 obtained as a red pigment from the Micrococcus sp. were investigated. It was found that compound 1 binds with DNA efficiently and facilitates copper-mediated DNA cleavage as well as peroxidation of membrane lipids by a process that does not require any external reducing agent. Compound 1 also showed impressive cytotoxicity to both mouse and human tumour cell lines. The membrane damaging ability of compound 1 might be vital in its nuclease and cytotoxicity properties. Interestingly, compared to the various DNA cleaving agents, compound 1 showed a preferential binding with the G-C rich domain.