Electrode potential-modulated cleavage of surface-confined DNA by hydroxyl radicals detected by an electrochemical biosensor

Damage to DNA frequently involves interruption of DNA sugar-phosphate strands (strand breaks, sb). Under aerobic conditions, transition metal ions cause DNA damage through production of reactive oxygen species (frequently via Fenton-type reactions). Formation of sb in covalently closed supercoiled (sc) DNA can be detected using an electrochemical biosensor based on a scDNA-modified mercury electrode. By controlling the potential of the electrode, this technique can be employed in studies of redox reactions involved in formation of DNA strand breaks, and to detect species involved in these reactions. ScDNA anchored at HMDE was cleaved by catalytic amounts of iron/EDTA ions in the absence of chemical reductants when appropriate electrode potential (sufficiently negative to reduce [Fe(EDTA)]- to [Fe(EDTA)]2-) was applied. The process required oxygen or hydrogen peroxide. The extent of DNA damage increased with the shift of the electrode potential to negative values, displaying a sharp inflection point matching the potential of [Fe(EDTA)]2-/[Fe(EDTA)]- redox pair. In the absence of transition metal ions, significant DNA damage was observed at potentials sufficiently negative for reduction of dioxygen at the mercury electrode. This observation suggests cleavage of the surface-attached scDNA by radical intermediates of oxygen reduction at HMDE.     

Mechanism of DNA strand breakage by piperidine at sites of N7-alkylguanines

The volatile, secondary amine piperidine is used in the Maxam-Gilbert chemical method of DNA sequencing to create strand breaks in DNA at sites of damaged bases. As such it is often used in generalized studies of DNA damage to identify 'alkali-labile lesions'. We confirm the mechanism proposed by Maxam and Gilbert (Maxam, A. and Gilbert, W. (1980) Methods Enzymol. 65, 499-560) by which aqueous piperidine creates strand breaks at sites of N7-guanine alkylations: alkaline conditions catalyze rupture of the C8-N9 bond, forming a formamido-pyrimidine structure which is displaced from the ribose moiety by piperidine. In keeping with this mechanism, the tertiary amine, N-methylpiperidine, does not catalyze the formation of strand breaks in alkylated DNA. Our data confirm the prediction that high pH in and of itself will not create strand breaks at sites of N7-alkylguanines.     

Effect of lipophilic chelators on oxyradical-induced DNA strand breaks in human granulocytes: paradoxical effect of 1,10-phenanthroline.

Strand breaks can be produced in the DNA of intact granulocytes by a flux of oxyradicals (O2- and H2O2) generated by tetradecanoylphorbol acetate (TPA) or by a flux of H2O2 generated by glucose oxidase. The mechanism by which such breaks are induced is still uncertain. Lipophilic chelators such as dipyridyl and 1,10-phenanthroline (OP) strongly inhibit strand breaks induced by H2O2, presumably because of their ability to chelate intracellular iron. We now report that dipyridyl also partially inhibits strand breaks in TPA-stimulated granulocytes while a "copper-specific" lipophilic chelator, neocuproine, has no effect. As opposed to these effects, OP increases the number of strand breaks in TPA-stimulated granulocytes. Superoxide dismutase (SOD) (but not catalase) partially blocks this increase. Both the cell-impermeable chelator, EDTA, and neocuproine strongly block the increase also. In fact, in the presence of EDTA, OP behaves like dipyridyl and inhibits strand breaks. Preformed OP2-copper(II) complex causes DNA breaks in TPA-stimulated granulocytes. The paradoxical effect of OP may be explained by assuming that OP may form two different metal complexes, a DNA-damaging complex with copper or an inhibitory complex with iron. If copper(II) and O2- are present, the first complex may form and the net effect may be an increase in strand breaks. If the formation of this complex is prevented by SOD, EDTA, or neocuproine, then OP may complex iron and the net effect may be (like dipyridyl) an inhibition of strand breaks. The source of the copper responsible for the formation of OP2-copper complex is unknown.     

In vivo formation of single-strand breaks in DNA by hydrogen peroxide is mediated by the Haber-Weiss reaction

Phenanthroline and bipyridine, strong chelators of iron, protect DNA from single-strand break formation by H2O2 in human fibroblasts. This fact strongly supports the concept that these DNA single-strand breaks are produced by hydroxyl radicals generated by a Fenton-like reaction between intracellular Fe2+ and H2O2: H2O2 + Fe2+----Fe3+ + OH- + OH: Corroborating this idea is the fact that thiourea, an effective OH radical scavenger, prevents the formation of DNA single-strand breaks by H2O2 in nuclei from human fibroblasts. The copper chelator diethyldithiocarbamate, a strong inhibitor of superoxide dismutase, greatly enhances the in vivo production of DNA single-strand breaks by H2O in fibroblasts. This supports the idea that Fe3+ is reduced to Fe2+ by superoxide ion: O divided by 2 + Fe3+----O2 + Fe2+; and therefore that the sum of this reaction and the Fenton reaction, namely the so-called Haber-Weiss reaction, H2O2 + O divided by 2----O2 + OH- + OH; represents the mode whereby OH radical is produced from H2O2 in the cell. EDTA completely protects DNA from single-strand break formation in nuclei. The chelator therefore removes iron from the chromatin, and although the Fe-EDTA complex formed is capable of reacting with H2O2, the OH radical generated under these conditions is not close enough to hit DNA. Therefore iron complexed to chromatin functions as catalyst for the Haber-Weiss reaction in vivo, similarly to the role played by Fe-chelates in vitro.     

Sites of gamma radiation-induced DNA strand breaks after alkali treatment

When DNA is gamma-irradiated in aerated aqueous solution, strand breaks are produced during irradiation or the next few hours. Subsequent piperidine treatment gives rise to further DNA strand ruptures at alkali-labile sites. These different types of DNA chain breaks provoked by gamma-irradiation have been studied with oligonucleotides having defined sequences. The breaks selectively developed inside the DNA chain at alkali-labile sites by piperidine treatment appeared at lower doses preferentially at guanine positions and the order G greater than A greater than T greater than or equal to C was observed. The total contribution of the direct DNA chain ruptures, formed during irradiation and the next few hours, and those obtained by piperidine treatment was studied at doses ranging from 10 to 120 Gy. The chain breaks appeared preferentially at thymine positions and the order T greater than G greater than A greater than or equal to C was shown for the higher doses.     

Ex-vivo and in vitro protective effects of kolaviron against oxygen-derived radical-induced DNA damage and oxidative stress in human lymphocytes and rat liver cells

The present study reports the protective effects of kolaviron, a Garcinia biflavonoid from the seeds of Garcinia kola widely consumed in some West African countries against oxidative damage to molecular targets ex-vivo and in vitro. Treatment with hydrogen peroxide (H2O2) at a concentration of 100 micromol/L increased the levels of DNA strand breaks and oxidized purine (formamidopyrimidine glycosylase (FPG) and pyrimidine (endonuclease III (ENDO III) sites) bases in both human lymphocytes and rat liver cells using alkaline single cell gel electrophoresis (the comet assay). Kolaviron was protective at concentrations between 30-90 micromol/L and decreased H2O2-induced DNA strand breaks and oxidized bases. Neither alpha-tocopherol nor curcumin decreased H2O2-induced DNA damage in this assay. In lymphocytes incubated with Fe3+/GSH, Fe3+ was reduced to Fe2+ by GSH initiating a free radical generating reaction which induced 11.7, 6.3, and 4.9 fold increase respectively in strand breaks, ENDO III and FPG sensitive sites compared with control levels. Deferoxamine (2 mmol/L), an established iron chelator significantly inhibited GSH/Fe3+-induced strand breaks and oxidized base damage. Similarly, kolaviron at 30 and 90 micromol/L significantly attenuated GSH/Fe3+-induced strand breaks as well as base oxidation. Kolaviron (100 mg/kg bw) administered to rats for one week protected rat liver cells against H2O2-induced formation of strand breaks, ENDO III, and FPG sensitive sites, Fe3+/EDTA/ascorbate-induced malondialdehyde formation and protein oxidation using gamma-glutamyl semialdehyde (GGS) and 2-amino-adipic semialdehyde (AAS) as biomarkers of oxidative damage to proteins. We suggest that kolaviron exhibits protective effects against oxidative damage to molecular targets via scavenging of free radicals and iron binding. Kolaviron may therefore be relevant in the chemoprevention of oxidant-induced genotoxicity and possibly human carcinogenesis.     

Charge dependence of Fe(II)-catalyzed DNA cleavage.

The effect of charge of the Fe(II) reagent used to induce DNA strand cleavage reactions in the presence of a source of reducing equivalents is investigated using two oligonucleotide models. The first consists of the two strands dA20 and dT20, and an equimolar complex between them. The second is a short four-arm branched DNA complex composed of four 16-mer strands. In the former case, cleavage of the 1:1 complex by three reagents with different formal charge, Fe(II).EDTA2-, Fe(II).EDDA and Fe2+, is comparable in rate to that of the individual dT20 and the dA20 strands. While the three reagents show similar cleavage rates for the duplex and single stranded molecules, they give distinctive cutting patterns in the DNA tetramer, consistent with the presence of a site of excess negative charge at the branch point. Scission induced by Fe(II).EDTA2- shows lower reactivity at the branch site relative to duplex controls, whereas Fe(II)2+ shows enhanced reactivity. Formally neutral Fe(II).EDDA shows weak loss of cutting reactivity at the branch. The position of attack by Fe(II)2+ in the branched tetramer is shifted with respect to those of Fe(II).EDTA2- or Fe(II).EDDA; a slower migrating species is also detected in the scission of dA20.dT20 duplex by Fe(II) reaction. These results suggest that the Fe(II)2+ reaction proceeds by a different mechanism from the other agents. The difference in cutting profiles induced by the neutral and negatively charged chelated complexes is consistent with a local electrostatic repulsion of a negatively charged source of radicals, not a positively charged one.     

Single-strand breakage on binding of DNA to cells in the genetic transformation of Diplococcus pneumoniae.

Mutants of Diplococcus pneumoniae that lack a membrane-localized DNAase are defective in transformation because entry of DNA into the cell is blocked. Such mutants still bind DNA on the outside of the cell. The bound DNA is double-stranded and its double-stranded molecular weight is unchanged. Its sedimentation behavior in alkali, however, shows that it has undergone single-strand breakage. The breaks are located randomly in both strands of the bound DNA at a mean separation of 2 × 10⁶ daltons of single-stranded DNA. Both binding and single-strand breakage occur in the presence of EDTA. Single-strand breaks are similarly formed on binding of DNA to normally transformable cells in the presence of EDTA. The single-strand breaks appear to be a consequence of attachment. DNA may be bound to the cell surface at the point of breakage.A mutant that is partially blocked in entry also binds DNA mainly on the outside of the cell. In the presence of EDTA, DNA bound by this mutant undergoes only single-strand breaks. In the absence of EDTA, however, double-strand breaks occur, apparently as a result of the initiation of entry. It is possible that the double-strand breaks arise from additional single-strand breaks opposite those that occurred on binding. The double-strand breaks presumably result from action of the membrane DNAase as it begins to release oligonucleotides from one strand segment while drawing the complementary strand segment into the cell.     

Iron(II)-mimosine catalyzed cleavage of DNA

Mimosine, DNA breaKs, Free Radicals, Fenton Reaction Supercoiled plasmid DNA was treated in vitro with H2O2, DTT and either Fe (II), Fe (II)-EDTA or Fe (II)-mimosine. The rate of DNA break formation was followed by the conversion of the supercoiled form into relaxed-circular and linear forms. In the concentration interval of 0-4 microM Fe (II), Fe (II)-EDTA slowed-down the formation of DNA breaks, while Fe (II)-mimosine enhanced the rate of break formation up to several times. A conclusion is drawn that this enhancement is due to the increased affinity of the Fe (II)-mimosine complex to DNA.     

Interaction of Topotecan,DNA Topoisomerase I Inhibitor,with Double-Stranded Polydeoxyribonucleotides. 5. Topotecan is Capable of Producing Single- and Double-Strand Breaks in Circular Supercoiled DNA in the Absence of the Enzyme

A study was made of the temperature, concentration, and time dependences for the emergence of breaks in the sugar-phosphate backbone of a circular supercoiled DNA (scDNA) in the presence of a campto-thecin derivative topotecan (TPT) and in the absence of DNA topoisomerase I (topo I). The experiments were carried out in low ionic strength solutions (10 mM sodium cacodylate) at neutral pH (6.8). The incubation time necessary for the appearance of double-strand breaks in scDNA in the presence of TPT correlated with the time of formation of strong TPT–DNA complex. This is the first demonstration that molecules of the camptothecin family can cause double-strand breaks in scDNA in the absence of the enzyme. A model is suggested for the complex composed of two crossed DNA duplexes bound through a bridge of two dimers of the TPT lactone form. According to this model, two carbonyl groups of D rings of different TPT dimers form hydrogen bonds with 2-amino groups of guanines located in the neighboring base pairs of different strands of one DNA duplex. At the same time, two other carbonyl groups of D rings of TPT dimers form hydrogen bonds with 2-amino groups of guanines 5 bp apart in one and the same strand of the second DNA duplex.     

Topoisomerase II-mediated breaks in spermatozoa cause the specific degradation of paternal DNA in fertilized oocytes

We have demonstrated that mouse spermatozoa can cleave their DNA into 50-kb fragments when treated with Triton X-100, MnCl(2), and CaCl(2). This cleavage, which is termed sperm chromatin fragmentation (SCF), is mediated by topoisomerase IIB (TOP2B) following stimulation by a factor in the epididymal fluid, most likely a nuclease, and can be at least partially religated by EDTA. When the protamines are removed, this DNA breakage is followed by digestion of the DNA by a nuclease(s). We tested whether the oocyte could repair TOP2B-induced sperm DNA breaks and whether partial religation by EDTA would allow spermatozoa to fertilize the oocytes normally. Oocytes injected with untreated spermatozoa developed normally. However, oocytes injected with spermatozoa treated with MnCl(2) and CaCl(2) to induce SCF, with or without subsequent EDTA treatment, failed to develop. In both of these treatment groups, the maternal pronuclei developed normally and replicated their DNA. However the paternal pronuclei did not replicate their DNA and this DNA began to disappear 6 h postinjection, which corresponded approximately to the time at which maternal DNA replication was initiated. These data suggest that when TOP2B is induced to cleave sperm DNA before fertilization, the paternal DNA is subsequently degraded by a highly regulated mechanism that does not affect the maternal chromatin. Furthermore, partial religation by EDTA of TOP2B-induced breaks prevents neither the inhibition of DNA synthesis nor DNA degradation.     

Metal-mediated oxidative damage to cellular and isolated DNA by gallic acid, a metabolite of antioxidant propyl gallate

Propyl gallate (PG), widely used as an antioxidant in foods, is carcinogenic to mice and rats. PG increased the amount of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a characteristic oxidative DNA lesion, in human leukemia cell line HL-60, but not in HP100, which is hydrogen peroxide (H2O2)-resistant cell line derived from HL-60. Although PG induced no or little damage to 32P-5'-end-labeled DNA fragments obtained from genes that are relevant to human cancer, DNA damage was observed with treatment of esterase. HPLC analysis of the products generated from PG incubated with esterase revealed that PG converted into gallic acid (GA). GA induced DNA damage in a dose-dependent manner in the presence of Fe(III)EDTA or Cu(II). In the presence of Fe(III) complex such as Fe(III)EDTA or Fe(III)ADP, GA caused DNA damage at every nucleotide. Fe(III) complex-mediated DNA damage by GA was inhibited by free hydroxy radical (*OH) scavengers, catalase and an iron chelating agent. These results suggested that the Fe(III) complex-mediated DNA damage caused by GA is mainly due to *OH generated via the Fenton reaction. In the presence of Cu(II), DNA damage induced by GA occurred at thymine and cytosine. Although *OH scavengers did not prevent the DNA damage, methional inhibited the DNA damage. Cu(II)-mediated DNA damage was inhibited by catalase and a Cu(I) chelator. These results indicated that reactive oxygen species formed by the interaction of Cu(I) and H2O2 participates in the DNA damage. GA increased 8-oxodG content in calf thymus DNA in the presence of Cu(II), Fe(III)EDTA or Fe(III)ADP. This study suggested that metal-mediated DNA damage caused by GA plays an important role in the carcinogenicity of PG.     

Bleomycin-iron can degrade DNA in the presence of excess ethylenediaminetetraacetic acid in vitro

The antineoplastic drug bleomycin, when complexed to Fe(II), causes both single- and double-stranded lesions in DNA in vitro. EDTA is commonly used to inhibit the reaction of bleomycin-Fe with DNA, presumably by removing the metal cofactor. In this study, we utilized a simple assay involving the conversion of supercoiled plasmid DNA to the nicked or linear forms to further investigate the ability of bleomycin-Fe to degrade DNA in the presence of EDTA. We found that a 1:1 complex of bleomycin and Fe can degrade plasmid DNA even in the presence of a 10(6) molar excess of EDTA over bleomycin. Furthermore, we found that the half-life for inactivation of bleomycin-Fe by excess EDTA is about 1.5 h. Finally, we demonstrate that excess bleomycin associated with the outer plasma membranes of cells can damage DNA after the cells are lysed in buffers containing EDTA and SDS. These results suggest that EDTA may not be an efficient inhibitor of the reaction of bleomycin-Fe with DNA.     

Copper-activated DNA photocleavage by a pyridine-linked bis-acridine intercalator

We report the synthesis of new photonuclease 4 consisting of two acridine rings joined by a pyridine-based copper binding linker. We have shown that photocleavage of plasmid DNA is markedly enhanced when this ligand is irradiated in the presence of copper(II) (419 nm, 22 degrees C, pH 7.0). Viscometric data indicate that 4 binds to DNA by monofunctional intercalation, and equilibrium dialysis provides an estimated binding constant of 1.13 x 105 M-1 for its association with calf thymus DNA. In competition dialysis experiments, 4 exhibits preferential binding to GC-rich DNA sequences. When Cu(II) is added at a ligand to metal ratio of 1:1, electrospray ionization mass spectrometry demonstrates that compound 4 undergoes complex formation, while thermal melting studies show a 10 degrees C increase in the Tm of calf thymus DNA. Groove binding and intercalation are suggested by viscometric data. Finally, colorimetric and scavenger experiments indicate that the generation of Cu(I), H2O2, and superoxide contributes to the production of DNA frank strand breaks by the Cu(II) complex of 4. Whereas the strand breaks are distributed in a relatively uniform fashion over the four DNA bases, subsequent piperidine treatment of the photolysis reactions shows that alkaline labile lesions occur predominantly at guanine.     

Interaction of topotecan-a DNA topoisomerase I inhibitor-with dual-stranded polydeoxyribonucleotides. V. Topotecan is able to cause single- and double-strand breaks in ring superhelical DNA in the absence of enzyme

Temperature, concentration, and time dependence for the emergence of breaks in the sugar-phosphate backbone in a circular supercoiled DNA (scDNA) was studied for the first time in the presence of topotecan (TPT) and in the absence of human DNA topoisomerase I (topo I). Because TPT is a comptothecin (CPT) derivative, it is the first example for the ability of molecules of CPT family to cause double-stranded breaks in scDNA in the absence of the enzyme. The experiments were carried out in low ionic strength solutions (10 mM sodium cacodylate) at neutral pH (6.8). Incubation time necessary for the appearance of double-stranded breaks in scDNA in the presence of TPT correlated with the time of formation of strong TPT-DNA complex. A model was suggested for the complex composed of two crossed DNA duplexes bound through a bridge of two dimers of TPT lactone form. According to this model, two carbonyl groups of D rings of different TPT dimers form hydrogen bonds with 2-amino groups of guanines located in the neighboring base pairs of diverse strands of one of DNA duplexes. At the same time, two other carbonyl groups of D rings of TPT dimers form hydrogen bonds with 2-amino groups of guanines spaced five bp apart in the same strand of the second DNA duplex.     

Design and synthesis of conformationally frozen peptide nucleic acid backbone: chiral piperidine PNA as a hexitol nucleic acid surrogate

The design and facile synthesis of novel chiral piperidine PNA from naturally occurring 4-hydroxy-L-proline is reported. The stereospecific ring-expansion reaction to get six-membered piperidine derivative from 5-membered pyrrolidine derivative is exploited for this synthesis. The resulting conformationally constrained PNA is utilized for the synthesis of PNA mixmers and the concept is substantiated by UV-Tm studies of the resulting PNA(2):DNA complexes.     

Photosensitization by antitumor agents, 4. Anthrapyrazole-photosensitized formation of single strand-breaks in DNA

Single-strand breaks can be introduced into PM2 closed-circular DNA upon illumination with blue light, in the presence of the anthrapyrazole antitumor agent, compound 1. Damage is observed already after 1 min of blue light illumination, and is significantly enhanced by the presence of electron donors such as NADH, ascorbic acid or Fe(III)/EDTA complex. The photosensitizing properties were not observed for anthrapyrazole analogues with one or more hydroxyl substituents in the chromophore of the drug. The inhibitory effects of sodium azide, methanol, mannitol, SOD, and catalase suggest an oxygen-dependent mechanism of strand-break production, probably involving hydroxyl radicals. However, a second mechanism involving drug molecules bound to the DNA is also indicated under anoxic conditions in the presence of NADH.     

Characterization of microbial communities removing nitrogen oxides from flue gas: the BioDeNOx process

BioDeNOx is an integrated physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gases. In this process, the flue gas is purged through a scrubber containing a solution of Fe(II)EDTA2-, which binds the NOx to form an Fe(II)EDTA.NO2- complex. Subsequently, this complex is reduced in the bioreactor to dinitrogen by microbial denitrification. Fe(II)EDTA2-, which is oxidized to Fe(III)EDTA- by oxygen in the flue gas, is regenerated by microbial iron reduction. In this study, the microbial communities of both lab- and pilot-scale reactors were studied using culture-dependent and -independent approaches. A pure bacterial strain, KT-1, closely affiliated by 16S rRNA analysis to the gram-positive denitrifying bacterium Bacillus azotoformans, was obtained. DNA-DNA homology of the isolate with the type strain was 89%, indicating that strain KT-1 belongs to the species B. azotoformans. Strain KT-1 reduces Fe(II)EDTA.NO2- complex to N2 using ethanol, acetate, and Fe(II)EDTA2- as electron donors. It does not reduce Fe(III)EDTA-. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene fragments showed the presence of bacteria closely affiliated with members of the phylum Deferribacteres, an Fe(III)-reducing group of bacteria. Fluorescent in situ hybridization with oligonucleotide probes designed for strain KT-1 and members of the phylum Deferribacteres showed that the latter were more dominant in both reactors.     

Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative.

A 3-azidoproflavine derivative was covalently linked to the 5'-end of an octathymidylate synthesized with the [alpha]-anomers of the nucleoside. Two target nucleic acids were used for this substituted oligo-[alpha]-thymidylate: a 27-mer single-stranded DNA fragment containing an octadeoxyadenylate sequence and a 27-mer duplex containing eight contiguous A.T base pairs with all adenines on the same strand. Upon visible light irradiation the octa-[alpha]-thymidylate was photocrosslinked to the single-stranded 27-mer. Chain breaks were induced at the crosslinked sites upon piperidine treatment. From the location of the cleavage sites on the 27-mer sequence it was concluded that a triple helix was formed by the azidoproflavine-substituted oligo-[alpha]-thymidylate with its complementary oligodeoxyadenylate sequence. When the 27-mer duplex was used as a substrate cleavage sites were observed on both strands after piperidine treatment of the irradiated sample. They were located at well defined positions which indicated that the octathymidylate was bound to the (dA)8.(dT)8 sequence in parallel orientation with respect to the (dA)8-containing strand. Specific binding of the [alpha]-octathymidylate involved local triple strand formation with the duplex (dA)8.(dT)8 sequence. This result shows that it is possible to synthesize sequence-specific molecules which specifically bind oligopurine-oligopyrimidine sequences in double-stranded DNA via recognition of the major groove hydrogen bonding sites of the purines.