Peroxy radical oxidation of thymidine

Tandem Lesions Arising from 5-(Uracilyl)methyl Peroxyl Radical Addition to Guanine: Product Analysis and Mechanistic Studies

The reaction of hydroxyl radical (HO^•) with thymine in DNA generates 5-(uracilyl)-methyl radicals (T^•) and the corresponding methylperoxyl radical (TOO^•) in the presence of O₂, which in turn propagates damage by reacting with a vicinal nucleobase. This leads to so-called double or tandem lesions. Because methyl oxidation products of thymine are major products, we investigated the reactivity of TOO^• using a photolabile precursor: 5-(phenylthiomethyl)uracil (T^SPh). The precursor was prepared and incorporated into a DNA trinucleotide: 5'-d(GpT^SPhpA)-3' (G-T^SPh-A). Upon photolysis, the resulting products were characterized by LC-MS/MS. Thereby, we identified four tandem lesions involving GpT, which include either 2,6-diamino-4-hydroxy-5-formamidopyrimidine (fapyG) or 8-oxo-7,8-dihydroguanine (oxoG) in tandem with either 5-formyluracil (fU) or 5-hydroxymethyluracil (hmU). The formation of these tandem lesions is explained by initial addition of TOO^• to the C8 of guanine moiety, giving an N7-guanine cross-linked radical. The latter radical undergoes either reduction to an 7,8-saturated endoperoxide or oxidation to an 7,8-unsaturated endoperoxide, which transform into fapyG-fU-A and oxoG-fU-A, respectively. This is supported by the effect of a reducing (dithiothreitol) and oxidizing agent (Fe³⁺) on product formation. This study expands the repertoire of tandem lesions that can occur at GpT sequences and underlines the importance of redox environment.

Reactivity of Nucleic Acid Radicals

Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.

A modified method for studying behavioral paradox of antioxidants and their disproportionate competitive kinetic effect to scavenge the peroxyl radical formation

We have described a modified method for evaluating inhibitor of peroxyl radicals, a well-recognized and -documented radical involved in cancer initiation and promotion as well as diseases related to oxidative stress and ageing. We are reporting hydrophilic and lipophilic as well as natural and synthetic forms of antioxidants revealing a diversified behaviour to peroxyl radical in a dose-dependent manner (1 nM–10 μM). A simple kinetic model for the competitive oxidation of an indicator molecule (ABTS) and a various antioxidant by a radical (ROO^•) is described. The influences of both the concentration of antioxidant and duration of reaction (70 min) on the inhibition of the radical cation absorption are taken into account while determining the activity. The induction time of the reaction was also proposed as a parameter enabling determination of antioxidant content by optimizing and introducing other kinetic parameters in 96-well plate assays. The test evidently improves the original PRTC (peroxyl radical trapping capacity) assay in terms of the amount of chemical used, simultaneous tracking, that is, the generation of the radical taking place continually and the kinetic reduction technique (area under curve, peak value, slope, and V_max).

Hepatoprotective effects and HSV-1 activity of the hydroethanolic extract of Cecropia glaziovii (embaúba-vermelha) against acyclovir-resistant strain

CONTEXT

Cecropia glaziovii Snethl. (Cecropiaceae), commonly known as "embaúba-vermelha", is widely distributed throughout Latin America and has been reported in Brazilian folk medicine to treat cough, asthma, high blood pressure and inflammation.

OBJECTIVE

Investigate the hepatoprotective properties of crude hydroethanolic extract of C. glaziovii as well as its in vitro antioxidant and antiviral (HSV-1 acyclovir resistant strain) activities.

MATERIALS AND METHODS

The hepatoprotective effect, the antioxidant properties and antiviral activity of crude hydroethanol extract (RCE40) from C. glaziovii leaves were evaluated by carbon-tetrachloride (CCl(4))-induced hepatotoxicity, by TBARS (thiobarbituric acid reactive species) and MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide] assays, respectively.

RESULTS

The RCE40 extract (20 mg/kg) inhibited lipid peroxidation on liver in post injury treatment and decreased serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). In addition, in this protocol the RCE40 (20 mg/kg) enhanced the activity of hepatic enzymes (SOD/CAT) which are involved in combating reactive oxygen species (ROS), suggesting that it possesses the capacity to attenuate the CCl(4)-induced liver damage. Moreover the RCE40 (20 mg/kg) inhibited TBARS formation induced by several different inductors of oxidative stress showing significant antioxidant activity, including physiologically relevant concentration, as low as 2 µg/mL. Concerning antiviral activity, the RCE40 was effective against herpes simplex virus type 1 replication (29R acyclovir resistant strain) with EC(50) = 40 µg/mL and selective index (SI) = 50.

DISCUSSION AND CONCLUSION

These results indicate that C. glaziovii could be a good source of antioxidant and anti-HSV-1 lead compounds.

Low energy electron stimulated desorption from DNA films dosed with oxygen

Desorption of anions stimulated by 1-18 eV electron impact on self-assembled monolayer (SAM) films of single DNA strands is measured as a function of film temperature (50-250 K). The SAMs, composed of 10 nucleotides, are dosed with O(2). The OH(-) desorption yields increase markedly with exposure to O(2) at 50 K and are further enhanced upon heating. In contrast, the desorption yields of O(-), attributable to dissociative electron attachment to trapped O(2) molecules decrease with heating. Irradiation of the DNA films prior to the deposition of O(2) shows that this surprising increase in OH(-) desorption, at elevated temperatures, arises from the reaction of O(2) with damaged DNA sites. These results thus appear to be a manifestation of the so-called "oxygen fixation" effect, well known in radiobiology.

Positioning effects of KillerRed inside of cells correlate with DNA strand breaks after activation with visible light

Fluorescent proteins (FPs) are established tools for new applications, not-restricted to the cell biological research. They could also be ideal in surgery enhancing the precision to differentiate between the target tissue and the surrounding healthy tissue. FPs like the KillerRed (KRED), used here, can be activated by excitation with visible day-light for emitting active electrons which produce reactive oxygen species (ROS) resulting in photokilling processes. It is a given that the extent of the KRED's cell toxicity depends on its subcellular localization. Evidences are documented that the nuclear lamina as well as especially the chromatin are critical targets for KRED-mediated ROS-based DNA damaging. Here we investigated the damaging effects of the KRED protein fused to the nuclear lamina and to the histone H2A DNA-binding protein. We detected a frequency of DNA strand breaks, dependent first on the illumination time, and second on the spatial distance between the localization at the chromatin and the site of ROS production. As a consequence we could identify defined DNA bands with 200, 400 and (600) bps as most prominent degradation products, presumably representing an internucleosomal DNA cleavage induced by KRED. These findings are not restricted to the detection of programmed cell death processes in the therapeutic field like PDT, but they can also contribute to a better understanding of the structure-function relations in the epigenomic world.

Oxidative Damage of Thymidines by the Atmospheric Free-Radical Oxidant NO3•

Analysis of the products formed in the reaction of nitrate radicals, NO3 •, with the N- and O-methylated and acetylated thymidines 1a and 1b revealed, for the first time, insight regarding how this important atmospheric free-radical oxidant can cause irreversible damage to DNA building blocks. Mechanistic studies indicated that the initial reaction step likely proceeds via NO3 • induced electron transfer at the pyrimidine ring, followed by deprotonation of the methyl group at C5. The oxidation ultimately leads to formation of nitrates 2, aldehydes 4 and, in the case of high [NO3 •], also to carboxylic acids 5. In addition to this, through a very minor pathway, loss of the methyl group at C5 also occurred to give the respective 2′-deoxyuridines 6. The nitrates 2 are highly labile compounds that undergo rapid hydrolysis during work-up and purification of the reaction mixtures, which could lead to serious misinterpretation of the experimental findings and reaction mechanism. Products resulting from NO3 • addition to the C5=C6 double bond in the pyrimidine ring were not observed. Also, no reaction of NO3 • with the 2′-deoxyribose moiety was detected.

Thymine hydroperoxide as a potential source of singlet molecular oxygen in DNA

The decomposition of organic hydroperoxides into peroxyl radicals is a potential source of singlet molecular oxygen [O2 (1Deltag)] in biological systems. This study shows that 5-(hydroperoxymethyl)uracil (5-HPMU), a thymine hydroperoxide within DNA, reacts with metal ions or HOCl, generating O2 (1Deltag). Spectroscopic evidence for generation of O2 (1Deltag) was obtained by measuring (i) the bimolecular decay, (ii) the monomolecular decay, and (iii) the observation of D2O enhancement of O2 (1Deltag) production and the quenching effect of NaN3. Moreover, the presence of O2 (1Deltag) was unequivocally demonstrated by the direct characterization of the near-infrared light emission. For the sake of comparison, O2 (1Deltag) derived from the H2O2/HOCl system and from the thermolysis of the N,N'-di(2,3-dihydroxypropyl)-1,4-naphthalenedipropanamide endoperoxide was also monitored. More evidence of O2 (1Deltag) generation was obtained by chemical trapping of O2 (1Deltag) with anthracene-9,10-divinylsulfonate (AVS) and detection of the specific AVS endoperoxide by HPLC/MS/MS. The detection by HPLC/MS of 5-(hydroxymethyl)uracil and 5-formyluracil, two thymine oxidation products generated from the reaction of 5-HPMU and Ce4+ ions, supports the Russell mechanism. These photoemission properties and chemical trapping clearly demonstrate that the decomposition of 5-HPMU generates O2 (1Deltag) by the Russell mechanism and point to the involvement of O2 (1Deltag) in thymidine hydroperoxide cytotoxicity.

Non-reductive Scavenging of 1,1-Diphenyl-2-picrylhydrazyl (DPPH) by Peroxyradical: A Useful Method for Quantitative Analysis of Peroxyradical

A stable radical 1,1-diphenyl-2-picrylhydrazyl (DPPH) has long been used as a convenient method for the antioxidant assay of biological materials such as cysteine, glutathione, ascorbic acid, tocopherol and polyhydroxy aromatic compounds (hydroquinone, pyrogallol, etc.). In this study, non-reductive scavenging of DPPH was investigated by electron spin resonance (ESR) analyses for the purpose of developing a useful method for quantitative determination of peroxyradical. Since DPPH was degraded in the presence of peroxyradical derived from UV-irradiated benzoylperoxide and the peroxyradical-induced degradation of DPPH was inhibited by the addition of a spin trapping agent 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), it is concluded that DPPH is non-reductively scavenged by peroxyradical. Therefore, it is suggested that DPPH could be a useful agent for the quantitative measurement of peroxyradical.

Nitroxides inhibit peroxyl radical-mediated DNA scission and enzyme inactivation

Nitroxides are cell-permeable stable radicals that protect biomolecules from oxidative damage in several ways. The mechanisms of protection studied to date include removal of superoxide radicals as SOD-mimics, oxidation of transition metal ions to preempt the Fenton reaction, and scavenging carbon-centered radicals. However, there is no agreement regarding the reaction of piperidine nitroxides with peroxyl radicals. The question of whether they can protect by scavenging peroxyl radicals is important because these radicals are formed in the presence of oxygen abundant in biological tissues. To further our understanding of the antioxidative behavior of piperidine nitroxides, we studied their effect on biochemical systems exposed to the water soluble radical initiator 2,2'-azobis (2-amidinopropane) hydrochloride (AAPH). AAPH thermally decomposes to yield tert-amidinopropane radicals (t-AP(*)) that readily react with oxygen to form peroxyl radicals (t-APOO(*)). It has recently been reported that piperidine nitroxides protect plasmid DNA from t-AP(*) though not from t-APOO(*). The present study was directed at the question of whether these nitroxides can protect biological systems from damage inflicted by peroxyl radicals. The reaction of nitroxides with AAPH-derived radicals was followed by cyclic voltammetry and electron paramagnetic resonance spectroscopy, whereas the accumulation of peroxide was iodometrically assayed. Assaying DNA damage in vitro, we demonstrate that piperidine nitroxides protect from both t-AP(*) and t-APOO(*). Similarly, nitroxides inhibit AAPH-induced enzyme inactivation. The results indicate that piperidine nitroxides protect the target molecule by reacting with and detoxifying peroxyl radicals.

Structure-dependent reactivity of oxyfunctionalized acetophenones in the photooxidation of DNA: base oxidation and strand breaks through photolytic radical formation (spin trapping, EPR spectroscopy, transient kinetics) versus photosensitization (electron transfer, hydrogen-atom abstraction)

The photooxidative damage of DNA, specifically guanine oxidation and strand-break formation, by sidechain-oxyfunctionalized acetophenones (hydroxy, methoxy, tert-butoxy and acetoxy derivatives), has been examined. The involvement of triplet-excited ketones and their reactivity towards DNA has been determined by time-resolved laser-flash spectroscopy. The generation of carbon-centered radical species upon Norrish-type I cleavage has been assessed by spin-trapping experiments with 5,5-dimethyl-1-pyrroline N-oxide, coupled with electron paramagnetic resonance spectroscopy. The observed DNA-base oxidation and strand-break formation is discussed in terms of the peroxyl radicals derived from the triplet-excited ketones by alpha cleavage and molecular oxygen trapping, as well as direct interaction of the excited states by electron transfer and hydrogen-atom abstraction. It is concluded that acetophenone derivatives, which produce radicals upon photolysis, in particular the hydroxy (AP-OH) and tert-butoxy (AP-O(t)Bu) derivatives, are more effective in oxidizing DNA.

Oxidation of thymine to 5-formyluracil in DNA promotes misincorporation of dGMP and subsequent elongation of a mismatched primer terminus by DNA polymerase

5-Formyluracil (fU) is a major oxidative thymine lesion generated by ionizing radiation and reactive oxygen species. In the present study, we have assessed the influence of fU on DNA replication to elucidate its genotoxic potential. Oligonucleotide templates containing fU at defined sites were replicated in vitro by Escherichia coli DNA polymerase I Klenow fragment deficient in 3'-5'-exonuclease. Gel electrophoretic analysis of the reaction products showed that fU constituted very weak replication blocks to DNA synthesis, suggesting a weak to negligible cytotoxic effect of this lesion. However, primer extension assays with a single dNTP revealed that fU directed incorporation of not only correct dAMP but also incorrect dGMP, although much less efficiently. No incorporation of dCMP and dTMP was observed. When fU was substituted for T in templates, the incorporation efficiency of dAMP (f(A) = V(max)/K(m)) decreased to (1/4) to (1/2), depending on the nearest neighbor base pair, and that of dGMP (f(G)) increased 1.1-5.6-fold. Thus, the increase in the replication error frequency (f(G)/f(A) for fU versus T) was 3.1-14.3-fold. The misincorporation rate of dGMP opposite fU (pK(a) = 8.6) but not T (pK(a) = 10.0) increased with pH (7.2-8.6) of the reaction mixture, indicating the participation of the ionized (or enolate) form of fU in the mispairing with G. The resulting mismatched fU:G primer terminus was more efficiently extended than the T:G terminus (8.2-11.3-fold). These results show that when T is oxidized to fU in DNA, fU promotes both misincorporation of dGMP at this site and subsequent elongation of the mismatched primer, hence potentially mutagenic.

Formation of abasic sites in DNA by t-butyl peroxyl radicals: implication for potent genotoxicity of lipid peroxyl radicals

We investigated abasic site formation in calf thymus DNA after exposure to a model compound of lipid-derived peroxyl radical that was generated by the reaction of tert-butyl hydroperoxide (t-BuOOH) with hemoglobin. Abasic site density in DNA was quantified by use of an enzyme-linked immunosorvent assay-like assay. In the presence of 10 mM t-BuOOH and 12.5 or 25 microM hemoglobin, 0.6-1.0 abasic sites/10(4) nucleotides were formed. However, abasic sites were not detected after replacing hemoglobin with nonheme iron, e.g. EDTA/Fe(2+), which initiates the production of alkyl and alkoxyl radicals. Therefore, the present results suggest that lipid peroxyl radicals may have a genotoxic potential through unique reactions, including depurination and depyrimidination, which lead to DNA strand breakage.

Independent generation and reactivity of 2-deoxy-5-methyleneuridin-5-yl, a significant reactive intermediate produced from thymidine as a result of oxidative stress

2'-Deoxy-5-methyleneuridin-5-yl (1) is produced in a variety of DNA damage processes and is believed to result in the formation of lesions that are mutagenic and refractory to enzymatic repair. 2'-Deoxy-5-methyleneuridin-5-yl (1) was independently generated under anaerobic conditions via Norrish Type I photocleavage during Pyrex filtered photolysis of the benzyl ketone 7. The radical (1) exhibits behavior consistent with that of a resonance-stabilized radical. The KIE for hydrogen atom transfer from t-BuSH was found to be 7.3 +/- 1.7. Competition studies between radical recombination and hydrogen atom donors (2,5-dimethyltetrahydrofuran, kTrap = 46.1 +/- 15.4 M(-1) s(-1); propan-2-ol, kTrap = 13.6 +/- 3.5 M(-1) s(-1)) chosen to mimic the carbohydrate components of 2'-deoxyribonucleotides suggest that 2'-deoxy-5-methyleneuridin-5-yl (1) may be able to transfer damage from the nucleobase to the deoxyribose of an adjacent nucleotide in DNA under hypoxic conditions.

Hydroperoxide-induced DNA damage and mutations

Hydroperoxides (ROOH) are believed to play an important role in the generation of free radical damage in biology. Hydrogen peroxide (R=H) is produced by endogenous metabolic and catabolic processes in cells, while alkyl hydroperoxides (R=lipid, protein, DNA) are produced by free radical chain reactions involving molecular oxygen (autooxidation). The role of metal ions in generating DNA damage from hydroperoxides has long been recognized, and several distinct, biologically relevant mechanisms have been identified. Identification of the mechanistic pathways is important since it will largely determine the types of free radicals generated, which will largely determine the spectrum of DNA damage produced. Some mechanistic aspects of the reactions of low valent transition metal ions with ROOH and their role in mutagenesis are reviewed with a perspective on their possible role in the biological generation of DNA damage. A survey of hydroperoxide-induced mutagenesis studies is also presented. In vitro footprinting of DNA damage induced by hydroperoxides provides relevant information on sequence context dependent reactivity, and is valuable for the interpretation of mutation spectra since it represents the damage pattern prior to cellular repair. Efforts in this area are also reviewed.

The effects of nitroxide radicals on oxidative DNA damage

The indolinonic and quinolinic aromatic nitroxides synthesized by us are a novel class of biological antioxidants, which afford a good degree of protection against free radical-induced oxidation in different lipid and protein systems. To further our understanding of their antioxidant behavior, we thought it essential to have more information on their effects on DNA exposed to free radicals. Here, we report on the results obtained after exposure of plasmid DNA and calf thymus DNA to peroxyl radicals generated by the water-soluble radical initiator, 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH), and the protective effects of the aromatic nitroxides and their hydroxylamines, using a simple in vitro assay for DNA damage. In addition, we also tested for the potential of these nitroxides to inhibit hydroxyl radical-mediated DNA damage inflicted by Fenton-type reactions using copper and iron ions. The commercial aliphatic nitroxides 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL), and bis(2,2, 6,6-tetramethyl-1-oxyl-piperidin-4-yl)sebacate (TINUVIN 770) were included for comparison. The results show that the majority of compounds tested protect: (i) both plasmid DNA and calf thymus DNA against AAPH-mediated oxidative damage in a concentration-dependent fashion (1-0.1 mM), (ii) both Fe(II) and Cu(I) induced DNA oxidative damage. However, all compounds failed to protect DNA against damage inflicted by the presence of the transition metals in combination with H(2)O(2). The differences in protection between the compounds are discussed in relation to their molecular structure and chemical reactivity.

Protection against radiation-induced degradation of DNA bases by polyamines

Polyamines have been reported to protect DNA against the formation of radiation-induced strand breaks and crosslinks to proteins. The present study was aimed at investigating the protective effect of spermine, spermidine and putrescine against the degradation of DNA bases upon exposure to gamma rays in aerated aqueous solution. The yield of 8-oxo-7,8-dihydroguanine and 5-hydroxycytosine was found to decrease for concentrations of spermine and spermidine greater than 0.1 mM. A protection factor of 10 was observed for a concentration of 1 mM of the latter two polyamines. Putrescine afforded a lower protection. In addition, the formation yield of a series of radiation-induced degradation products of the purine and pyrimidine bases was determined within DNA in the presence or absence of spermine. The protection factor was within the same range for all the lesions measured. The latter observation ruled out the possibility of degradation of DNA by radiation-induced polyamine peroxyl radicals. This was confirmed by studies involving radiolysis of DMSO and decomposition of 2,2'-azobis(2-methyl-propionamidine) as sources of alkylperoxyl radicals. Therefore, it is likely that the polyamine-mediated protection against the radiation-induced degradation of DNA bases is due to the compaction of the DNA structure and the reduction in the accessibility of DNA to .OH rather than by scavenging .OH in the bulk solution or in the vicinity of the DNA.

Internal hazards: baseline DNA damage by endogenous products of normal metabolism

Recent improvements in the ability to detect chemically modified bases in DNA have revealed that not only does the genetic material incur damage by foreign chemicals, but that it also sustains injury by reactive products of normal physiological processes. This review summarises current understanding of the DNA-damaging potential of various substances of endogenous origin, including oxidants, lipid peroxidation products, alkylating agents, estrogens, chlorinating agents, reactive nitrogen species, and certain intermediates of various metabolic pathways. The strengths and weaknesses of the existing database for DNA damage by each class of substance are discussed, as are future strategies for resolving the difficult question of whether endogenous chemicals are significant contributors to spontaneous mutagenesis and cancer development in vivo.

Oxidation of DNA bases, deoxyribonucleosides and homopolymers by peroxyl radicals

DNA base oxidation is considered to be a key event associated with disease initiation and progression in humans. Peroxyl radicals (ROO. ) are important oxidants found in cells whose ability to react with the DNA bases has not been characterized extensively. In this paper, the products resulting from ROO. oxidation of the DNA bases are determined by gas chromatography/MS in comparison with authentic standards. ROO. radicals oxidize adenine and guanine to their 8-hydroxy derivatives, which are considered biomarkers of hydroxyl radical (HO.) oxidations in cells. ROO. radicals also oxidize adenine to its hydroxylamine, a previously unidentified product. ROO. radicals oxidize cytosine and thymine to the monohydroxy and dihydroxy derivatives that are formed by oxidative damage in cells. Identical ROO. oxidation profiles are observed for each base when exposed as deoxyribonucleosides, monohomopolymers and base-paired dihomopolymers. These results have significance for the development, utilization and interpretation of DNA base-derived biomarkers of oxidative damage associated with disease initiation and propagation, and support the idea that the mutagenic potential of N-oxidized bases, when generated in cellular DNA, will require careful evaluation. Adenine hydroxylamine is proposed as a specific molecular probe for the activity of ROO. in cellular systems.

DNA cleavage induced by alkoxyl radicals generated in the photolysis of N-alkoxypyridinethiones

The photolysis of N-isopropoxypyridine-2-thione (1b) and of N-tert-butoxypyridine-2-thione (1c) generated alkoxyl radicals as confirmed by trapping experiments with DMPO and subsequent EPR spectroscopy. Upon UVA irradiation, the alkoxyl-radical sources induce strand breaks in supercoiled pBR 322 DNA, which was analyzed by gel electrophoresis. The participation of type I (electron transfer, H abstraction) or type II (1O2) photosensitization in the DNA cleavage by the oxyl-radical sources 1a-d or their photoproducts could be excluded. The present study establishes unequivocally that alkoxyl and benzoyloxyl, as well as hydroxyl radicals, cause strand breaks in DNA and, thus, may play a significant role in the DNA cleavage by peroxides.