DNA phosphotriesters as indicators of cumulative carcinogen-induced damage

Methyl DNA Phosphate Adduct Formation in Rats Treated Chronically with 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone and Enantiomers of Its Metabolite 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol

The tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a powerful lung carcinogen in animal models and is considered a causative factor for lung cancer in tobacco users. NNK is stereoselectively and reversibly metabolized to 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), which is also a lung carcinogen. Both NNK and NNAL undergo metabolic activation by α-hydroxylation on their methyl groups to form pyridyloxobutyl and pyridylhydroxybutyl DNA base and phosphate adducts, respectively. α-Hydroxylation also occurs on the α-methylene carbons of NNK and NNAL to produce methane diazohydroxide, which reacts with DNA to form methyl DNA base adducts. DNA adducts of NNK and NNAL are important in their mechanisms of carcinogenesis. In this study, we characterized and quantified methyl DNA phosphate adducts in the lung of rats treated with 5 ppm of NNK, (S)-NNAL, or (R)-NNAL in drinking water for 10, 30, 50, and 70 weeks, by using a novel liquid chromatography-nanoelectrospray ionization-high resolution tandem mass spectrometry method. A total of 23, 21, and 22 out of 32 possible methyl DNA phosphate adducts were detected in the lung tissues of rats treated with NNK, (S)-NNAL, and (R)-NNAL, respectively. Levels of the methyl DNA phosphate adducts were 2290-4510, 872-1120, and 763-1430 fmol/mg DNA, accounting for 15-38%, 8%, and 5-9% of the total measured DNA adducts in rats treated with NNK, (S)-NNAL, and (R)-NNAL, respectively. The methyl DNA phosphate adducts characterized in this study further enriched the diversity of DNA adducts formed by NNK and NNAL. These results provide important new data regarding NNK- and NNAL-derived DNA damage and new insights pertinent to future mechanistic and biomonitoring studies of NNK, NNAL, and other chemical methylating agents.

Genetic sensor for strong methylating compounds

Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl adducts on the phosphoester backbone of DNA. We characterize this system as a genetic sensor and engineer it to lower the detection threshold. By overexpressing Ada from a plasmid, we improve the sensor’s dynamic range to 350-fold induction and lower its detection threshold to 40 μM for methyl iodide. In eukaryotes, there is no known sensor of methyl adducts on the phosphoester backbone of DNA. By fusing the N-terminal domain of Ada to the Gal4 transcriptional activation domain, we built a functional sensor for methyl phosphotriester adducts in Saccharomyces cerevisiae. This sensor can be tuned to variable specifications by altering the expression level of the chimeric sensor and changing the number of Ada operators upstream of the Gal4-sensitive reporter promoter. These changes result in a detection threshold of 28 μM and 5.2-fold induction in response to methyl iodide. When the yeast sensor is exposed to different SN1 and SN2 alkylating compounds, its response profile is similar to that observed for the native Ada protein in E. coli, indicating that its native function is retained in yeast. Finally, we demonstrate that the specifications achieved for the yeast sensor are suitable for detecting methylating compounds at relevant concentrations in environmental samples. This work demonstrates the movement of a sensor from a prokaryotic to eukaryotic system and its rational tuning to achieve desired specifications.

Mechanistic and biological aspects of helicase action on damaged DNA

Helicases catalytically unwind structured nucleic acids in a nucleoside-triphosphate-dependent and directionally specific manner, and are essential for virtually all aspects of nucleic acid metabolism. ATPase-driven helicases which translocate along nucleic acids play a role in damage recognition or unwinding of a DNA tract containing the lesion. Although classical biochemical experiments provided evidence that bulky covalent adducts inhibit DNA unwinding catalyzed by certain DNA helicases in a strand-specific manner (i.e., block to DNA unwinding restricted to adduct residence in the strand the helicase translocates), recent studies suggest more complex arrangements that may depend on the helicase under study, its assembly in a protein complex, and the type of structural DNA perturbation. Moreover, base and sugar phosphate backbone modifications exert effects on DNA helicases that suggest specialized tracking mechanisms. As a component of the replication stress response, the single-stranded DNA binding protein Replication Protein A (RPA) may serve to enable eukaryotic DNA helicases to overcome certain base lesions. Helicases play important roles in DNA damage signaling which also involve their partnership with RPA. In this review, we will discuss our current understanding of mechanistic and biological aspects of helicase action on damaged DNA.

Creating context for the use of DNA adduct data in cancer risk assessment: II. Overview of methods of identification and quantitation of DNA damage

The formation of deoxyribonucleic acid (DNA) adducts can have important and adverse consequences for cellular and whole organism function. Available methods for identification of DNA damage and quantification of adducts are reviewed. Analyses can be performed on various samples including tissues, isolated cells, and intact or hydrolyzed (digested) DNA from a variety of biological samples of interest for monitoring in humans. Sensitivity and specificity are considered key factors for selecting the type of method for assessing DNA perturbation. The amount of DNA needed for analysis is dependent upon the method and ranges widely, from <1 microg to 3 mg. The methods discussed include the Comet assay, the ligation-mediated polymerase reaction, histochemical and immunologic methods, radiolabeled ((14)C- and (3)H-) binding, (32)P-postlabeling, and methods dependent on gas chromatography (GC) or high-performance liquid chromatography (HPLC) with detection by electron capture, electrochemical detection, single or tandem mass spectrometry, or accelerator mass spectrometry. Sensitivity is ranked, and ranges from approximately 1 adduct in 10(4) to 10(12) nucleotides. A brief overview of oxidatively generated DNA damage is also presented. Assay limitations are discussed along with issues that may have impact on the reliability of results, such as sample collection, processing, and storage. Although certain methodologies are mature, improving technology will continue to enhance the specificity and sensitivity of adduct analysis. Because limited guidance and recommendations exist for adduct analysis, this effort supports the HESI Committee goal of developing a framework for use of DNA adduct data in risk assessment.

Detection of phosphodiester adducts formed by the reaction of benzo[a]pyrene diol epoxide with 2'-deoxynucleotides using collision-induced dissociation electrospray ionization tandem mass spectrometry

In this study, we investigated the products formed following the reaction of benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (B[a]PDE) with 2'-deoxynucleoside 3'-monophosphates. The B[a]PDE plus 2'-deoxynucleotide reaction mixtures were purified using solid phase extraction (SPE) and subjected to HPLC with fluorescence detection. Fractions corresponding to reaction product peaks were collected and desalted using SPE prior to analysis for the presence of molecular ions corresponding to m/z 648, 632, 608 and 623 [M-H]- consistent with B[a]PDE adducted (either on the base or phosphate group) 2'-deoxynucleotides of guanine, adenine, cytosine and thymine, respectively, using LC-ESI-MS/MS collision-induced dissociation (CID). Reaction products were identified having CID product ion spectra containing product ions at m/z 452, 436 and 412 [(B[a]Ptriol+base)-H]-, resulting from cleavage of the glycosidic bond between the 2'-deoxyribose and base, corresponding to B[a]PDE adducts of guanine, adenine and cytosine, respectively. Further reaction products were identified having unique CID product ion spectra characteristic of B[a]PDE adduct formation with the phosphate group of the 2'-deoxynucleotide. The presence of product ions at m/z 399 and 497 were observed for all four 2'-deoxynucleotides, corresponding to [(B[a]Ptriol+phosphate)-H]- and [(2'-deoxyribose+phosphate+B[a]Ptriol)-H]-, respectively. In conclusion, this investigation provides the first direct evidence for the formation of phosphodiester adducts by B[a]PDE following reaction with 2'-deoxynucleotides.

Evaluation of phosphodiesterase I-based protocols for the detection of multiply damaged sites in DNA: the detection of abasic, oxidative and alkylative tandem damage in DNA oligonucleotides

It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection of MDS in DNA. In the present study we demonstrate the potential of protocols incorporating an exonucleolytic snake venom phosphodiesterase (SVPD) digestion stage to permit the direct detection of certain tandem damage, in which two lesions are immediately adjacent to each other on the same DNA strand. A series of prepared oligonucleotides containing either single or pairs of tetrahydrofuran moieties (F), thymine glycol lesions (T(g)) or methylphosphotriester adducts (Me-PTE) were digested with SVPD and the digests examined by either (32)P-end-labelling or electrospray mass spectrometry. The unambiguous observation of SVPD-resistant 'trimer' species in the digests of oligonucleotides containing adjacent F, T(g) and Me-PTE demonstrates that the SVPD digestion strategy is capable of allowing direct detection of certain tandem damage. Furthermore, in studies to determine the specificity of SVPD in dealing with pairs of lesions on the same strand, it was found mandatory to have the two lesions immediately adjacent to each other in order to generate the trimer species; pairs of lesions separated by as few as one or two normal nucleotides behave principally as single lesions towards SVPD.

Time versus replication dependence of EMS-induced delayed mutation in Chinese hamster cells

We have previously observed in Chinese hamster cells that ethyl methane sulfonate (EMS) induces mutations which are distributed over at least 10-14 cell divisions following treatment. This delayed appearance of mutations could be explained by EMS-induced lesions which remain in DNA and have a probability that is significantly less than 1.0 of producing base mispairing errors during successive replication cycles (replication-dependent). Alternatively, delayed mutation may be a time-dependent process in which a slow acting or damage inducible error-prone repair process removes persistent DNA lesions and replaces them with an incorrect base during the course of 7-10 days of colony growth following EMS exposure. To address this question, the distribution of HGPRT delayed mutation events (fifth division or later) in cells plated immediately for exponential growth after EMS treatment was compared with the distribution in cells which remained under confluent growth conditions for 8 days and then were replated. Both the distribution and rate of accumulation of delayed mutations (mutations/cell division) were similar in the two culture conditions. In contrast, the frequency of early mutations (before the fifth division) in the confluent population was reduced more than 2-fold compared to dividing cells. A comparison of the frequency of EMS-induced DNA lesions in the two populations revealed that the density inhibited population contained one third the DNA lesions of the exponential population. These results argue against a time-dependent process since, if this mechanism applies, one would expect an increase in early mutant events and a decrease in delayed events in the confluent population. The results, however, are consistent with a replication model in which potential early mutant lesions are preferentially removed in the density inhibited culture during the 8 days of incubation while lesions producing late mutants are not removed.

Studies of transalkylation of phosphotriesters in DNA: reaction conditions and requirements on nucleophiles for determination of DNA adducts

Reactive compounds form adducts at several sites in DNA. One of these sites, the phosphate groups, forms phosphotriesters (PTE) which are both chemically stable and little repaired. A measurement of PTE in DNA could therefore be advantageous for the determination of doses in vivo of mutagens/cancer initiators. In this paper, the possibilities of utilizing the weakly alkylating properties of PTE for the transfer of adducts to strong nucleophiles have been investigated. Model compounds, thymidine 3'-[thymidine 5'-(methyl phosphate)], TpMeT, and thymidine 3'-[thymidine 5'-(2-hydroxyethyl phosphate)], TpHOEtT, were incubated with thiosulfate, a relatively strong nucleophile and the formation of dealkylated model PTE, thymidine 3'-(thymidine 5'-phosphate), TpT, was followed by HPLC. Transalkylation to thiosulfate or aniline of methyl PTE in DNA alkylated by [3H]N-methyl-N-nitrosourea was demonstrated. The methyl groups transferred, forming methyl thiosulfate and N-methylaniline, respectively, were determined by HPLC. These experiments demonstrate that it is possible to transfer alkyls from DNA phosphate to nucleophiles. Kinetic aspects of the transalkylation and requirement on nucleophiles for a practically useful method for determination of DNA adducts are discussed. Constants of reaction rates are presented.

Two expressed human genes sustain slightly more DNA damage after alkylating agent treatment than an inactive gene

Alkylating agent damage was quantified in human T-lymphocytes by calculating gene-specific lesion frequencies and repair rates. At 3 time points after exposure to methyl methanesulfonate (0, 6, and 24 h), T-lymphocyte DNA was extracted, digested with HindIII, and divided into 2 aliquots. Apurinic sites were formed in the DNA fragments of both aliquots by heat-induced liberation of the N-methylpurines. The methoxyamine-treated aliquot provided gene fragments which were refractory to alkaline hydrolysis (full-length fragments), while the fragments in the untreated aliquot were cleaved at apurinic sites by hydroxide. After Southern blotting, lesion frequencies were calculated by comparing the band intensity of the full-length fragment to its unprotected counterpart. The restriction fragments analyzed were from the constitutively active dihydrofolate reductase (dhfr) plus hypoxanthine phosphoribosyltransferase (hprt) genes and from the transcriptionally inactive Duchenne muscular dystrophy gene (dmd). In decreasing order, the fragments containing the most lesions per kb of DNA were: hprt greater than dhfr greater than dmd. T-Lymphocytes from 2 females had 30% more heat-labile N-methylpurines in the active X-linked hprt gene than in the inactive X-linked dmd gene. The lesion frequency found in the male's lone hprt allele was the highest observed. These lesion frequency differences are discussed in terms of chromatin structure. After 6 and 24 h, no significant repair rate differences were observed among the 3 genes.

Specific DNA alkylation damage and its repair in carcinogen-treated rat liver and brain

The in vivo formation and repair of specific DNA lesions produced by alkylating agents of contrasting carcinogenic potencies were investigated. Male Sprague-Dawley rats were treated with direct-acting alkylating agents methylmethane sulfonate (MMS) or methylnitrosourea (MNU). The amounts of N-3-methyladenine (3-meA), N-7-methylguanine (7-meG), and methylphosphotriesters (mePTE) in the DNA of liver and brain were determined following selective removal of the methylated bases by enzyme 3-meA N-glycosylase from Micrococcus luteus and thermal depurination at neutral pH. Both enzyme- and heat-induced alkali-labile apurinic sites were converted to single-strand breaks on incubation with 0.1 M NaOH. The number of such sites was quantitated following centrifugation of the DNA in alkaline sucrose gradients, fluorescent detection of unlabeled DNA, and estimation of number-average molecular weight. The results show a carcinogen dose-dependent initial linear increase in the number of enzyme- and heat-induced DNA strand breakage in both liver and brain DNA. With a half-life of approximately 3 h, 3-meA was removed from the tissues, whereas 45 to 55% of 7-meG remained unrepaired at 48 h. The study of the alkylation damage induced by MNU treatment of rats showed that the kinetics of repair for 3-meA and 7-meG was similar to the MMS-treated tissues and that mePTE persisted over a 7-day period. The technique developed does not require the use of radiolabeled reagents of DNA and allows for the selective quantitation of DNA alkylation lesions like 3-meA and 7-meG in the presence of nitrosourea-induced phosphotriesters.

Formation of phosphodiesters in thymidine monophosphate by styrene oxide

Three products were isolated by high-performance liquid chromatography (HPLC) from the reaction between thymidine-5'-monophosphate (TMP) and styrene oxide in aqueous solution. None of the products was digested by alkaline phosphatase, but each was digested by vernom phosphodiesterase. The digestion products were identified by their mobility in HPLC and UV-spectra as phenylethylene glycol, thymidine, TMP, and hydroxyethylphenyl phosphoric acid, of which phenylethylene glycol and TMP were most abundant.

Is there more than one critical lesion relevant for experimental liver carcinogenesis?

The present study was designed to determine whether there is one or more than one critical lesion, induced by a carcinogen, relevant for initiation. The experimental approach consisted of administering a non-necrogenic dose of the carcinogen 1,2-dimethylhydrazine 2HCl (100 mg/kg, i.p.) to male Fischer 344 rats (120-140 g) and completing the initiation process by two different methods: (i) induction of liver cell proliferation by partial hepatectomy, or (ii) creation of hypomethylation in DNA by giving 5-azacytidine, an agent that inhibits DNA methylation. The initiated hepatocytes were assayed as gamma-glutamyltransferase positive foci. The rationale for the approach was based on the premise that the two methods used for completing the initiation step might give either the same or a different pattern in the incidence of initiated hepatocytes depending on whether one or more than one lesion was important for initiation, particularly if some of the lesions were allowed to repair before applying the cell proliferative stimulus or administering the 5-azacytidine. The results obtained indicated that 5-azacytidine facilitated the induction of the same number of foci whether given 12 or 96 hours after the carcinogen indicating that the critical lesion involved in this mode of initiation persisted up to at least 96 hours. In contrast, our earlier results showed that there was a reduction in the number of gamma-glutamyltransferase positive foci when partial hepatectomy was delayed beyond 24 hours after the carcinogen administration, indicating that the critical lesion involved in this mode of initiation has a half-life of not more than 24 hours.(ABSTRACT TRUNCATED AT 250 WORDS)

Template properties of DNA alkylated with N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea

Alkylation of DNA with N-methyl-N-nitrosourea (MeNU) and N-ethyl-N-nitrosourea (EtNU) reduces its ability to support RNA synthesis catalyzed by exogenously added RNA polymerase. It is likely that 7-alkylguanine and alkyl phosphotriester in DNA are mainly responsible for the inhibition of RNA synthesis. The inhibitory effect of alkyl groups varies depending upon divalent metal ions and the type of RNA polymerase used as well as upon the presence of chromosomal proteins on DNA templates. Analyses of RNA products indicate that inhibition occurs primarily at the initiation step.

Induction of single-strand breaks plus alkali-labile bonds by N-nitrosoureas in rat tissues in vivo: ethylnitrosourea versus benzylnitrosourea

Alkaline sucrose sedimentation procedures were used to quantitate the amount of single-strand breaks plus alkali-labile bonds (SSB + ALB) induced and repaired following a single intraperitoneal injection of the neurocarcinogen N-ethyl-N-nitrosourea (ENU) and its non-neurocarcinogenic analog N-benzyl-N-nitrosourea (BNU) in the brain, liver and kidney of female Sprague-Dawley rats. SSB + ALB were measured and used as an indicator of apurinic/apyrimidinic sites, phosphotriesters and in situ breaks. ENU induced a dose-dependent increase in the number of SSB + ALB at the doses studied (0, 0.39, 0.77, 1.54 mmoles/kg) in all 3 tissues. At 1 h postinjection with 0.77 mmoles/kg of these compounds there were 50-70% fewer breaks induced by BNU than ENU. The SSB + ALB induced by ENU persisted over a 7-day period, while those induced by BNU did not. Thus, these studies showed that 2 homologues of nitrosoureas, ENU and BNU, exhibited different potentials to induce and to persist SSB + ALB in vivo.

Quantitative estimation of the extent of alkylation of DNA following treatment of mammalian cells with non-radioactive alkylating agents

Alkaline sucrose sedimentation has been used to quantitate phosphotriester formation following treatment of human cells with the monofunctional alkylating agents methyl and ethyl methanesulfonate. These persistent alkaline-labile lesions are not repaired during short-term culture conditions and thus serve as a useful and precise index of the total alkylation of the DNA. Estimates of alkylation by this procedure compare favorably with direct estimates by use of labeled alkylating agents.

Reactions of beta-propiolactone, beta-butyrolactone and gamma-butyrolactone with nucleic acids

Reactivity of beta-propiolactone, beta-butyrolactone and gamma-butyrolactone with guanosine, RNA, DNA and 4-(p-nitrobenzyl)pyridine was studied. beta-Propiolactone was 50--100 times more reactive with all the nucleophiles than beta-butyrolactone whereas gamma-butyrolactone was completely inactive. The rate of alkylation by the lactones was guanosine greater than RNA = denatured DNA greater than double-stranded DNA. The type of the adducts formed were characterized by fluorescence and ultraviolet spectroscopy. Similar alkylation products were formed by the two lactones. The main sites alkylated were N-1 at adenosine, N-3 at cytidine and N-7 at guanosine. The results suggest that the carcinogenic potency of the lactones correlates with their reactivity rather than with specificity of the adducts formed.

Interaction of chemical carcinogens with macromolecules

The nature of certain critical cellular reactions is discussed in terms of both mutagenic and carcinogenic effects. Emphasis is placed on the ability of the ultimate carcinogen, normally formed in vivo by metabolism, to react with nucleic acids and, in particular, with nuclear DNA. The actions of N-nitroso compounds is examined in some detail and a possible correlation of the carcinogenic action of these compounds with their ability to react with oxygen-atoms in nucleic acids in considered. The formation of a specific lesion, O6-alkylguanine, in DNA and the capacity for its repair in different tissues is discussed with respect to tissue susceptibility to tumor induction. This discussion is extended to compare differences between species in the (tissue) specificity of action of particular N-nitroso compounds.

Esolation of 3-(2-carboxyethyl)thymine following in vitro reaction of beta-propiolactone with calf thymus DNA

3-(2-Carboxyethyl)thymine (3-CET) was synthesized from beta-propiolactone (BPL) and dThd 5'P at pH 9.0--9.5 via the intermediate 3-(2-carboxyethyl)-thymidine-5'-monophosphoric acid (3-CEdThd5'P). 3-CEdThd5'P was converted to 3-CET by hydrolysis in 1.5 N HCl at 100 degrees C for 2 h. The structure of 3-CET was assigned on the basis of UV spectra, electron impact (EI) and isobutane chemical ionization mass spectra and the EI mass spectrum of a trimethylsilyl derivative of 3-CET. BPL was reacted in vitro with calf thymus DNA at pH 7.5. 100 A units of BPL-reacted DNA yielded, following perchloric acid hydrolysis and preparative paper chromatography, 3 A units of 3-CET. Reaction of BPL with the phosphodiester thymidylyl-(3'-5')-thymidine gave 3-(2-carboxyethyl)thymidylyl-(3'-5')-3-(2-carboxyethyl)-thymidine (approximately 3%). Phosphotriester formation was not detected.

The stability of methylated purines and of methylphosphotriesters in the DNA of V79 cells after treatment with N-methyl-N-nitrosourea

V79-379A cells growing in suspension culture were treated with N-methyl-N-nitrosourea at concentrations of 0.6 and 1.2 mM. After incubation for periods from 1 to 48 h DNA was isolated from the cells and the concentrations of 7-methylguanine, O6-methylguanine, 3-methyladenine and methyl phosphotriesters were determined. After correction for dilution resulting from DNA synthesis during the incubation it was found that no loss of O6-methylguanine or methylphosphotriesters occurred; 7-methylguanine disappeared with a half-life of 22 h and 3-methyladenine was detectable only immediately after the initial treatment. The results show that these cells eliminate 7-methylguanine and 3-methyladenine from DNA by a repair process but are unable to excise or repair O6-methylguanine or methyl phosphotriesters.