Identification and characterization of 2'-deoxyadenosine adducts formed by isoprene monoepoxides in vitro.

Isoprene, the 2-methyl analogue of 1,3-butadiene, is ubiquitous in the environment, with major contributions to total isoprene emissions stemming from natural processes despite the compound being a bulk industrial chemical. Additionally, isoprene is a combustion product and a major component in cigarette smoke. Isoprene has been classified as possibly carcinogenic to humans (group 2B) by IARC and as reasonably anticipated to be a human carcinogen by the National Toxicology Program. Isoprene, like butadiene, requires metabolic activation to reactive epoxides to exhibit its carcinogenic properties. The mode of action has been postulated to be that of a genotoxic carcinogen, with the formation of promutagenic DNA adducts being essential for mutagenesis and carcinogenesis. In rodents, isoprene-induced tumors show unique point mutations (A→T transversions) in the K-ras protooncogene at codon 61. Therefore, we investigated adducts formed after the reaction of 2'-deoxyadenosine (dAdo ) with the two monoepoxides of isoprene, 2-ethenyl-2-methyloxirane (IP-1,2-O) and propen-2-yloxirane (IP-3,4-O), under physiological conditions. The formation of N1-2'-deoxyinosine (N1-dIno) due to the deamination of N1-dAdo adducts was of particular interest, since N1-dIno adducts are suspected to have high mutagenic potential based on in vitro experiments. Major stable adducts were identified by HPLC, UV-spectroscopy, and LC-MS/MS and characterized by (1)H NMR and (1)H,(13)C HSQC and HMBC NMR experiments. Adducts of IP-1,2-O that were fully identified are R,S-C1-N(6)-dAdo, R-C2-N(6)-dAdo, and S-C2-N(6)-dAdo; adducts of IP-3,4-O are S-C3-N(6)-dAdo, R-C3-N(6)-dAdo, R,S-C4-N(6)-dAdo, S-C4-N1-dIno, R-C4-N1-dIno, R-C3-N1-dIno, S-C3-N1-dIno, and C3-N7-Ade. Both monoepoxides formed adducts on the terminal and internal oxirane carbons. This is the first study to describe adducts of isoprene monoepoxides with dAdo. Characterization of adducts formed by isoprene monoepoxides with deoxynucleosides and subsequently with DNA represent the first step toward evaluating their potential for being converted into a mutation or as biomarkers of isoprene metabolism and exposure.

Synthesis of uniformly 13C-labeled polycyclic aromatic hydrocarbons.

Convergent synthetic pathways were devised for efficient synthesis of a series of uniformly (13)C labeled polycyclic aromatic hydrocarbons de novo from U-(13)C-benzene and other simple commercially-available (13)C-starting compounds. All target products were obtained in excellent yields, including the alternant PAH U-(13)C-naphthalene, U-(13)C-phenanthrene, U-(13)C-anthracene, U-(13)C-benz[a]anthracene, U-(13)C-pyrene and the nonalternant PAH U-(13)C-fluoranthene.

New immunoaffinity-LC-MS/MS methodology reveals that Aag null mice are deficient in their ability to clear 1,N6-etheno-deoxyadenosine DNA lesions from lung and liver in vivo.

The mouse alkyladenine DNA glycosylase (Aag) initiates base excision repair with a broad substrate range that includes the highly mutagenic exocyclic etheno DNA base adduct 1,N6-ethenodeoxyadenosine ((epsilon)dA). Previous attempts to determine the in vivo role of Aag in (epsilon)dA repair were complicated by technological difficulties in measuring low levels of (epsilon)dA in genomic DNA. Here we describe the development of a new method for (epsilon)dA detection in genomic DNA that couples an immunoaffinity purification with LC-MS/MS analysis and that utilizes an isotopically labeled internal standard. We go on to describe the application of this method to measuring the in vivo repair of (epsilon)dA base lesions in liver and lung tissue of wild type and Aag null mice. Our results demonstrate that while Aag clearly represents the major DNA repair enzyme for the in vivo removal (epsilon)dA bases, these lesions can also be eliminated from the genome via an alternative mechanism.

The effect of aging on pyrene transformation in sediments.

The effect of aging on pyrene transformation and pyrene association with fractions of the sedimentary organic matrix (SdOM) was evaluated using [4,9-(13)C2]pyrene. Sediments were collected from a site of previous petroleum hydrocarbon contamination (New Orleans, LA, USA). Aged sediments were autoclaved for 1 h, amended with pyrene, and then stored in the dark in a 0.05% NaN3 solution for 120 d. Both aged and nonaged sediments were incubated in aerated microcosms for 120 d. Microcosms were acidified to collect evolved carbon dioxide (CO2); sediments were fractionated and lipid extracted to quantify pyrene in SdOM fractions. Cross-polarization magic angle spinning 13C-nuclear magnetic resonance (CPMAS 13C-NMR) spectra indicated that synthetic aging techniques did alter SdOM structure to some degree, but these changes did not affect SdOM affinity for pyrene. Aging delayed pyrene mineralization and increased pyrene concentrations extracted from bulk sediment and humic fractions. Aging also reduced the toxicity of sediment humin. Pyrene-4,5-dione and pyrene cis-4,5-dihydrodiol were identified in extracts of aged sediments by 13C-NMR and gas chromatography mass spectrometry, respectively.

Ethenoguanines undergo glycosylation by nucleoside 2'-deoxyribosyltransferases at non-natural sites.

Deoxyribosyl transferases and functionally related purine nucleoside phosphorylases are used extensively for synthesis of non-natural deoxynucleosides as pharmaceuticals or standards for characterizing and quantitating DNA adducts. Hence exploring the conformational tolerance of the active sites of these enzymes is of considerable practical interest. We have determined the crystal structure at 2.1 Å resolution of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine) at the active site. The active site electron density map was compatible with four orientations, two consistent with sites for deoxyribosylation and two appearing to be unproductive. In accord with the crystal structure, Lactobacillus helveticus PDT glycosylates the 8,9-dihydro-9-oxoimidazo[2,1-b]purine at N7 and N1, with a marked preference for N7. The activity of Lactobacillus helveticus PDT was compared with that of the nucleoside 2'-deoxyribosyltransferase enzymes (DRT Type II) from Lactobacillus leichmannii and Lactobacillus fermentum, which were somewhat more effective in the deoxyribosylation than Lactobacillus helveticus PDT, glycosylating the substrate with product profiles dependent on the pH of the incubation. The purine nucleoside phosphorylase of Escherichia coli, also commonly used in ribosylation of non-natural bases, was an order of magnitude less efficient than the transferase enzymes. Modeling based on published active-site structures as templates suggests that in all cases, an active site Phe is critical in orienting the molecular plane of the purine derivative. Adventitious hydrogen bonding with additional active site residues appears to result in presentation of multiple nucleophilic sites on the periphery of the acceptor base for ribosylation to give a distribution of nucleosides. Chemical glycosylation of O9-benzylated 8,9-dihydro-9-oxoimidazo[2,1-b]purine also resulted in N7 and N1 ribosylation. Absent from the enzymatic and chemical glycosylations is the natural pattern of N3 ribosylation, verified by comparison of spectroscopic and chromatographic properties with an authentic standard synthesized by an unambiguous route.

Identification and quantification of uncultivated Proteobacteria associated with pyrene degradation in a bioreactor treating PAH-contaminated soil.

Uncultivated bacteria associated with the degradation of pyrene in a bioreactor treating soil contaminated with polycyclic aromatic hydrocarbons (PAH) were identified by DNA-based stable-isotope probing (SIP) and quantified by real-time quantitative PCR. Most of the 16S rRNA gene sequences recovered from (13)C-enriched DNA fractions clustered phylogenetically within three separate groups of beta- and gamma-Proteobacteria unassociated with described genera and were designated "Pyrene Groups 1, 2 and 3". One recovered sequence was associated with the Sphingomonas genus. Pyrene Groups 1 and 3 were present in very low numbers in the bioreactor but represented 75% and 7%, respectively, of the sequences recovered from 16S rRNA gene clone libraries constructed from (13)C-enriched DNA. In a parallel time-course incubation with unlabelled pyrene, there was between a 2- and 4-order-of-magnitude increase in the abundance of 16S rRNA genes from Pyrene groups 1 and 3 and from targeted Sphingomonas spp. over a 10 day incubation. Sequences from Pyrene Group 2 were 11% of the SIP clone libraries but accounted for 14% of the total bacterial 16S rRNA genes in the bioreactor community. However, the abundance of this group did not increase significantly in response to pyrene disappearance. These data indicate that the primary pyrene degraders in the bioreactor were uncultivated, low-abundance beta- and gamma-Proteobacteria not previously associated with pyrene degradation.

LC/MS/MS method for the quantitation of trans-2-hexenal-derived exocyclic 1,N(2)-propanodeoxyguanosine in DNA.

trans-2-Hexenal is an alpha,beta-unsaturated aldehyde to which humans are exposed daily in small amounts. Hexenal has demonstrated mutagenicity and genotoxicity in vitro and reacts with deoxyguanosine to form diastereomeric hexenal-derived exocyclic 1,N(2)-propanodeoxyguanosine (Hex-PdG) adducts. A highly sensitive and specific method for the measurement of Hex-PdG in DNA has not previously been available. An LC/MS/MS assay for the quantitation of Hex-PdG, using [(13)C4(15)N2]Hex-PdG as an internal standard, was developed, to assess binding of hexenal to DNA. Samples were purified prior to analysis by centrifuge filtration and solid phase extraction and analyzed by LC/MS/MS in the selected reaction monitoring (SRM) mode (SRM m/z 366.2 --> 250.2 for Hex-PdG; SRM m/z 372.2 --> 256.2 for [(13)C4(15)N2]Hex-PdG). Recovery of standards was 89% or greater, and quantitation was unaffected by the addition of increasing concentrations of calf thymus DNA (ctDNA). The limit of quantitation, determined in samples of 200 microg of ctDNA spiked with analyte standard, was 0.015 fmol/microg DNA, which corresponds to approximately 5 Hex-PdG/10(9) unmodified nucleotides. Hex-PdG was detected in ctDNA treated with 0.021 microM, 0.21 microM, or 2.1 mM hexenal but not in untreated DNA. Furthermore, Hex-PdG was not detected in DNA exposed to reactive oxygen species-mediated deoxyribose attack and lipid peroxidation, which resulted in a significant increase in the malondialdehyde-derived pyrimido[1,2-a]purin-10(3H)one. Hex-PdG was not detected in DNA of untreated rat liver, but Hex-PdG in hexenal-treated calf thymus DNA was quantifiable when spiked into the rat liver DNA at 0.035 or 0.35 fmol/microg DNA. These data indicate that Hex-PdG is formed following hexenal treatment and that this method is suitable for in vitro or in vivo assessment of Hex-PdG formation.

Profiling of ecdysteroids in complex biological samples using liquid chromatography/ion trap mass spectrometry.

A sensitive method using high-performance liquid chromatography coupled to a mass spectrometer with electrospray ionization source (HPLC/ESI-MS) was developed for detection of ecdysteroids in biological samples. We report here for the first time that ecdysteroids can be classified into three groups based on ESI full-scan mass spectra: group 1 (ecdysone (E), 2-deoxyecdysone (2dE), 2,22-dideoxyecdysone (3beta5beta-KT), and 3alpha5alpha[H]-dihydroxycholest-7-en-6-one (3alpha5alpha-KD)), in which loss of one molecule of water from the protonated molecular ion ([M+H](+)) represents the dominant ion; group 2 (20-hydroxyecdysone (20E), makisterone A (MakA), 3beta5beta-KD, and 3beta5alpha-KD), in which [M+H](+) is a major ion but some water loss is observed; and group 3 (muristerone A (MurA) and ponasterone A (PonA)), in which [M+H](+) is the dominant ion with no water loss observed. Based on the analytical procedure in combination with structural information from the group classification and with the application of source-induced dissociation, we identified free ecdysteroids in biological samples: 20,26-dihydroxyecdysone and ecdysonic acid in the larval hemolymph, and the progressive metabolism of 26-hydroxyecdysone (26E) to 3alpha-26E from day-1 to day-3 embryos of the tobacco hornworm Manduca sexta.

Characterization and quantification of cysteinyl adducts of benzene diol epoxide.

The production of macromolecular adducts of benzene diol epoxide (BDE), a toxic metabolite of benzene, has received little attention despite the demonstrated mutagenicity and carcinogenicity of BDE in rodents. Syn and anti enantiomers of BDE were relatively stable in 0.1 M ammonium acetate buffer, pH 7.6 (half times were greater than 5 h), and showed evidence of pseudo-first-order reactions with albumin (half times were about 4 h) and glutathione (GSH) (half times were about 0.3-0.4 h). Reaction products of BDE isomers with l-cysteine, N-acetyl-l-cysteine, N-acetyl-l-cysteine methyl ester, and GSH were characterized by a combination of electrospray ionization mass spectrometry and/or gas chromatography-mass spectrometry with electron impact ionization of trimethylsilyl derivatives of the adducts. Products corresponded to 1:1 addition of BDE isomers with each nucleophilic species, suggesting that adduction occurred primarily at the free sulfhydryl group. To investigate the disposition of the BDEs in vivo, we developed an assay for cysteinyl BDE-protein adducts. The assay involves enzymatic hydrolysis of the protein followed by derivatization of the released adducts and gas chromatography-negative ion chemical ionization-mass spectrometry. Preliminary applications of the assay showed linear increases in the formation of BDE-GSH adducts in samples of GSH incubated with increasing concentrations of BDE (10-300 microM) and showed the presence of BDE-albumin following incubation of albumin with 10 microM BDE.

Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil.

[13C6]salicylate, [U-13C]naphthalene, and [U-13C]phenanthrene were synthesized and separately added to slurry from a bench-scale, aerobic bioreactor used to treat soil contaminated with polycyclic aromatic hydrocarbons. Incubations were performed for either 2 days (salicylate, naphthalene) or 7 days (naphthalene, phenanthrene). Total DNA was extracted from the incubations, the "heavy" and "light" DNA were separated, and the bacterial populations associated with the heavy fractions were examined by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Unlabeled DNA from Escherichia coli K-12 was added to each sample as an internal indicator of separation efficiency. While E. coli was not detected in most analyses of heavy DNA, a low number of E. coli sequences was recovered in the clone libraries associated with the heavy DNA fraction of [13C]phenanthrene incubations. The number of E. coli clones recovered proved useful in determining the relative amount of light DNA contamination of the heavy fraction in that sample. Salicylate- and naphthalene-degrading communities displayed similar DGGE profiles and their clone libraries were composed primarily of sequences belonging to the Pseudomonas and Ralstonia genera. In contrast, heavy DNA from the phenanthrene incubations displayed a markedly different DGGE profile and was composed primarily of sequences related to the Acidovorax genus. There was little difference in the DGGE profiles and types of sequences recovered from 2- and 7-day incubations with naphthalene, so secondary utilization of the 13C during the incubation did not appear to be an issue in this experiment.

Analysis of M1G-dR in DNA by aldehyde reactive probe labeling and liquid chromatography tandem mass spectrometry.

A novel method for the measurement of pyrimido[1,2-a]purin-10(3H)one (M1G) has been developed. Previous methods for analysis of M1G have been confounded by the fact that this lesion exists in equilibrium between a ring-closed form and a ring-opened aldehyde form. Poor detection sensitivity of the aldehydic form can result from loss of the adduct during analysis by its reaction with amines or proteins. We utilized the aldehyde reactive probe (ARP) to produce a stable ARP-M1G-deoxyribose (ARP-M1G-dR) conjugate to minimize adduct loss. This conjugate has increased the hydrophobicity that enhances separation of ARP-M1G-dR from unmodified DNA nucleosides by using solid phase extraction. In addition, measuring ARP-M1G-dR by selective reaction monitoring (SRM) of the [ARP-M1G-dR + H]+ (635) --> [M1G + H]+ (188) transition increases the detection sensitivity by nearly an order of magnitude relative to the measurement of M1G-dR by SRM. For accurate measurement, analytical standard (AS) DNA and internal standard (IS) DNA were used. High purity 15N-labeled DNA was isolated from Escherichia coli that had been grown in minimum salt medium containing (15NH4)2SO4. The 15N-DNA and calf thymus DNA were treated with malondialdehyde to induce a high number of M1G adducts to prepare the IS and AS DNA, respectively. A consistent calibration curve was established from the analysis of 200 microg of blank DNA, 23 ng of IS DNA (400 fmol of 15N5-M1G-dR), and AS DNA containing 0-810 fmol of M1G-dR. With the use of this novel IS DNA and selective labeling, this assay is a useful tool for monitoring oxidative stress-induced DNA damage from small amounts of DNA without the need of a specific antibody or laborious procedures. By this assay, two M1G adducts/10(8) guanines can readily be detected. Furthermore, this approach should be applicable to the analysis of other aldehydic DNA adducts as well as the measurement of an array of DNA lesions.

Synthesis, characterization, and identification of N7-guanine adducts of isoprene monoepoxides in vitro.

Isoprene (IP, 2-methylbuta-1,3-diene) is ubiquitous in the environment through emission by plants, combustion processes, and endogenous formation and exhalation by mammals, including humans. IP is also an industrial chemical, widely used in the manufacture of synthetic rubber and plastics. Like butadiene, IP is metabolized to reactive epoxides, which form adducts with macromolecules, and is a demonstrated carcinogen in mice. To date, DNA adducts of IP monoepoxides have not been reported. We report here on the formation of N7-guanine (N7-Gua) adducts of isoprene-1,2-oxide (IP-1,2-O, 2-ethenyl-2-methyloxirane) and isoprene-3,4-oxide (IP-3,4-O, propen-2-yloxirane). DNA adducts are useful as biomarkers to estimate exposure, as well as to investigate mechanisms of IP carcinogenesis. Incubation of 2'-deoxyguanosine with the monoepoxides followed by deglycosylation gave four N7-Gua adducts that were isolated by HPLC and characterized by high-resolution FAB(+)-MS, ESI(+)-MS, ESI(+)-MS/MS, and (1)H NMR and two-dimensional heteronuclear (1)H, (13)C correlation NMR spectrometry. IP-1,2-O and IP-3,4-O reacted at both terminal and internal oxirane carbons to form the following regioisomeric adducts at Gua N7: N7-(2'-hydroxy-2'-methyl-3'-buten-1'-yl)guanine, N7-(1'-hydroxy-2'-methyl-3'-buten-2'-yl)guanine, N7-(1'-hydroxy-3'-methyl-3'-buten-2'-yl)guanine, and N7-(2'-hydroxy-3'-methyl-3'-buten-1'-yl)guanine. The same adducts were identified by UV spectra, HPLC retention times, and LC/ESI(+)-MS in the neutral thermal hydrolysates of single- and double-stranded calf thymus DNA after incubation with IP monoepoxides. Characterization of the N7-Gua adducts identified in incubations of DNA with IP monoepoxides represents the first step toward establishing biomarkers of IP metabolism and exposure.