On-line identification of diastereomeric dibenzo[a,l]pyrene diol epoxide-derived deoxyadenosine adducts by capillary electrophoresis-fluorescence line-narrowing and non-line narrowing spectroscopy

A capillary electrophoretic method for the separation and on-line identification of closely related analytes using low-temperature fluorescence spectroscopy is reported for the eight diastereomeric deoxyadenosine (dA) adducts derived from dibenzo[a,l]pyrene diol epoxide (DB[a,l]PDE). Electrophoretic separation of stereoisomers was accomplished by application of a mixed surfactant buffer [dioctyl sulfosuccinate (DOSS) and Brij-S], which was below the critical micelle concentration (CMC) due to the high concentration (approximately 25%) of organic solvent. Addition of multiple surfactant additives to the separation buffer provided electrophoretic resolution, which was unattainable under single surfactant conditions. It is shown that the CE-separated analyte zones could be identified on-line via low-temperature (4.2 K) fluorescence non-line narrowing and fluorescence line-narrowing (FLN) spectroscopy. In addition, it was determined that in CE buffer trans-syn-,cis-syn- and cis-anti-DB[a,l]PDE-14-N6dA diastereomeric adducts exist mostly with the -dA and DB[a,l]P moiety in an "open"-type conformation while the trans-anti-DB[a,l]PDE-14-N6dA adducts exist in two different conformations whose relative distribution depends on matrix composition. The above conformations have also been revealed by selective laser excitation. Thus, the low-temperature methodology not only provides fingerprint structure via vibrationally resolved 4.2 K fluorescence spectra for adduct identification, but also provides conformational information on the spatial relationship of the carcinogen and dA moiety. These results, taken together with those for DB[a,l]P-DNA adducts formed in standard glasses and mouse epidermis exposed to DB[a,l]P, support our earlier findings that DB[a,l]P-derived adducts exist in different conformations [Jankowiak et al., Chem. Res. Toxicol. 11 (1998) 674]. Therefore, the combination of the separation power of CE and spectral selectivity of low-temperature fluorescence spectroscopy at NLN and FLN conditions provides a powerful methodology which should prove useful for identification of closely related DNA adducts formed at low levels in biological systems.

Lipid peroxidation-induced etheno-DNA adducts in the liver of patients with the genetic metal storage disorders Wilson's disease and primary hemochromatosis

To assess DNA damage caused by lipid peroxidation due to copper and iron storage disorders in the human liver, the formation of the etheno adducts 1,N6-ethenodeoxyadenosine (epsilon dA) and 3,N4-ethenodeoxycytine (epsilon dC) was measured in liver DNA from normal subjects and from patients with Wilson's disease (WD) and primary hemochromatosis. The mean epsilon dA and epsilon dC levels per 10(9) parent nucleotides in normal liver were 19.3 +/- 4.9 and 27.5 +/- 10.0, respectively. The mean epsilon dA and epsilon dC levels per 10(9) parent nucleotides in WD were 61.03 +/- 7.95 and 91.50 +/- 36.02, and in primary hemochromatosis, they were 46.62 +/- 32.83 and 64.32 +/- 11.55, respectively, two to three times higher than those in the normal liver. The etheno adduct levels were highly correlated with the copper content of the liver in the normal and WD samples. This study demonstrates for the first time the formation of promutagenic etheno adducts in humans in association with copper and iron storage-induced lipid peroxidation. Thus, the etheno adducts are implicated as initiating DNA damage in copper/iron-induced carcinogenesis in humans and should also be explored as biomarkers in disease progression and prevention trials.

[Determination of adenosine and 3'-deoxyadenosine in Cordyceps militaris (L.) Link. by HPLC]

The establishment of a quantitative determination method by HPLC for adenosine and 3'-deoxyadenosine in Cordyceps militaris is reported. The sample was extracted with water under ultrasonic management for 2 hours. Chromatographic conditions: YWG C18 10 microns 5 mm x 200 mm; mobile phase consisted of NaH2PO4-NaOH buffer solution (pH 6.8); UV detection at 260 nm. The recoveries of adenosine and 3'-deoxyadenosine were 95.8% +/- 0.64% and 100.6% +/- 0.65% (n = 5) respectively.

Mass spectrometric analysis of 2-deoxyribonucleoside and 2'-deoxyribonucleotide adducts with aldehydes derived from lipid peroxidation

An important emerging issue in chemical carcinogenesis is the role that products of endogenous metabolism play in formation of covalently modified DNA. One example is the formation of alpha, beta-unsaturated aldehydes as a result of endogenous and drug-stimulated lipid peroxidation. Malondialdehyde (MDA), crotonaldehyde (CR), 2-hexenal (HX), and 4-hydroxy-2-nonenal (HNE) react covalently with 2'-deoxyguanosine (dG) and 2'-deoxyadenosine (dA) residues on DNA to form promutagenic cyclic adducts that may be important in the etiology of cancer in humans and animals. The accurate quantification of such adducts provides a powerful tool in molecular epidemiology for assessing carcinogenic risks from various lifestyle choices (e.g. diet, drug use) in humans. 32P-Postlabeling is recognized as one of the most sensitive methods available for detection of DNA adducts in human tissues, but without adequate validation such methodology can yield inaccurate quantitative measurements. We have used LC separations in conjunction with electrospray ionization MS and tandem MS (triple quadrupole and hybrid quadrupole-orthogonal acceleration time of flight analyzers) to characterize MDA-, CR-, HX- and HNE-modified dG and nucleotide (3'- and 5'-monophosphate; 3',5'-bisphosphate) adducts. These data have been used to validate 32P-postlabeling methods for quantification of low level MDA-dG adducts formed in DNA of human and animal tissues. Availability of reliable methods for quantification of endogenous DNA damage in humans and animals is essential for determining unknown etiologies of cancer and for the assessment of cancer risks in humans.

Analysis of 7-methylbenz[a]anthracene-DNA adducts formed in SENCAR mouse epidermis by 32P-postlabeling

The present study has analysed the DNA adducts formed in SENCAR mouse epidermis following topical application of 7-methylbenz[a]anthracene (7-MBA). Mice were treated with 400 nmol of 7-MBA, which represents an initiating dose of this hydrocarbon for SENCAR mice. DNA adducts were analysed 24 h after topical application of the hydrocarbon by 32P-postlabeling coupled with either HPLC analysis or an improved TLC procedure giving better resolution of DNA adducts through the use of a D6 solvent [isopropanol:4N NH4OH (1:1)] following D5. Twenty-four hours after topical application of 400 nmol 7-MBA, the level of total covalent binding was 0.37 +/- 0.07 pmol/mg DNA as determined by 32P-postlabeling. This level of binding correlated well with the relative tumor initiating activity of this hydrocarbon compared to 7,12-dimethylbenz[a]anthracene (6.4 +/- 0.01 pmol/mg DNA) and dibenz[a,j]anthracene (0.03 +/- 0.01 pmol/mg DNA). Analysis of the 32P-labeled 3',5'-diphosphodeoxyribonucleosides by HPLC and TLC revealed the presence of deoxyguanosine (dGuo) and deoxyadenosine (dAdo) adducts formed from both the anti- and syn-bay-region diol-epoxides of 7-MBA (anti- and syn-7-MBADEs). The major DNA adduct derived from 7-MBA in mouse epidermis was tentatively identified as (+) anti-7-MBADE-trans-N2-dGuo. In addition, a minor dGuo adduct derived from the bay-region syn-diol-epoxide of 7-MBA was detected as well as a minor dAdo adduct from this diol-epoxide. Another minor dAdo adduct was also detectably present which arose from either the anti- or syn-diol epoxide. Furthermore, several unidentified DNA adducts were present in both HPLC and TLC chromatograms of DNA samples from 7-MBA-treated mice. These results are discussed in terms of the role of specific 7-MBA-DNA adducts in tumor initiation by this hydrocarbon.

Lipid peroxidation-induced putative malondialdehyde-DNA adducts in human breast tissues

The etiology of the majority of human breast cancers is unknown; however, oxidative stress and lipid peroxidation have been suggested to play a role in breast carcinogenesis. To address this possibility, DNA adducts induced by malondialdehyde (MDA), an end product of lipid peroxidation, were analyzed in surgical specimens of normal breast tissues of 51 breast cancer patients using the nuclease P1-enhanced version of the 32P-postlabeling assay. Normal breast tissue samples from 28 noncancer patients receiving reduction mammoplasty served as controls. Two previously characterized putative MDA-deoxyadenosine (dA) and one MDA-deoxyguanosine adduct were detected in all tissue samples examined. Normal breast tissues from cancer patients exhibited significantly higher levels of the putative MDA adducts [median (42.5) and range (2.2-202.8) of relative adduct labeling x 10(9) values] than those found in noncancer controls (median, 15.67; range, 2.4-382.1; P = 0.0001, Mann-Whitney U test). Ten of the 51 cancer patients and 1 of the 28 controls were found to contain the putative MDA adducts at the level of > 1/10(7) nucleotides, a frequency comparable to that found in human liver. Age and body mass did not significantly influence the levels of these adducts. However, the presence of a previously detected benzo(a)pyrene-like DNA adduct in the breast tissues was associated with higher levels of the putative MDA-dA adducts in cancer patients (P = 0.012). The level of the putative MDA-dA adducts was significantly lower in smokers and former smokers compared to nonsmokers among cases after adjusting for age, body mass index, and status of the benzo(a)pyrene-like adduct (P = 0.009). Tumor tissues (n = 11) displayed significantly lower levels of the putative MDA adducts (median, 10.2; range, 5.3-20.6) than their corresponding normal adjacent tissues (median, 25.5; range, 10.5-138; P < 0.01). These findings provide evidence that lipid peroxidation products can accumulate in human breast tissues and reach relatively high levels in the breast tissues of women with breast cancer. There seems to be an interaction between these endogenous DNA modifications and carcinogen exposure-induced DNA adducts. Detection and quantitation of the putative MDA-DNA adducts may potentially be a useful tool in the understanding of breast cancer etiology.

Detection of 1,N6-ethenodeoxyadenosine and 3,N4-ethenodeoxycytidine by immunoaffinity/32P-postlabelling in liver and lung DNA of mice treated with ethyl carbamate (urethane) or its metabolites

The capacity of the chemical carcinogen ethyl carbamate (EC, urethane) and its metabolites vinyl carbamate (VC) and vinyl carbamate epoxide (VCO) to form ethenobases was studied in liver and lung DNA of 12-day-old and adult CD-1, B6C3F1, C3H/HeJ and C57BL/6J mice. Following single and multiple doses of EC, VC or VCO, the formation of 1,N6-ethenodeoxyadenosine (epsilon dA) and 3,N4-ethenodeoxycytidine (epsilon dC) was quantified by an immunoaffinity chromatography/32P-postlabelling technique. Both etheno adducts were detected in untreated control DNA samples from liver and lung in the range of 2-15 adducts/10(9) parent nucleotides. Following five repeated injections of 250 or 280 nmol/g body wt VC to adult mice, 51, 57 and 78 epsilon dA/10(9) dA and 28, 42 and 42 epsilon dC/10(9) dC (means of duplicate analyses) were detected in liver DNA of CD-1, C3H/HeJ and C57BL/6J mice respectively. In lung DNA of these VC-treated mice, the levels were 87, 49 and 58 (epsilon dA/10(9) dA) and 64, 39 and 43 (epsilon dC/10(9) dC) respectively. Under similar dose regimens, lower levels of etheno adducts were detected in B6C3F1 mice. Etheno-DNA adducts were also formed in liver and lung upon treatment with EC in adult mice, but at 3-fold lower levels as compared with VC. In 12-day-old C3H/HeJ and C57BL/6J mice, 2- to 3-fold higher etheno adduct levels were detected in liver DNA, when compared with adults, upon a single treatment with 250 nmol/g body wt VC, suggesting that young animals are more susceptible to adduct formation. Combined analysis of adduct formation in adult CD-1, C3H/HeJ and C57BL/6J mice at the higher dose showed a statistically significant increase in etheno adduct formation in the order EC > VC. The results demonstrate that EC and its activated intermediates bind to liver and lung DNA to form epsilon dA and epsilon dC, and the differences in DNA binding further support the hypothesis that metabolic activation of EC to VC is involved. Preliminary data also suggest that background levels of epsilon dA and epsilon dC in DNA are affected by the type of diet given to the animals.

Observation and prevention of an artefactual formation of oxidized DNA bases and nucleosides in the GC-EIMS method

Gas chromatography coupled to electron impact mass spectrometry (GC-EIMS) analysis following hydrolysis of DNA is a widely used assay for the detection of oxidized nucleobases and nucleosides. However, evidence was recently provided for an oxidation of guanine residues of hydrolysed DNA during the silylation prior to GC-EIMS analysis. This reaction accounts for the overestimation of the yield of 8-oxo-7,8-dihydroguanine by GC-EIMS. In the present work, we showed that adenine, cytosine, thymine and thymidine also give rise to oxidized derivatives during the derivatization. This was inferred from the measurement of the amount of 5-formyluracil, 5-hydroxymethyluracil, 5-hydroxycytosine (5-OHCyt), 8-oxo-7,8-dihydroadenine (8-OxoAde) and 5-hydroxymethyl-2'-deoxyuridine (5-HMdUrd) in a series of experiments based on the use of purified bases and nucleosides. Isotopically labelled oxidized bases and 5-HMdUrd were used as internal standards to control the quantitative aspect of the silylation reaction. Support for an artefactual oxidation of hydrolysed DNA was provided by the comparison of the amount of 8-OxoAde and 5-OHCyt detected within native and gamma-irradiated DNA by HPLC-EC and GC-EIMS. To prevent the artefactual formation of oxidized bases during the silylation, an approach based on an HPLC prepurification was developed to remove the precursors of the oxidized bases measured in the DNA sample. The HPLC/GC-EIMS assay was successfully applied to the quantitation of 8-OxoAde and 5-OHCyt in calf thymus DNA. In addition, the detection of the dose-dependent formation of 5-HMdUrd in isolated DNA exposed to ionizing radiation was achieved using the same approach.

1,N6-ethenodeoxyadenosine and 3,N4-ethenodeoxycytine in liver DNA from humans and untreated rodents detected by immunoaffinity/32P-postlabeling

The etheno-bridged exocyclic DNA adducts 1,N6-ethenodeoxyadenosine (epsilon dA) and 3,N4-ethenodeoxycytine (epsilon dC) can be formed by several structurally diverse carcinogens and mutagens that include vinyl chloride and urethane. In order to investigate the occurrence and persistence of these adducts in rodents exposed to such DNA-damaging agents, an ultra-sensitive detection method has been developed. It is based on immunoaffinity purification of the etheno adducts and subsequent 32P-postlabelling followed by separation as 5'-monophosphates on polyethyleneimine-cellulose-coated thin-layer plates. Normal nucleotides in the DNA samples were quantitated by HPLC. Optimal conditions for enzymatic hydrolysis of DNA are described: deoxyuridine 3'-monophosphate was used as internal standard to correct for labelling efficiency of the etheno adducts. The method had a detection limit of 25 amol of epsilon dA and epsilon dC for a 50 micrograms DNA sample. Using this technique, analysis of liver DNA from humans with unknown exposure revealed the presence of epsilon dA and epsilon dC residues in the range of 0-27 adducts per 10(9) parent bases. Liver DNA obtained from untreated mice and rats was also shown to contain similar low but variable levels of these etheno adducts. In vitro studies indicated that these promutagenic DNA lesions could arise from endogenously formed lipid peroxidation products.

pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2'-deoxyadenosine

The ability of homopyrimidine oligonucleotides containing 8-oxo-2'-deoxyadenosine to form stable, triple helical structures with the sequence containing the recognition site for the class II-S restriction enzyme, Ksp632-I, was studied as a function of pH. The 8-oxo-2'-deoxyadenosine-substituted oligomers were shown to inhibit enzymatic cleavage and to bind within the physiological pH range in a pH-independent fashion without compromising specificity.

A comparison of two ultrasensitive methods for measuring 1,N6-etheno-2'-deoxyadenosine and 3,N4-etheno-2'-deoxycytidine in cellular DNA

1,N6-Ethenodeoxyadenosine (edA) and 3,N4-ethenodeoxycytidine (edC) are two mutagenic adducts associated with exposure to ethyl carbamate (urethane) and vinyl chloride. We have recently developed two ultrasensitive methods for determining the molecular dose of these adducts in cellular DNA. In both methods, purified DNA was first enzymatically digested to 2c-deoxyribonucleotide 3c-monophosphates. Etheno-modified nucleotides were then separated from normal nucleotides in one of two ways: either by reverse phase, ion-pair HPLC coupled with 260 nm UV detection, or by immunoaffinity chromatography using reusable microcolumns containing specific monoclonal antibodies coupled to Protein A-Sepharose. Fractions enriched for the adducted nucleotides were labeled using T4 poly-nucleotide kinase and [32P]ATP, and individual nucleotides were subsequently resolved by two-dimensional TLC, visualized by autoradiography, and quantified by liquid scintillation counting. When used to analyze the same sample of etheno-modified calf thymus DNA, both assays produced similar results. However, when both methods were used to analyze rat liver DNA 'spiked' with known amounts of etheno nucleotide standards, the immuno-affinity/32P TLC procedure proved to be more sensitive and more reproducible than the HPLC/32P TLC method: while the detection limit of the immunoaffinity/32P TLC technique was < 4 etheno adducts/10(9) parent deoxynucleotides, the HPLC/32P TLC method often failed to detect adducts at concentrations < 2/10(8). In other experiments, the immunoaffinity/32P TLC method was used to demonstrate formation of edA and edC in cells treated with vinyl chloride monomer. Because of its exquisite sensitivity, the immunoaffinity/32P TLC method promises to be extremely useful for measuring both background and induced levels of etheno adducts, making it possible to examine the role of these adducts in inducing mutations and/or carcinogenesis.

Fluorescence HPLC methods for detecting benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide-deoxyadenosine adducts in enzyme-digests of modified DNA: improved sensitivity

The fluorescence of mononucleoside adducts derived from the binding of anti-7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo [a]pyrene (BPDE I) to N6-deoxyadenosine (BPDE-dA adducts) is 10-100 times stronger (depending on the methanol/water solvent composition) than the fluorescence of adducts derived from the binding of this diol epoxide derivative to N2-deoxyguanosine. It is shown here that these fluorescence characteristics can be used to quantitate the relatively low yields of BPDE-dA adducts by fluorescence detection when BPDE-modified DNA is subjected to enzymatic degradation to the mononucleoside levels, followed by HPLC analysis of the digests.

A comparative study of the reversed-phase HPLC retention behaviour of S-adenosyl-L-methionine and its related metabolites on Hypersil ODS and Supelcosil LC-ABZ stationary phases

S-Adenosyl-L-methionine (SAM) and its metabolites S-adenosyl-L-homocysteine (SAH) and methyl-thioadenosine (MTA) are endogenous compounds that are heavily involved in a variety of biochemical processes, and have therefore been the target for several assays in body fluids and tissues. Reversed-phase chromatographic behaviour of SAM and its metabolites has been studied by using Supelcosil LC-ABZ column, specially designed for analysis of acidic, basic, zwitterionic and neutral compounds, and on a Hypersil ODS column as a function of mobile phase pH. The retentions of the compounds, expressed by the capacity ratio (k'), are measured on both column with mobile phases comprised of 10% acetonitrile and 10 mM ammonium formate buffer with pH values ranging from 2 to 9. Higher selectivity is observed on Supelcosil LC-ABZ within pH range 4-6. Different retention properties are observed at very low pH and seemed as if the Supelcosil LC-ABZ column reduced the effect of the mobile phase pH by about 1 pH unit. Whilst the Supelcosil column can be recommended for the routine analysis of SAM and its related metabolites in biological fluids by using mobile phase pH 5, the Hypersil ODS column may be suggested for use with mobile phase pH values of 3-4.

Novel deletion and a new missense mutation (Glu 217 Lys) at the catalytic site in two adenosine deaminase alleles of a patient with neonatal onset adenosine deaminase- severe combined immunodeficiency

Mutations at the adenosine deaminase (ADA) locus result in a spectrum of disorders, encompassing a fulminant neonatal onset severe combined immunodeficiency (SCID) and childhood onset immunodeficiency, as well as apparently normal immune function. The extent of accumulation of the toxic metabolite, deoxyATP, correlates directly with severity of disease. We have now determined the mutations on both alleles of a child with fulminant, neonatal onset ADA- SCID and accumulation of extremely high concentrations of deoxyATP. The genotype was consistent with the severely affected phenotype. One allele carried a large deletion that arose by non-homologous recombination and included the first five exons and promoter region. The second allele carried a missense mutation (G649A) resulting in replacement of Glu217, an amino acid involved in the catalytic site, by Lys and predicting a major alteration in charge. Expression of the mutant cDNA in Cos cells confirmed that the mutation abolished enzyme activity. We have previously reported that a missense mutation at the preceding codon is similarly associated with neonatal onset ADA- SCID and accumulation of extremely high deoxyATP. These findings suggest that genotype-phenotype correlations may be apparent for ADA- SCID, despite the role that random variation in exposure to environmental pathogens may play in the initial phenotype. Such genotype-phenotype correlations may be important to consider in evaluating results of ongoing trials of "gene" and enzyme replacement therapy.

Etheno adducts formed in DNA of vinyl chloride-exposed rats are highly persistent in liver

Preweanling rats were exposed to 600 p.p.m. (4h/day) of the human carcinogen vinyl chloride for 5 days to determine the molecular dosimetry of DNA adducts in liver, lung and kidney. 7-(2'-Oxoethyl)guanine (7OEG) was the major DNA adduct detected, representing approximately 98% of all adducts. N2,3-Ethenoguanine (epsilon G) and 3,N4-etheno-2'-deoxycytidine (epsilon dC) were present at approximately 1% of the 7OEG concentration, while 1,N6-etheno-2'-deoxyadenosine was present in even lower concentrations. Liver had 3- to 8-fold higher amounts of the DNA adducts than lung and kidney. The persistence of all four adducts was determined at 3, 7 and 14 days post-exposure. Whereas 7OEG had a t 1/2 of -62 h, all three etheno adducts were highly persistent. After accounting for dilution due to growth-related cell proliferation, epsilon G had a t 1/2 of approximately 30 days, while epsilon dC and epsilon dA were not repaired. These data suggest that these cyclic adducts are poorly recognized by liver DNA repair enzymes and have the potential for accumulation upon chronic exposure. This, coupled with the known miscoding properties of the ethenobases, provides a strong rational for examining their role in vinyl chloride-induced cancer and their utility as biomarkers of exposure.

Detection of 1,N6-propanodeoxyadenosine in acrolein-modified polydeoxyadenylic acid and DNA by 32P postlabeling

The interaction of acrolein, an alpha,beta-unsaturated aldehyde, with polydeoxyadenylic acid and DNA has been investigated using 32P-postlabeling analysis. In preliminary experiments, polydeoxyadenylic acid was incubated with excess acrolein and then digested to 3' monophosphates prior to transfer of 32P from [gamma-32P]ATP with T4 polynucleotide kinase. The 3',5'-bisphosphates were 3'-dephosphorylated prior to two-dimensional thin layer chromatography on polyethyleneimine-cellulose layers. Autoradiography provided evidence for the formation of one extra spot of radioactivity, compared to the control. To determine the adduct structure, deoxyadenosine-5'-monophosphate was incubated with a 3-fold excess of acrolein. This material was mixed with a 32P-labeled digest of acrolein-polydeoxyadenylic acid, and the sample was analyzed by ion-pair high performance liquid chromatography. The spot of 32P observed by thin layer chromatography co-eluted with the major product of the acrolein nucleotide reaction mixture, which was purified by ion-pair high performance liquid chromatography. Two-dimensional nuclear magnetic resonance spectroscopy and mass spectrometry showed the adduct to be 3-(2'-deoxyribosyl-5'-monophosphatyl)-7,8,9-trihydro-9-hydro xy- pyrimido[2,3-i]purine(1,N6-propanodeoxyadenosine-5'-monophosphate) . High performance liquid chromatography was used to fractionate digests of acrolein-modified DNA prior to detection of this exocyclic adduct by 32P-postlabeling.

Nucleic acid hybridization assays employing dA-tailed capture probes. I. Multiple capture methods

A quantitative hybridization assay termed "reversible target capture" is described. The technique is designed to extensively purify the target nucleic acid from crude cell lysates in about 1 h without phenol extraction. Simple, rapid methods are described that explain how each process in the assay is optimized. The procedure involves hybridizing the target nucleic acid in solution with a dA-tailed capture probe and a labeled probe. The capture probe-target-labeled probe "ternary complex" is then captured on magnetic beads containing oligo(dT). After the excess unhybridized labeled probe, cell debris, and other sample impurities are washed away, the intact ternary complex is further purified by chemical elution from the beads and recapture on fresh beads. The ternary complex is then eluted thermally and recaptured on a third set of beads or on poly(dT) filters. This triple capture method results in a detection limit of approximately 0.2 amol (100 fg) of target with 32P-labeled riboprobes. This is approximately 1000 times more sensitive than sandwich assays employing only a single capture step. The method is illustrated by detecting Listeria cells in the presence of heterologous bacteria. With three rounds of target capture, as few as six Listeria cells have been detected in the presence of 1.25 x 10(7) control cells.

HPLC-32P-postlabelling analysis of 1,N6-ethenodeoxyadenosine and 3,N4-ethenodeoxycytidine

A 32P-postlabelling procedure coupled with HPLC has been developed to detect and measure the cyclic nucleic acid adducts 1,N6-ethenodeoxyadenosine and 3,N4-ethenodeoxycytidine in DNA. Chloroacetaldehyde-modified DNA containing these adducts was enzymatically digested to 3'-monophosphates and adducts were separated by ion-pair reverse-phase HPLC on PL RP-S prior to 32P-postlabelling with carrier free [gamma-32P]ATP. Following 3'-dephosphorylation with nuclease P1 the resulting [5'-32P]monophosphate adducts were finally resolved by HPLC on PL RP-S and assayed by liquid scintillation counting.

1,N6-etheno-2'-deoxyadenosine and 3,N4-etheno-2'-deoxycytidine detected by monoclonal antibodies in lung and liver DNA of rats exposed to vinyl chloride

1,N6-Etheno-2'-deoxyadenosine (epsilon dAdo) and 3,N4-etheno-2'-deoxycytidine (epsilon dCyd) are formed in vitro by reaction of DNA with the electrophilic metabolites of vinyl chloride (VC), chloroethylene oxide and chloroacetaldehyde. To detect and quantitate these DNA adducts in vivo, we have raised a series of specific monoclonal antibodies (Mab). Among those, Mab EM-A-1 and Mab EM-C-1, respectively, were used for detection of epsilon dAdo and epsilon dCyd by competitive radioimmunoassay (RIA), following pre-separation of the etheno adducts from DNA hydrolysates by high performance liquid chromatography. At 50% inhibition of tracer-antibody binding, both Mab had a detection limit of 187 fmol and antibody affinity constants (K) of 2 x 10(9) l/mol. The levels of epsilon dAdo and epsilon dCyd were quantitated in the DNA of lung and liver tissue of young Sprague-Dawley rats exposed to 2000 p.p.m. of VC for 10 days. The epsilon dAdo/2'-deoxyadenosine and epsilon dCyd/2'-deoxycytidine molar ratios were 1.3 x 10(-7) and 3.3 x 10(-7), respectively, in lung DNA, and 5.0 x 10(-8) and 1.6 x 10(-7) in liver DNA. When hydrolysates of 3 mg of DNA were analyzed by RIA at 25% inhibition of tracer-antibody binding, epsilon dAdo and epsilon dCyd were not detected in liver DNA from untreated rats above the limiting epsilon dAdo/2'-deoxyadenosine and epsilon dCyd/2'-deoxycytidine molar ratios of 2.2 x 10(-8) and 3.1 x 10(-8), respectively.

Ion microscopy: a new approach for subcellular localization of labelled molecules

Secondary ion mass spectroscopy (SIMS) was used to obtain images representing the intracellular distribution of molecules labelled with carbon 14. Deoxyadenosine labelled with carbon 14 was added to a cultured human fibroblast cell medium, and the intracellular distribution of this molecule was studied using three different SIMS instruments: the CAMECA IMS 3F and SMI 300 ion microscopes and the UC-HRL scanning ion microprobe. Carbon 14 distribution images obtained by this method show that deoxyadenosine U-C14 is present in the cytoplasm as well as the nucleus, with a higher concentration in the nucleoli. Our study clearly demonstrates that ion microscopy is well suited for carbon 14 detection and localization at the subcellular level, permitting a wide variety of microanalytical tracer experiments.

7,12-Dimethylbenz[a]anthracene-DNA adducts in mouse skin, dermis and epidermis

Female NIH Swiss mice were treated topically with either 0.01 or 0.1 mumol 7,12-[3H]dimethylbenz[a]anthracene and DNA was isolated either from the whole skin, the dermis or the epidermis. Levels of binding to DNA and levels of individual adducts formed were similar in all 3 tissue fractions for a given dose of carcinogen with levels for the epidermis being marginally greater than in the other fractions. In all tissue fractions, the syn dihydrodiol epoxide-deoxyribonucleoside adducts were responsible for a greater fraction of total binding at the higher, than at the lower, carcinogen dose. The mechanism of metabolic activation of 7,12-dimethylbenz[a]anthracene for DNA binding is, therefore, qualitatively the same in both the dermis and epidermis. Quantification of adducts suggests some subtle differences between the DMBA activating systems in dermis and epidermis.

CpG and TpA frequencies in the plant system

Higher plant nuclear sequences reveal avoidance of CpG and TpA doublets. Chloroplast sequences avoid the TpA doublet in all codon positions. The chloroplast genome is not methylated but codon positions II-III and untranslated regions avoid CpG. The mitochondrial genome, also unmethylated, avoids CpG in all codon positions. We therefore deduce that methylation is not sufficient to explain CpG avoidance in the higher plant systems. Other factors must be taken into account such as amino acid composition, codon choices and perhaps stability of the DNA helix.

DNase VII of human placenta. Mechanism studies

The mechanism of the human placental DNase VII, described previously (Hollis, G. F., and Grossman, L. (1981) J. Biol. Chem. 256, 8074-8079) has been investigated in further detail. The enzyme initiates exonucleolytic hydrolysis from the 3'-end of DNA in a nonprocessive, or distributive, manner, regardless of whether the carbohydrate moiety associated with the 3'-terminal nucleotide contains H or OH at its 2' and 3' positions. DNase VII does not have associated RNase H activity; however, it is capable of removing 3'-terminal ribonucleotides. The enzyme also can hydrolyze DNA containing a terminal nucleotide lacking a purine or pyrimidine as well as termini containing noncomplementary nucleotides. DNase VII activity is product-inhibited by deoxynucleoside 5'-monophosphates. From kinetic studies, the mononucleotide deoxyadenylic acid is a noncompetitive inhibitor with a Ki = 0.3 mM. The resemblance of DNase VII to the 3'----5' exonuclease activity of Escherichia coli DNA polymerase I and its possible role in excision repair and proofreading are discussed.

Search for DNA alterations in Alzheimer's disease

The DNA of brain cortex obtained from autopsy specimens of eight patients with Alzheimer's disease and eight controls was examined for content of normal and abnormal bases. DNA, purified by hydroxyapatite chromatography, was hydrolyzed under mild conditions and the deoxynucleosides were measured by high performance liquid chromatography (HPLC). No differences in the mole percentages of deoxynucleosides in DNA were detected in patients with Alzheimer's disease compared to controls, nor were abnormal deoxynucleosides found. Restriction-nuclease digests examined by agarose gel electrophoresis also showed no changes. Thus, diffuse and persistent damage to the DNA in brain in Alzheimer's disease was not detected by these methods.

[A simple enzymatic method for the quantitative determination of cordycepin and [3'-deoxy]ATP in rat brain tissue]

A procedure for quantitative estimation of cordycepin (3'-deoxyadenosine), a specific inhibitor of post-transcriptional polyadenylation of pre-mRNA and of a metabolite of cordycepin 3'-deoxyATP in rat brain tissue is described. The procedure is based on evaluation of an inhibitory effect on the synthesis of polyA in vitro of total nucleoside and nucleoside and nucleoside triphosphate preparations isolated from the animal brain after cordycepin administration. Homogenates of intact animal brain were used as a source of "crude" polyA polymerase preparations.

A dose-response study on opening of imidazole ring of adenine in DNA by ionizing radiation

A dose-response relationship between gamma-irradiation and the cleavage of the imidazole ring of adenine in DNA to form formamidopyrimidine has been demonstrated. When the DNA aqueous solution was irradiated with 0.1 Gy under N2O, there is little evidence of imidazole ring cleavage. A significant increase in cleavage begins to be noticed above 1 Gy reaching a plateau at 1000 Gy. No formamidopyrimidine was formed when 2'-deoxyadenosine was irradiated with up to 1000 Gy. A dose of 100 Gy converts 18 per cent of adenine in DNA to formamidopyrimidine. In irradiated DNA aqueous solution 1000 Gy convert 25 per cent of adenine to formamidopyrimidine under N2O. Some of the adenine was converted to 7,8-dihydro-8-oxoadenine but in amount that is 20 per cent of that converted to formamidopyrimidine under N2O. There was more adenine in DNA converted to formamidopyrimidine under N2O than under N2.

Quantitative estimate of unlabelled cordycepin in acid-soluble pool isolated from rat brain tissue after intraperitoneal injection of the inhibitor

A technique for the quantitative estimation of intraperitoneally injected unlabelled cordycepin in an acid-soluble pool (ASP) isolated from rat brain tissue is suggested. It consists in consecutive chromatography of ASP on Dowex 1 X 8, Dihydroxyboryl = SP500 and Sephasorb-HP. The fraction containing 2'-deoxyriboadenosine and 3'-deoxyriboadenosine (cordycepin) has been isolated from brain tissue ASP of experimental animals after a cordycepin injection. 2'-Deoxyriboadenosine fraction has been isolated from tissue ASP of the control animals not subjected to an inhibitor injection. Brain tissue antibiotic content has been estimated by the difference in nucleoside quantity values (microM) in these two fractions (control/experiment).

[2'Deoxyadenosine/adenosine deaminase ratio in pleural and peritoneal effusions. Diagnostic significance]

It has been observed that adenosine deaminase activity in human beings differ between serum and tissues reference to optimal pH, Km and relative substrate specificity. Based upon the ratio between the activity of deaminase on 2'deoxyadenosine and adenosine, we may distinguish between a "serum type" enzyme and a "tissue type" enzyme. In sample of pleural and peritoneal fluid extracted from 92 patients with variable pathology, we have found the existence of a "tissue type" enzyme in three patients having empyemic pleural effusions and ten with malignant systemic pathology.

Formation and removal of benzo(a)pyrene adducts of DNA in hamster tracheal epithelial cells

A cloned cell line derived from normal hamster tracheal epithelium has been characterized with respect to its response to the environmental pollutant and carcinogen benzo(a)pyrene [B(a)P]. These cells metabolize B(a)P to ultimate reactive forms as assayed by alkylation of DNA. Alkylation with radiotracer amounts of B(a)P was maximum at 8 hr, at which time 70% of the applied hydrocarbon had been converted to water-soluble forms. At longer incubation times, the rate of removal of adducts exceeded the rate of formation. When B(a)P-containing medium was replaced with fresh medium at two or four hr, a subsequent biphasic removal of adducts occurred, a rapid removal for the first four hr postincubation and then a slower repair. About 50% of the DNA-bound hydrocarbon remained in DNA after 48 hr. Cells were able to divide in the presence of these lesions, undergoing five doublings (five days), while only 60% of the adducts were removed from the DNA. Integrity of DNA during this period was monitored by the alkaline elution technique. A toxic dose of B(a)P was required to cause any increase in the rate of elution. Minimal single-strand breakage was observed from two to eight hr of B(a)P treatment, but at 15 hr DNA appeared normal. Comparison was made with a nontoxic dose of methyl methanesulfonate which caused very rapid elution of DNA after only one hr treatment. At least 15 deoxyribonucleoside-bound B(a)P adducts were separated by high-pressure liquid chromatography. Four adducts, probably deoxyadenosine-B(a)P, were removed almost completely in 24 hr, while the others appeared to be poorly removed. The possible significance to neoplasia of persistent and repairable lesions is discussed.

[Absorption spectra of nucleic acids and related compounds in the spectral region 120--280 nm]

The absorption spectra of thin films of nucleic acids, nucleosides, nucleotides, D-ribose, Na3PO4 in vacuum ultraviolet region are measured. In the spectral region 280--160 nm the absorption spectra consist of the bands of nucleic acid bases. In the range shorter than 160 nm the absorption is determined by phosphate and D-ribose groups. The methods of thin films preparation are discussed.

The crystal and molecular structure of an intermolecular complex between riboflavin and an adenosine derivative

Riboflavin and the adenosine derivative 5'-bromo-5'-deoxyadenosine form a crystalline 1:1 intermolecular complex, the structure of which has been solved by x-ray diffraction analysis. The adenine ring is found to be joined by two hydrogen bonds to the uracillike end of the riboflavin isoalloxazine ring. In addition, the riboflavin and the adenosine molecules associate through the formation of stacks of alternating parallel adenine and isoalloxazine rings. These intermolecular associations are considered to be models for intramolecular association in the coenzyme flavin adenine dinucleotide (FAD), which contains both adenosine and riboflavin.