Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A.

Multiple studies have indicated that the TET oxidases and, more controversially, the activation-induced cytidine deaminase/APOBEC deaminases have the capacity to convert genomic DNA 5-methylcytosine (MeC) into altered nucleobases that provoke excision repair and culminate in the replacement of the original MeC with a normal cytosine (C). We show that human APOBEC3A (A3A) efficiently deaminates both MeC to thymine (T) and normal C to uracil (U) in single-stranded DNA substrates. In comparison, the related enzyme APOBEC3G (A3G) has undetectable MeC to T activity and 10-fold less C to U activity. Upon 100-fold induction of endogenous A3A by interferon, the MeC status of bulk chromosomal DNA is unaltered, whereas both MeC and C nucleobases in transfected plasmid DNA substrates are highly susceptible to editing. Knockdown experiments show that endogenous A3A is the source of both of these cellular DNA deaminase activities. This is the first evidence for nonchromosomal DNA MeC to T editing in human cells. These biochemical and cellular data combine to suggest a model in which the expanded substrate versatility of A3A may be an evolutionary adaptation that occurred to fortify its innate immune function in foreign DNA clearance by myeloid lineage cell types.

BRCA1 required for transcription-coupled repair of oxidative DNA damage.

The breast and ovarian cancer susceptibility gene BRCA1 encodes a zinc finger protein of unknown function. Association of the BRCA1 protein with the DNA repair protein Rad51 and changes in the phosphorylation and cellular localization of the protein after exposure to DNA-damaging agents are consistent with a role for BRCA1 in DNA repair. Here, it is shown that mouse embryonic stem cells deficient in BRCA1 are defective in the ability to carry out transcription-coupled repair of oxidative DNA damage, and are hypersensitive to ionizing radiation and hydrogen peroxide. These results suggest that BRCA1 participates, directly or indirectly, in transcription-coupled repair of oxidative DNA damage.

Inducible repair of thymine glycol detected by an ultrasensitive assay for DNA damage.

An ultrasensitive assay for measuring DNA base damage is described that couples immunochemical recognition with capillary electrophoresis and laser-induced fluorescence detection. The method provides a detection limit of 3 x 10(-21) moles, an improvement of four to five orders of magnitude over current methods. Induction and repair of thymine glycols were studied in irradiated A549 cells (a human lung carcinoma cell line). Exposure of these cells to a low dose of radiation (0.25 Gray) 4 hours before a clinically relevant dose (2 Gray) enhanced removal of thymine glycols after the higher dose. These data provide evidence for an inducible repair response for radiation-induced damage to DNA bases.

Production of thymine glycols in DNA by N-hydroxy-2-naphthylamine as detected by a monoclonal antibody.

We have quantitated the production of thymine glycols in DNA following treatment of cultured human fibroblasts or DNA in solution with the carcinogen N-hydroxy-2-naphthylamine. Thymine glycols, detected by using a monoclonal antibody specific to this base damage, were produced in DNA in a dose dependent manner both in vitro and in vivo. Exposure of DNA to N-hydroxy-2-naphthylamine in the presence of catalase and superoxide dismutase, which break down hydrogen peroxide and superoxide anions, respectively, inhibited the production of this base damage. Thymine glycols were efficiently removed from DNA in both normal human fibroblasts and in cells from a patient with xeroderma pigmentosum complementation group A, which are deficient in nucleotide excision repair.

Immunoanalytical detection of O4-ethylthymine in liver DNA of individuals with or without malignant tumors.

The detection and quantitation of carcinogen-DNA adducts in human cells are the key parameters in the molecular dosimetry of human exposure to environmental carcinogens. For investigating the possible relevance of alkylating N-nitroso compounds as causative agents in human carcinogenesis, we have quantitated O4-ethyl-2'-deoxythymidine (O4-EtdThd) in human liver DNA obtained from 33 autopsy specimens, i.e., 13 cases with primary liver cancer (LC), 8 with cancers other than liver cancer (OC), and 12 with noncancerous diseases (NC). None of the cases analyzed had a history of known occupational exposure to ethylating agents. The detection limit for O4-EtdThd was 3 X 10(-8) as a O4-EtdThd/dThd molar ratio in DNA, which was attained by the combination of prefractionation of DNA hydrolysates (= 20 mg of DNA/sample) by high performance liquid chromatography and competitive radioimmunoassay using anti-(O4-EtdThd) monoclonal antibody ER-01. Except for one case in each group, O4-EtdThd [or, alternatively, (an) unidentified structural modification(s) of DNA recognized by monoclonal antibody ER-01] was detected at mean (+/- SD) O4-EtdThd/dThd molar ratios of 39.9 +/- 40.2 x 10(-8), 53.5 +/- 74.0 X 10(-8), and 11.7 +/- 6.5 X 10(-8), respectively, in LC, OC, and NC. The difference of the O4-EtdThd content in DNA between LC and NC, or between LC + OC and NC, was statistically significant at P less than 0.05. These results suggest that humans are exposed to ethylating agents in vivo and that a premutagenic DNA lesion (O4-EtdThd) eventually accumulates in DNA, possibly to a biologically significant extent.

Reactive oxygen species modified thymine and poly(dT) present unique epitope for human anti-DNA autoantibodies.

Hydroxyl radical, one of the most potent of all reactive oxygen species has been implicated in many human degenerative diseases and is known to modify adenine and thymine in cellular DNA. In the present studies, adenine, thymine and their synthetic homopolymers poly(dA), poly(dT) were ROS-modified and subsequently used as inhibitors of native DNA binding to human anti-DNA autoantibodies. Besides nDNA, modified thymine and poly(dT) were effective inhibitors of DNA-anti-DNA antibody interaction. The relative affinity of ROS-modified poly(dT) was better than that of native DNA. Visual detection of modified thymine and poly(dT) binding to affinity purified anti-DNA IgG by an indirect band shift assay support competition inhibition data. The enhanced recognition of ROS-DNA by anti-DNA autoantibodies, as reported earlier, could be due to the ROS-induced modification of thymine.

Properties of antibodies to thymine glycol, a product of the radiolysis of DNA.

Anti-thymine glycol antibodies were elicited by immunizing rabbits with thymine glycol monophosphate (TMP-glycol) conjugated by carbodiimide to BSA. The antibodies produced are specific for thymine glycol as measured by immunoprecipitation of TMP-glycol-RSA conjugates and hapten inhibition of reactivity with OsO4-treated DNA in an enzyme immunoassay. Using the enzyme immunoassay, the antibody is capable of detecting femtomole and picomole levels of thymine glycol in direct and competitive assays, respectively. This immunochemical assay is potentially suitable for measuring the production and repair of thymine glycol damage in cellular DNA.

Specificities and rates of binding of anti-(6-4) photoproduct antibody fragments to synthetic thymine photoproducts.

Pyrimidine (6-4) pyrimidone photoproducts are some of the major DNA photolesions induced by ultraviolet (UV) light. A monoclonal antibody (64M5) specific to a (6-4) photoproduct has been established and the corresponding single-chain antibody (64M5scFv) has been prepared. In this study, we characterized the ligand selectivities of 64M5 and 64M5scFv using synthetic octadeoxynucleotides containing either a central cis-syn cyclobutane thymine dimer (T[c,s]T), the (6-4) photoproduct of TpT (T[6-4]T), or its Dewar isomer (T[Dewar]T) by means of enzyme-linked immunosorbent assays (ELISA). Both 64M5 and 64M5scFv recognized T[6-4]T, but not the other photoproducts. We synthesized several biotinylated oligonucleotides of different lengths containing (T[6-4]T) to analyze the effects of the antigen size on the binding rates of an antigen binding fragment (64M5Fab) and 64M5scFv by means of surface plasmon resonance. The association rate constants for oligonucleotides of different sizes containing T[6-4]T as to 64M5Fab were found to be almost the same (1.9-5.6 x 10(5) M(-1) x s(-1)), while the dissociation rate constant for the largest oligonucleotide (d8mer, 8.0 x 10(-5) s(-1)) was significantly smaller than that for the d2mer (4.2 x 10(-2) s(-1)). These results indicate that 64M5Fab recognized the d2mer as the epitope and that the binding affinity for T[6-4]T depended on the flanking oligonucleotides. The dissociation rate constants for 64M5scFv as to the antigen analogs were almost the same as those for the various T[6-4]T-oligonucleotides as to 64M5Fab, suggesting that the conformations of these antibody binding regions are pretty similar to each other.

Melanin both causes and prevents oxidative base damage in DNA: quantification by anti-thymine glycol antibody.

The present study employs immunological methods to measure modified bases in DNA. A polyclonal antibody specific for thymine glycol was used to quantify the level of thymine glycol in calf thymus DNA gamma-irradiated in solutions containing varying concentrations of DOPA-eumelanin. Melanin decreased the number of thymine glycols produced by 200 Gy at low melanin concentrations. At high melanin concentrations, the number of thymine glycols increased. Thymine glycol was also produced in unirradiated DNA-eumelanin mixtures. DOPA-eumelanin was found to produce single-strand breaks in supercoiled phi X174 RF DNA. The breaks were measured by conversion of form I to form II as detected by agarose gel electrophoresis. The level of damage produced by melanin could be modulated by agents known either to stabilize or to scavenge active oxygen species. These studies demonstrate that melanin can both scavenge and generate active free radicals.

Development and characterization of a monoclonal antibody with cross-reactivity towards uracil and thymine, and its potential use in screening patients treated with 5-fluorouracil for possible risks.

BACKGROUND: Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in catabolism of pyrimidines including 5-fluorouracil. There have been efforts to isolate a monoclonal antibody that will bind selectively to pyrimidine and can be used to measure the concentration of pyrimidine in blood and/or in urine that may reflect the activity of dihydropyrimidine dehydrogenase. However, the monoclonal antibodies selective to pyrimidine have not been available. METHODS: Using 1-carboxymethyl-uracil as a hapten, in which steric conformation of uracil is thought to be well maintained, extensive screening was done to isolate a monoclonal antibody specific to uracil. RESULTS: We established the first monoclonal antibody that reacted with uracil and thymine but not with pseudouridine, dihydrouracil, dihydrothymine, cytosine, uridine, or N-carbamyl-beta-alanine at the concentration of 100 microg/ml. CONCLUSIONS: The monoclonal antibody can be used to develop a simple screening assay for patients with dihydropyrimidine dehydrogenase deficiency. This may increase the safety of 5-fluorouracil treatment.

Relationship between the induction of mitotic gene conversion and the formation of thymine glycols in yeast S. cerevisiae treated with hydrogen peroxide.

The effects of hydrogen peroxide on yeast Saccharomyces cerevisiae were assessed by measuring gene conversion at the trp 5 locus and the amount of thymine glycols in DNA using a monoclonal antibody specific to this base modification. Our results show that: (a) hydrogen peroxide-induced mitotic gene conversion in yeast strain D7M1 was dose-dependent in the low dose range where no toxicity was observed; (b) in the low dose range, the frequency of gene conversion depended on the temperature of the treatment, with more conversion at 25 degrees C than at 15 degrees C; (c) thymine glycols were induced in DNA in a dose-dependent manner following exposure of cells to up to 400 mM hydrogen peroxide; (d) there was little difference in the amount of thymine glycols formed in DNA when treatment occurred at either 25 degrees C or 15 degrees C.

Characterization of antibodies to dihydrothymine, a radiolysis product of DNA.

Antibodies to dihydrothymine were elicited by immunizing rabbits with dihydrothymidine monophosphate conjugated by carbodiimide to BSA. By use of an ELISA assay, the antibodies produced were found to be specific for dihydrothymine. Hapten inhibition studies showed that dihydrothymidine monophosphate was 3 orders of magnitude more effective as an inhibitor than thymidine monophosphate and 4 orders of magnitude more effective than thymidine glycol monophosphate. With DNA containing dihydrothymine, antibody reactivity was observed at 20 fmol of dihydrothymine, which is approximately 0.1 dihydrothymine per 10,000 bases. Thus, the assay is very sensitive. The antibody reacted with denatured DNA containing dihydrothymine but not with native DNA containing this lesion. The antibody was used for measurement of in vivo incorporation of dihydrothymidine in wild-type Escherichia coli or mutants defective in their ability to remove dihydrothymine from DNA or in the de novo synthesis of thymidylate. Lastly, antibodies to dihydrothymine were use to quantitate the formation of dihydrothymine in DNA X-irradiated under N2. Production of dihydrothymine in irradiated DNA correlated with the level of reducing species produced by X-rays, and dihydrothymine was produced preferentially in irradiated single-stranded or denatured DNA as compared to irradiated duplex DNA.

TMP-reactive autoantibodies in human SLE sera demonstrate thymine-dependent oligonucleotide specificity.

Autoantibodies present in the sera of lupus patients and specific for single-stranded (ss) DNA were fractionated into subsets based upon their reactivity towards 5' nucleotide haptens. As evaluated by ELISA testing, antibodies retained by TMP-agarose bound to TMP-BSA and ssDNA but not to other nucleotide-BSA conjugates or to double-stranded (ds) DNA. Competition-inhibition studies further revealed that TMP-enriched oligo- and polynucleotides were the preferred antigens for these affinity purified antibodies. Similar assays with sequence- or size- defined oligonucleotides further implied that those oligonucleotides comprised entirely of TMP residues were most antigenic and that antigenicity increased with size (length). These results document the existence of a TMP-dependent oligonucleotide specificity among a diverse population of autoanti-ssDNA antibodies.

The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation.

Somatic mutation is a fundamental component of acquired immunity. Although its molecular basis remains undetermined, the sequence specificity with which mutations are introduced has provided clues to the mechanism. We have analyzed data representing over 1700 unselected mutations in V gene introns and nonproductively rearranged V genes to identify the sequence specificity of the mutation spectrum-the distribution of resultant nucleotides. In other words, we sought to determine what effects the neighboring bases have on what a given base mutates "to." We find that both neighboring bases have a significant effect on the mutation spectrum. Their influences are complicated, but much of the effect can be characterized as enhancing homogeneity of the mutated DNA sequence. In contrast to what has been reported for the sequence specificity of the "targeting" mechanism, that of the spectrum is notably symmetric under complementation, indicating little if any strand bias. We compared the spectrum to that found previously for germline mutations as revealed by analyzing pseudogene sequences. We find that the influences of nearest neighbors are quite different in the two datasets. Altogether, our findings suggest that the mechanism of somatic hypermutation is complex, involving two or more stages: introduction of mis-pairs and their subsequent resolution, each with distinct sequence specificity and strand bias.

Characteristics of sequences around individual nucleotide substitutions in IgVH genes suggest different GC and AT mutators.

Somatic hypermutation affects Ig genes during T-dependent B cell responses and is characterized by a high frequency of single base substitutions. Hypermutation is not a completely random process; a study of mutations in different systems has revealed the presence of sequence motifs that target mutation. In a recent analysis of the sequences surrounding individual mutated bases in out-of-frame human IgVH genes, we found that the target motifs around mutated G's and C's are reverse complements of each other. This finding suggests that hypermutation acts on both strands of DNA, which contradicts evidence of a strand-dependent mechanism as suggested by an observed bias in A and T mutations and the involvement of transcriptional machinery. We have now extended our database of out-of-frame genes and determined the sequence motifs flanking mutated A and T nucleotides. In addition, we have analyzed the flanking sequences for different types of nucleotide substitutions separately. Our results confirm the relationship between the motifs for G and C mutations and show that the motifs surrounding mutated A's and T's are weaker and do not have the same relationship. Taken together with our observation of A/T strand bias in out-of-frame genes, this observation suggests that there is a semitargeted G/C mutator that is strand-independent and a separate A/T mutator that is strand-dependent and is less reliant on the local target sequence.

Immune suppression to nucleosides: differences between NZB and NZW mice.

Previous studies (Y. Borel and M.C. Young, Proc. Natl. Acad. Sci. USA 1980 77: 1593) have shown that one can raise nucleic acid-specific suppressor T cells which diminish either the T-dependent immune response in vivo or the T-independent immune response in vitro. The results presented here confirm and extend these observations in several different strains of mice. Administration of nucleoside-modified spleen cells diminishes antibody-forming cells to nucleoside in mice immunized with nucleoside linked to keyhole limpet hemocyanin (KLH), Immune suppression was obtained in all strains except SJL and NZW, which are known to be high responders to denatured DNA. Both the primary and secondary immune responses were suppressed in C57BL/6 mice. Autologous cells exhibit a different ability to function as carriers. Spleen cells are the most effective, and to a certain extent, thymus cells. In contrast, bone marrow cells and red cells fail to induce immune suppression. A strain difference was found between NZB and NZW mice in their susceptibility to immunosuppression by nucleoside-modified spleen cells. Whereas NZB mice are high responders to nucleoside-KLH, they were easily suppressed by nucleoside coupled to spleen cells. In contrast, NZW mice, although relatively low responders to nucleoside-KLH, were not suppressed by administration of nucleoside coupled to spleen cells. Both male and female (NZB X NZW) F1 mice appeared to behave like the NZW parental strain and were resistant to immunosuppression by nucleoside-modified spleen cells. The significance of this observation for the pathogenesis of murine systemic lupus erythematosus is discussed.