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PubMed1991

Chemical modification of DNA: quantitation of O6-methyldeoxyguanosine by tandem mass spectrometry.

Methodology is described which allows quantitation of O6-methyldeoxyguanosine generated as a product of in vitro methylation of calf thymus DNA by methyl methanesulfonate (MeMS). Quantitative precision of 10% is achieved on samples of 10(-11)-10(-12) mol generated in 0.02% yield (expressed as O6-methyldeoxyguanosine versus deoxyguanosine) when DNA is treated with the weak carcinogen MeMS. These results show the potential application of this method to the analysis of DNA chemical modifications at the low levels that are relevant to the induction of biological effects of many alkylating agents. The methodology utilizes enzymatic degradation, reverse-phase chromatography and finally analysis by tandem mass spectrometry using desorption chemical ionization. Multiple reaction monitoring was used to increase sensitivity and the CD3-labeled nucleoside was used as an internal standard for quantification.

Chromatography, High Pressure Liquid↗
PubMed1990

Mechanism of formation and 32P-postlabeling of DNA adducts derived from peroxidative activation of carcinogenic non-aminoazo dye 1-phenylazo-2-hydroxynaphthalene (Sudan I).

Horseradish peroxidase in the presence of hydrogen peroxide mediates the activation of carcinogenic 1-phenylazo-2-hydroxynaphthalene (Sudan I) to DNA-bound products in vitro. The peroxidase activating system is greater than 10 times more effective with respect to DNA modification by Sudan I than the microsomal enzymes containing cytochrome P450. The DNA-binding reaction of the Sudan I metabolite(s) formed by the peroxidase system is dependent on Sudan I and H2O2 concentration and pH. Reactive intermediate(s) or product(s) of the Sudan I oxidation by peroxidase with a short half-life are responsible for the DNA modification. DNA modified by peroxidase-activated Sudan I becomes colored and has an absorption maximum at approximately 480 nm. The modification of DNA by Sudan I metabolites(s) formed by the peroxidase system is inhibited by some compounds of physiological importance (ascorbate, glutathione, Mg2+ ions) and by radical trapping agents (nitrosobenzene, methyl viologen). 32P-Postlabeling assay of the DNA modified by Sudan I activated by the peroxidase system indicates that the covalent DNA adduct formation is the principal type of the DNA modification. Four major and several minor adducts of deoxyribonucleotide 3',5'-bisphosphate from DNA with Sudan I metabolite(s) were detected by the classical Randerath 32P-postlabelling assay as well as by the nuclease P1 version of the same method.

Animals↗
PubMed1998

Oxidative DNA base modifications as factors in carcinogenesis.

Reactive oxygen species can cause extensive DNA modifications including modified bases. Some of the DNA base damage has been found to possess premutagenic properties. Therefore, if not repaired, it can contribute to carcinogenesis. We have found elevated amounts of modified bases in cancerous and precancerous tissues as compared with normal tissues. Most of the agents used in anticancer therapy are paradoxically responsible for induction of secondary malignancies and some of them may generate free radicals. The results of our experiments provide evidence that exposure of cancer patients to therapeutic doses of ionizing radiation and anticancer drugs causes base modifications in genomic DNA of lymphocytes. Some of these base damages could lead to mutagenesis in critical genes and ultimately to secondary cancers such as leukemias. This may point to an important role of oxidative base damage in cancer initiation. Alternatively, the increased level of the modified base products may contribute to genetic instability and metastatic potential of tumor cells.

Animals↗
PubMed1994

Visible light generates oxidative DNA base modifications in high excess of strand breaks in mammalian cells.

The DNA damage induced by visible light in L1210 mouse leukaemia cells was analysed by an alkaline elution assay with specific repair endonucleases. DNA single-strand breaks and DNA modifications sensitive to FPG protein (formamidopyrimidine-DNA glycosylase), endonuclease III and exonuclease III were quantified in parallel. The light-induced cellular DNA damage was found to consist of many base modifications sensitive to FPG protein, which most probably are predominantly 7,8-dihydro-8-oxoguanine (8-hydroxyguanine) residues. Base modifications sensitive to endonuclease III are virtually absent. The yield of the FPG-sensitive base modifications is 10-fold higher than that of single-strand breaks plus AP sites (sites of base loss). The described ratios of the various modifications indicate that the damage most probably results from a reaction of DNA with singlet oxygen (type II reaction) or directly with an excited endogenous photosensitizer (type I reaction) and is not mediated by hydroxyl radicals. Experiments with cut-off filters indicate that wavelengths between 400 and 500 nm are responsible for most of the modifications. The FPG-sensitive base modifications are repaired efficiently (t1/2 approximately 1 h at 37 degrees C). This is perhaps why the light-induced DNA damage is apparently associated with only low mutagenicity.

Animals↗
PubMed1978

Effect of chemical modification of supercoiled simian virus 40 DNA on the rate of in vitro transcription.

Superhelical simian virus 40 FI DNA could be modified with the single-strand-specific reagent N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide (CMC). A limited reaction, of less than 2% of the base pairs, resulted in almost total inhibition of in vitro transcription by DNA-dependent RNA polymerase from Escherichia coli. This effect was shown to be due to DNA modification and not to inhibition of polymerase activity by the reagent. Inhibition of enzyme activity occurred if the contaminating reagent was not absorbed with another protein before polymerase addition. No inhibition was observed when DNA and polymerase were incubated together to allow the formation of pre-initiation complexes before CMC was added. Studies of template saturation with polymerase showed that the inhibition of transcription by DNA modification was due to a loss of binding ability of the enzyme to the reacted, supercoiled DNA when reaction times of less than 2 h were used.

CME-Carbodiimide↗
PubMed2026

DREAMS illuminates spatial DNA and RNA modification landscapes.

DNA and RNA modifications regulate gene expression and RNA processing, but their spatial organization in complex tissues remains elusive. Here we developed DNA RNA Elements Areal Mass Spectrometry (DREAMS), a mass spectrometry imaging platform that spatially maps diverse nucleic acid modifications simultaneously. Applying DREAMS to TET-deficient mouse brains (Tet1Δ/Δ and triple Tet1/2/3Δ/Δ), we uncover TET1's unexpected role in modulating N1-methyladenosine (m1A), a pivotal RNA modification. While DREAMS reveals broad modification landscapes altered across TET knockouts, we identify TET1-mediated changes in m1A that correlate with transcriptome alterations. Our work establishes DREAMS as a transformative tool for spatial epigenomics/epitranscriptomics and suggests that TET enzymes could influence multiple DNA and RNA modifications with potential gatekeeping roles in nucleic acid regulation.

Animals↗
PubMed1993

Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition.

We have characterized a novel mutant of EcoDXXI, a type IC DNA restriction and modification (R-M) system, in which the specificity has been altered due to a Tn5 insertion into the middle of hsdS, the gene which encodes the polypeptide that confers DNA sequence specificity to both the restriction and the modification reactions. Like other type I enzymes, the wild type EcoDXXI recognizes a sequence composed of two asymmetrical half sites separated by a spacer region: TCA(N7)RTTC. Purification of the EcoDXXI mutant methylase and subsequent in vitro DNA methylation assays identified the mutant recognition sequence as an interrupted palindrome, TCA(N8)TGA, in which the 5' half site of the wild type site is repeated in inverse orientation. The additional base pair in the non-specific spacer of the mutant recognition sequence maintains the proper spacing between the two methylatable adenine groups. Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl-terminal DNA binding domain which recognizes the 3' half of the EcoDXXI binding site. The truncated hsdS gene still encodes both the amino-terminal DNA binding domain and the conserved repeated sequence that defines the length of the recognition site spacer region. We propose that the EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize its binding site. The implications of this finding in terms of subunit interactions and the malleability of the type I R-M systems will be discussed.

Base Sequence↗
PubMed1994

The interaction of intercalators and groove-binding agents with DNA triple-helical structures: the influence of ligand structure, DNA backbone modifications and sequence.

The effects of ligand structure and properties, DNA backbone modifications and DNA sequence on the interaction of a variety of well-known groove-binding agents and intercalators with DNA duplexes and triplexes have been evaluated by thermal melting experiments and molecular modeling. Both methylphosphonate and phosphorothioate substitutions generally destabilize DNA duplexes and triplexes. Modified duplexes can be strongly stabilized by both groove-binding agents and intercalators whereas triplexes are primarily stabilized by intercalators. Of the compounds tested, the intercalators coralyne and quinacrine provide the largest stabilization of the triplex dT19.dA19.dT19. Molecular modeling studies suggest that the large intercalating ring system of coralyne stacks well with the triplex bases whereas the alkylamino side chain of quinacrine fits snugly into the remaining space of the major groove of dT19.dA19.dT19 triplex and forms extensive van der Waals contacts with the thymine methyl groups that line the groove. Converting some of the T.A.T base triples to C+.G.C (e.g. dT19.dA19.dT19 to d(T4C+)3T4.d(A4G)3A4.(T4C)3T4) causes very significant decreases in observed Tm increases for compounds such as quinacrine and coralyne. Although removal of thymine methyl groups and addition of positive charge on substitution of C+.G.C for T.A.T should reduce binding of cationic intercalators, the large difference observed between the pure AT and the mixed sequence triplexes suggest that they may also have differences in structure and properties.

Base Sequence↗
PubMed1986

Modification of DNA and metabolism of ethyl carbamate in vivo: formation of 7-(2-oxoethyl)guanine and its sensitive determination by reductive tritiation using 3H-sodium borohydride.

The modification of liver DNA of mice and rats by ethyl carbamate and its putative proximate metabolite, vinyl carbamate, has been investigated. Following treatment with [ethyl-1-14C]-ethyl carbamate, the main radioactive DNA adduct was identified as 7-(2-oxoethyl)guanine by cochromatography with the authentic marker in several separation systems. After reduction by sodium borohydride (NaBH4) to 7-(2-hydroxyethyl)guanine, the radioactive material again cochromatographed with the respective marker. Reduction of modified liver DNA by 3H-NaBH4, following administration of unlabelled ethyl carbamate or vinyl carbamate, allowed the quantitation of 7-(2-oxoethyl)guanine (as 7-(2-hydroxy-2-[3H]-ethyl)guanine). Vinyl carbamate led to about 100 times as much 7-(2-oxoethyl)guanine (on a molar basis) as did ethyl carbamate. Both the formation of 7-(2-oxoethyl)guanine by ethyl carbamate and vinyl carbamate, and the much higher activity of the latter compound, strongly support the existence of the metabolic activation pathway, ethyl carbamate----vinyl carbamate----epoxyethyl carbamate, as proposed by Dahl et al. (1978, 1980). The possible role of 7-(2-oxoethyl)guanine in the initiation of the carcinogenic process is discussed in view of the structural equilibrium with its hemiacetal conformation, O6,7-(1'-hydroxyethano)guanine. In the latter conformation, it is assumed to represent a promutagenic lesion. In addition, intrastrand cross-links between modified guanine and adjacent cytosine or adenine seem possible and may have promutagenic consequences. Replication of DNA containing such lesions may lead to the induction of mutations. This may be a critical event in the initiation, and eventually progression, of the carcinogenic process as determined by ethyl carbamate and other carcinogens, such as vinyl chloride, which lead to the same DNA modification.

Animals↗
PubMed1986

Modification of calf thymus DNA by methyl methanesulfonate. Quantitative determination of 7-methyldeoxyguanosine by mass spectrometry.

Quantitation of 7-methyldeoxyguanosine (m7dG) produced in the in vitro methyl methanesulfonate (MeMS) action on calf-thymus DNA is achieved by enzymatic degradation, liquid chromatographic separation and chemical ionization mass spectrometry. The total degree of methylation, measured by uptake of [14C]MeMS was 0.35%. Mass spectral analysis shows that m7dG constitutes 84% of the total methylated product. It is also shown that tandem mass spectrometry allows detection of m7dG, as the protonated base, down to 1 pmol level, suggesting that MS/MS analysis can be the method of choice in quantitation of the adducts of in vivo DNA modifications.

Animals↗
PubMed1983

Site specific cleavage of phi X-174 replicative form DNA after modification by N-acetoxy-N-2-acetylaminofluorene.

Three kinds of structural disturbances were found in an 88 base pair (bp) fragment of phi X-174 DNA after exposure to N-acetoxy-N-2-acetylaminofluorene (N-Aco-AAF). (i) Frequent strand scissions at two specific guanine sites on the 5' 32P-end-labeled fragment were identified by base sequence analysis. Scissions at these two sites were induced at neutral pH and they were not increased by treatment with apurinic endonuclease. They are an immediate consequence of N-Aco-AAF action and are not primarily apurinic sites. (ii) Alkali treatment with 1 M piperidine at 90 degrees C induced strand scissions at every guanine, demonstrating adduct slices, depurination and strand scissions. (iii) Adducted DNA was sensitive to single-strand specific nuclease digestion, suggesting unwound DNA. These studies indicate the prediliction of N-Aco-AAF for certain DNA sites and they suggest three kinds of DNA modifications which can be expected after adduction by this carcinogen. Some of the sites may be premutational carcinogen-induced DNA structural modifications.

2-Acetylaminofluorene↗
PubMed1998

Fanconi's anaemia cells have normal steady-state levels and repair of oxidative DNA base modifications sensitive to Fpg protein.

Cells from Fanconi's anaemia (FA) patients are abnormally sensitive to oxygen. However, a distinct genetic defect in either the cellular defence against reactive oxygen species (ROS) or in their metabolic generation has not been identified to date. Recently, the gene for the human 8-hydroxyguanine (8-oxoG) glycosylase, which removes this oxidative base modification from the genome, has been localized on chromosome 3p25, i.e., in the same region as the FA complementation group D (FAD) gene. We therefore studied the removal of photosensitization-induced 8-oxoG residues from the DNA of FA cells, using Fpg protein, the bacterial 8-oxoG glycosylase, to quantify the lesions by alkaline elution. Similar repair kinetics (approx. 50% removal within 2 h) were observed in Epstein-Barr virus (EBV) immortalized lymphoid cells from FA complementation groups A, B, C and D and in control cells from normal donors, as well as in primary fetal lung fibroblasts not yet assigned to a specific complementation group. The susceptibility for the induction of oxidative DNA modifications by photosensitization was similar in all cells. In addition, the background (steady-state) levels of Fpg-sensitive oxidative DNA base modifications, which reflect the balance between generation and removal of the lesions, were similar in control and FA cells. It is concluded that both the generation and the overall removal of 8-oxoG residues in nuclear DNA is not impaired in FA cells.

Cell Division↗
PubMed1987

Light-induced modifications of DNA by gilvocarcin V and its aglycone.

Gilvocarcins are antitumor agents that have been reported to damage DNA upon activation by visible light. This activation is dependent on interaction with DNA. Here it is shown that gilvocarcin V and its synthetic aglycone analogue can both introduce single-strand scission into plasmid DNA. Light irradiation is required for the reaction. The binding of gilvocarcin V to plasmid DNA in the absence of light decreased the DNA linking number in a fashion similar to known intercalating agents such as ethidium bromide. The use of oligonucleotides as substrates for gilvocarcin V demonstrated that one of the steps of the reaction following binding of gilvocarcin V to DNA involves covalent modification at thymidine and to a lesser extent, cytosine residues.

Aminoglycosides↗
PubMed1999

Modification of DNA bases by photosensitized one-electron oxidation.

PURPOSE: To determine the distribution of base damage within isolated DNA upon oxidation by three type I photosensitizers in aerated aqueous solution. MATERIALS AND METHODS: Aqueous solutions of DNA were exposed to UVA in the presence of riboflavin, benzophenone or menadione. Then, eight modified nucleobases were measured, using HPLC-EC, GC-MS or HPLC with fluorescence detection. RESULTS: The three photosensitizers led to a predominant degradation of guanine bases within DNA. The relative yield of the three main guanine degradation products measured in DNA was similar with the three sensitizers. 8-OxodAdo was also produced in an almost constant yield with respect to its guanine analogue. The yield of oxidized pyrimidines was lower and was found to depend on the photosensitizer used. The results were compared with the yield of photosensitization-induced degradation of the 2'-deoxyribonucleosides. CONCLUSION: The favoured photosensitized degradation of guanine within DNA may be explained by its lower oxidation potential with respect to that of the other bases, together with the occurrence of charge transfer through DNA. The base modification pattern determined in the present work is different from that obtained upon reaction of hydroxyl radicals. Under the latter conditions, pyrimidine oxidation products were generated more efficiently than by photosensitized one-electron oxidation.

Benzophenones↗
PubMed1976

A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA.

Genetic analyses of DNA restriction and modification mechanisms have been encumbered by the inability to rigorously select for mutant phenotypes associated with these systems. The application of restriction endonucleases has now proved to be a successful approach to the genetic analyses of small genomes that are recalcitrant to the more standard genetic techniques. Restriction endonucleases EcoRI and HindIII were used to analyze the structure of the plasmid genome responsible for the EcoRI restriction endonuclease and modification methylase. This plasmid in the original clinical isolate of Escherichia coli appears to be identical to the ColE 1 plasmid except for a 1.95 kilobase pair segment which contains these genes. A preliminary restriction map of this plasmid is presented.

Base Sequence↗
PubMed1999

Influence of glutathione levels and heat-shock on the steady-state levels of oxidative DNA base modifications in mammalian cells.

The effects of thiols, ascorbic acid and thermal stress on the basal (steady-state) levels of oxidative DNA base modifications were studied. In various types of untreated cultured mammalian cells, the levels of total glutathione were found to be inversely correlated with the levels of DNA base modifications sensitive to the repair endonuclease Fpg protein, which include 8-hydroxyguanine (8-oxoG). A depletion of glutathione by treatment with buthionine sulphoximine increased the steady-state level in AS52 Chinese hamster cells by approximately 50%. However, additional thiols in the culture medium did not reduce the level of Fpg-sensitive base modifications: 0-10 mM N-acetylcysteine had no effect, whereas cysteine ethylester even increased the oxidative DNA damage at concentrations >0.1 mM. Similarly, ascorbic acid (0-20 mM) failed to reduce the steady-state levels. When AS52 cells were grown at elevated temperature (41 degrees C), the steady-state level of the oxidative DNA modifications increased by 40%, in spite of a concomitant 1.6-fold increase of the cellular level of total glutathione. Depletion of glutathione at 41 degrees C nearly doubled the already elevated level of oxidative damage. A constitutive expression of the heat-shock protein Hsp27 in L929 mouse fibrosarcoma cells at 37 degrees C increased the glutathione level by 60%, but had little effect on the level of oxidative DNA damage.

Animals↗
PubMed1998

DNA damage in mononuclear leukocytes of farmers measured using the alkaline comet assay: modifications of DNA damage levels after a one-day field spraying period with selected pesticides.

The alkaline comet assay was used to assess DNA damage in mononuclear leukocytes of farmers before and after a 1-day spraying period with selected pesticides under usual conditions. Two blood samples were collected, one in the morning of the day of spraying (S0) and the second in the morning of the day after (S1). Here, we assessed variations in DNA damage levels between these two sampling times. Four groups of farmers were formed, according to exposure to: (a) various fungicide-insecticide mixtures (including chlorothalonil; group 1, n = 8), (b) the herbicide isoproturon (group 2, n = 11), (c) fungicide triazoles (group 3, n = 14), and (d) a fungicide (chlorothalonil)-insecticide mixture (group 4, n = 8). An increase in DNA damage levels was observed at S1 for groups 1 and 4, who were exposed to similar pesticides. This increase was correlated with area sprayed between S0 and S1 and with the number of spraying tanks used over this 1-day period. No effect was observed on cell viability or on hematological parameters for these two groups. No statistically significant modification of DNA damage level was observed the day after spraying for groups 2 and 3, when each was observed as a whole. However, some farmers presented significantly more DNA damage after exposure, and others presented less damage. In these two groups, a significant decrease of neutrophils was observed at S1, and a decrease of red blood cells was observed in group 3. In parallel, a significant loss of lymphocyte viability was observed in these two groups. A 1-day spraying period seems to be sufficient to significantly modify DNA damage levels in mononuclear leukocytes, but the correlation of this change with pesticide-related exposure parameters depends on the kind of pesticide concerned.

Adult↗