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At least 1,153 records · Page 64Linked to original sources
PubMed1983

New methods for detection of low levels of DNA damage in human populations.

The use of a postlabeling method to characterize and to detect infrequent base modifications in DNA is outlined. This method has the advantage that low levels of DNA modifications, approximately 1 modified base per 10(5) nucleotides, can be detected. Moreover, a broad spectrum of modification can be identified by using this methodology. The basis for the method involves transfer of a radioactive phosphate from the gamma position of ATP to the 5'-hydroxyl terminus of 3'-phosphoryl nucleotides that are derived from modified DNA by appropriate nuclease digestion. The second method involves use of a defined DNA sequence within human cells. The alpha sequence is used as a probe for DNA damage to specific nucleotides. The alpha DNA sequence is reiterated approximately 300,000 times in the human genome and exists in tandem arrays. It comprises approximately 1% of the entire genome. The reiterated sequence is sufficiently homogeneous to permit its use as a probe for a site specific in DNA damage. Examples of the application of both of these methodologies to DNA damage inflicted in human cells by chemicals and ultraviolet light are provided.

Alkylating Agents↗
PubMed1984

Implications of multiple mechanisms of carcinogenesis for short-term testing.

The attempt has been made recently to categorize carcinogens into two mechanistic types based on their mechanism of action: genotoxic (capable of reacting with and damaging DNA) and epigenetic (unable to damage DNA to any detectable extent). By requiring that a given chemical fit into one or the other of these narrowly defined categories for regulatory purposes, we are probably oversimplifying potential biological effects. In fact, based on our limited understanding of carcinogenic mechanisms, this artificial distinction should probably be abandoned in favor of a more precise statement of each chemical's mechanism or relative potency of initiating and promoting effects. Since the standard short-term tests by which carcinogenicity of chemicals is screened were designed to detect certain chemical classes with active electrophilic intermediates, weak or specialized carcinogens may be missed and may be assumed erroneously to be nongenotoxic. The mechanisms of carcinogenicity for such carcinogens may include particulate deposition, active radical formation, liver toxicity, and hormonal interactions. Not all of these secondary mechanisms depend upon a detectable level of binding to DNA, damage to DNA, or modification of the DNA sequence, even though they may demonstrate other characteristics of a complete carcinogen (that is, irreversibility and lack of a threshold). Certain agents have been labeled as epigenetic. However, a consideration of the literature on sample agents (diethylstilbestrol, asbestos, and urethane) reveals that these are not epigenetic carcinogens despite their being labeled as such. Agents with irreversibility and no threshold have initiating potential and, as such, are genotoxic, whereas carcinogens that are classified as nongenotoxic are largely agents that promote the growth of liver tumors. Even promotion can be a mechanistically specialized phenomenon. For example, some promoters are cytotoxic to the liver, but not all liver toxins are liver tumor promoters or liver carcinogens. Further, the carcinogens commonly labeled as epigenetic might cause a unique specialized genotoxicity not detected by common screening tests routinely used for detecting genotoxicity. If we assume that this unrecognized but necessary initiating potential is mediated by some specialized genotoxicity, extra care must be taken to establish a genuine lack of genotoxicity before an agent can be classified (and regulated) as a promoter (lacking the ability to initiate tumor growth but still enhancing tumor development).(ABSTRACT TRUNCATED AT 400 WORDS)

Asbestos↗
PubMed2000

The feasibility of PCR-based diagnosis of Prader-Willi and Angelman syndromes using restriction analysis after bisulfite modification of genomic DNA.

We have developed a novel PCR-based method for studying DNA methylation in the proximal region of 15q, using restriction analysis after bisulfite treatment of genomic DNA. This protocol can be used for the diagnosis of Prader-Willi and Angelman syndromes. Unlike the recently reported methylation-specific PCR protocol, our method avoids the use of multiplex amplification, thus overcoming the need to adjust relative primer amounts and the risk of obtaining false-negative results.

Angelman Syndrome↗
PubMed1980

Modification of the DNA content in translocated regions of Drosophila polytene chromosomes.

The DNA content of translocated polytene chromosome regions in Drosophila melanogaster is affected by heterochromatic position effect. Microdensitometric studies on wm258-21 translocation heterozygotes showd (Hartmann-Goldstein and Cowell, 1976; Cowell and Hartmann-Goldstein, 1980) that band region 3D1-E2, adjacent to the breakpoint, contained less DNA than the homologous non-translocated region whereas the neighbouring 3C1-10 region contained more DNA than its non-translocated counterpart. In the nuclei selected for measurement the translocated X chromosome was morphologically euchromatic, but both regions undergo heterochromatisation in other nuclei within the same salivary gland. To explore the relationship between changes in DNA content and heterochromatisation, the effect on DNA content of two known modifiers of heterochromatisation has now been studied. Larvae cultured at 15 degrees C, which exhibit more heterochromatisation than those grown in 25 degrees C, have the same relative DNA contents as at the higher temperature. The addition of a Y chromosome markedly reduced heterochromatisation; in XXY larvae there was no difference between the DNA contents of translocated and non-translocated 3D1-E2 regions, and in region 3C1-10 the percentage excess of DNA in the translocated homolgue was approximately double that found in XX larvae. The relationship between replication behaviour and compaction suggested by these results is discussed.

Animals↗
PubMed1990

Base modifications in plasmid DNA caused by potassium permanganate.

KMnO4 is a powerful oxidizing agent which has been used to modify DNA bases. In previous studies, mild KMnO4 treatment has been shown to preferentially modify Thy; Cyt and Gua are modified only under harsher conditions to as yet unidentified products. In the present study, denatured plasmid pCMV beta gal DNA was exposed to 0.015-1.5 mM KMnO4, pH 8.6, at 4 degrees C for 5 min, after which the DNA was hydrolyzed in formic acid, trimethylsilylated, and analyzed for modified base content by gas chromatography-mass spectrometry/selected ion monitoring. KMnO4 treatment, even at concentrations as low as 0.015 mM, caused a concentration-dependent increase in the Thy products Thy glycol and 5-hydroxy-5-methylhydantoin, the Cyt products Cyt glycol, 5,6-dihydroxycytosine, and 5-hydroxyhydantoin, the Ade product 8-hydroxyadenine, and the Gua product 8-hydroxyguanine. The Ade product 4,6-diamino-5-formamidopyrimidine and the Gua product 2,6-diamino-4-hydroxy-5-formamidopyrimidine were minimally (less than or equal to 2-fold) increased by treatment with greater than or equal to 0.8 mM KMnO4. These data demonstrate that, in addition to Thy, Cyt, Gua, and Ade bases in plasmid DNA may be modified by treatment with KMnO4, even under mild conditions. They represent the first identification of Cyt, Gua, and Ade products caused by KMnO4 treatment. Furthermore, these data suggest that previous studies which have used treatment with KMnO4 to study the mutagenicity of Thy glycol specifically or as a Thy-specific probe in DNA structure should be interpreted with caution.

Adenine↗
PubMed1992

Circadian rhythm of covalent modifications in liver DNA.

32P-postlabeling analysis recently revealed that in addition to 5-methylcytosine, mammalian DNA contains covalently modified nucleotides of unknown structures and functions termed I-compounds whose levels increase with age. I-compound levels, in addition, depend on species, strain, sex, tissue, and diet and are generally lowered by carcinogen exposure. As shown here, levels of several non-polar I-compounds in liver DNA of untreated male C3H mice were elevated 2 to 8.5 times at 1800 h and 2400 h as compared to 0600 h and 1200 h, while polar I-compounds and persistent carcinogen-DNA adducts induced by safrole were unaffected by time of day. In liver DNA of male F-344 rats 4 non-polar I-compounds and 4 polar I-compounds showed significant circadian rhythm at 2000 h compared to 0800 h. This novel circadian variation of DNA structure implies mechanisms precisely regulating I-compound levels in vivo and may conceivably be linked to diurnal differences of DNA synthesis and gene expression.

Animals↗
PubMed1980

Carcinogenic purine N-oxide ester modifies covalently all common bases in polynucleotides.

The carcinogen 1-methyl-3-hydroxyxanthine after esterification binds covalently to polynucleotides, RNA and DNA. All four ribopolynucleotides and poly(dT) are targets. Depending on reaction conditions, covalent binding is greatest to poly(A) followed by poly(U), poly(dT), poly(G), poly(C), RNA and DNA. Maximal covalent modification of DNA is one moiety per 360 nucleotides. All modified polynucleotides, RNA and DNA, except poly guanylic acid have been enzymatically digested and the major adducts characterized as nucleosides.

Binding Sites↗
PubMed1992

Structure of UvrABC excinuclease-UV-damaged DNA complexes studied by flow linear dichroism. DNA curved by UvrB and UvrC.

The interaction between UvrABC excinuclease from Escherichia coli and ultraviolet light-(UV) damaged DNA was studied by flow linear dichroism. The dichroism signal from DNA was drastically decreased in intensity upon incubation with UvrA and UvrB or whole enzyme in the presence of effector ATP. The change was specific for UV-damaged DNA, and a concluded suppressed DNA orientation suggests the wrapping of DNA around the protein. The incubation with the UvrC subunit alone also somewhat reduces the signal, however, in this case the change was smaller and not specific for UV-damaged DNA. The structural modification of DNA, promoted by the (UvrA2-UvrB) complex, probably facilitates or stabilizes the interaction of the UvrC subunit with DNA for the excision.

Adenosine Triphosphatases↗
PubMed1981

O6-alkylguanine and structural modifications in liver DNA of dialkylnitrosamine-treated rats.

Isolated rat liver DNA was fractionated on benzoylated-naphthoylated-DEAE-cellulose (BND-cellulose) columns. In experiments with dimethyl-nitrosamine (DMN)-treated (1-30 mg/kg) rats killed 24 h after injection, the amount of DNA eluting in the formamide fraction (i.e., containing single-stranded or partially denatured regions) was increased in a dose-dependent way. The absence of an effect at 6 days after DMN indicated that above regions disappear much more rapidly from rat liver DNA than do those DMN-induced lesions that give rise to more persistent DNA fragmentation in alkaline sucrose gradients. This indicates that 2 different lesions are involved. When the extents of alkylation at the O6- and 7-position of guanine in the NaCl-eluted and formamide-eluted DNA were compared, no significant differences were observed. Our results indicate that, at least in the present system, neither the presence nor the repair of O6-alkylguanine is related to the formation of single-stranded regions in rat liver DNA.

Animals↗
PubMedDate not supplied

Modification of lymphocyte DNA synthesis by alpha 1-antitrypsin.

Purified human alpha 1-antitrypsin (alpha 1-AT) was shown to inhibit 3H-thymidine incorporation into mouse or human lymphocytes stimulated by various mitogens or by allogeneic cells. In the mouse, both B- and T-cell responses were affected. In the human, proliferative responses of peripheral blood lymphocytes, thymocytes and T-enriched tonsillar lymphocytes to phytohaemagglutinin were inhibited as well as that of tonsillar lymphocytes to Salmonella typhi-murium lipopolysaccharide. Spontaneous 3H-thymidine incorporation was moderately and inconstantly decreased, without evidence of altered cell viability. The inhibitory effect of alpha 1-AT appears to be related to its protease inhibitory capacity. These data bring further evidence for the role of proteolytic enzymes in the early events of lymphocyte activation, and support the hypothesis that serum inhibitors of proteases may contribute to the modulation of the immune response.

Animals↗
PubMed1988

Modification of the DNA colony hybridization technique for multiple filter analysis.

Inexpensive fiberglass mesh window screens were used as spacers between colony blot filters to increase the number of bacterial isolates that could be tested by DNA colony hybridization. Sixty filters with up to 48 isolates per filter were tested at one time. This modified technique reduced the amount of radiolabelled probe and other materials needed for simultaneous analysis of up to 2880 test isolates.

Animals↗
PubMed2005

A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening.

We have developed a nonradioactive assay method for DNA methyltransferases based on the ability to protect substrate DNA from restriction. DNA immobilized to a microplate well was treated sequentially with methyltransferase and an appropriate endonuclease. The amount of methylated DNA product is reflected by a proportional decrease in endonuclease cleavage, which is in turn reflected by increased retention of the end-labeled affinity probe. A single universal substrate was designed to assay multiple methyltransferases including those that do not have a cognate endonuclease. The methodology developed is suited to screen a large number of compounds for inhibitors of various methyltransferases.

Base Sequence↗