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At least 307 records · Page 17Linked to original sources

PubMed1999

Acute elevation by short-term dietary restriction or food deprivation of type I I-compound levels in rat liver DNA.

Type I I-compounds are bulky endogenous DNA modifications detectable by 32P postlabeling that exhibit age, species, tissue, genotype, gender, and diet dependence. Their formation appears unrelated to oxidative stress. In fact, several lines of indirect evidence suggest that many type I I-compounds may represent normal functional DNA modifications. For example, long-term dietary restriction (DR), which retards the development of age-related diseases including cancer and extends median and maximum life spans, unexpectedly elicits significant increases rather than decreases in the levels of many I-compounds in different rodent tissues. Positive linear correlations have been observed between such levels and median life spans of the animals. In the present work we have investigated 1) whether elevation of I-compound levels does not depend on chronic DR, i.e., occurs after a short period of DR or fasting, and 2) whether I-compound levels return to control values after the animals are returned to unrestricted feeding after food deprivation. Female Fischer 344 rats (approx 140 g each) were randomized into three groups. Group I was fed a natural ingredient (Purina 5001) diet ad libitum (AL) throughout the study, Group 2 was switched to 60% of the AL amount (40% DR) at 0 hour, and Group 3 was given no food for up to 72 hours and then returned to AL feeding until the end of the experiment. Liver DNA of individual rats (n = 4) was isolated for I-compound analysis at 24, 72, and 240 hours. Restricted and food-deprived rats showed elevated levels of hepatic I-compounds, with fasting eliciting the highest levels. These effects were seen as early as the 24-hour time point. Refeeding after 72 hours of food deprivation restored the levels to control values, measured at 240 hours. Our observations are discussed in relation to carcinogenesis and tumor promotion. The almost instantaneous changes of endogenous DNA modifications showed their exquisite sensitivity to nutritional factors and provided strong new evidence for precise regulation of their formation and removal.

Animals↗

PubMed2000

Combined effects of okadaic acid and cadmium on lipid peroxidation and DNA bases modifications (m5dC and 8-(OH)-dG) in Caco-2 cells.

Okadaic acid (OA) is a marine toxin, a tumour promoter and an inducer of apoptosis. It mainly inhibits protein-phosphatases, protein synthesis and enhances lipid peroxidation. Cadmium (Cd) is known to be carcinogenic in animals and humans (group 1 according to the International Agency for Research on Cancer (IARC) classification). Cd also induces oxidative stress in living organisms. Since they are sometimes found simultaneously in mussels, we have evaluated in the present investigation, the lipid peroxidation, as malondialdehyde (MDA) production, in the variation of the ratios of 8-(OH)-dG/10(5)dG and m5dC/(dC + m5dC) induced by OA and/or Cd in Caco-2 cells. When cells were treated exclusively by OA (15 ng/ml) or Cd (0.625 and 5 microg/ml) for 24 h, protein synthesis was inhibited (by 42 +/- 5%, 18 +/- 13%, and 90 +/- 4% respectively) while MDA production was 2,235 +/- 129, 1710 +/- 20, and 11,496 +/-1,624 pmol/mg protein respectively. In addition, each toxicant induced modified bases in DNA; increases in oxidised bases and methylated dC. The combination of OA and cadmium was more cytotoxic and caused more DNA base modifications; the ratio m(5)dC/(m(5)dC + dC) was increased from 3 +/- 0.15 to 9 +/- 0.15 and the ratio 8-(OH)-dG/10(5) dG also (from 36 +/- 2 to 76 +/- 6). The combination of OA and Cd also increased the level of MDA (1,6874 +/- 2,189 pmole/mg protein). The present results strongly suggest that DNA damage resulting from the oxidative stress induced by these two toxicants may significantly contribute to increasing their carcinogenicity via epigenetic processes.

5-Methylcytosine↗

PubMed2006

Chromatin modifications and DNA double-strand breaks: the current state of play.

The packaging and compaction of DNA into chromatin is important for all DNA-metabolism processes such as transcription, replication and repair. The involvement of chromatin modifications in transcriptional regulation is relatively well characterized, and the distinct patterns of chromatin transitions that guide the process are thought to be the result of a code on the histone proteins (histone code). In contrast to transcription, the intricate link between chromatin and responses to DNA damage has been given attention only recently. It is now emerging that specific ATP-dependent chromatin remodeling complexes (including the Ino80, Swi/Snf and RSC remodelers) and certain constitutive (methylation of lysine 79 of histone H3) and DNA damage-induced covalent histone modifications (the most well characterized being the rapid phosphorylation of histone H2A) facilitate responses to double-strand breaks. Indeed, evidence is already accumulating for a DNA repair-specific histone code. In this review, the recent advances in our understanding of the relationship between chromatin modifications and double-strand break signaling and repair is discussed.

Animals↗

PubMed2026

TRIM28 regulates the G2/M transition via histone modification and DNA damage repair during mouse oocyte meiosis.

TRIM28, a member of the tripartite motif (TRIM) family, functions as a transcriptional coregulator involved in maintaining genome stability during mitosis. In this study, we explored the role of TRIM28 in mouse oocyte meiotic maturation, where transcriptional activity is barely detectable. We found that TRIM28 was constitutively expressed during the early stages of oocyte meiotic maturation, with predominant nuclear localization in germinal vesicle (GV)-stage oocytes. TRIM28 depletion caused defective germinal vesicle breakdown (GVBD), but oocytes that successfully underwent GVBD displayed unimpaired first polar body (PB1) extrusion. TRIM28 depletion impaired CDK1 activity and reduced cyclin B1 levels, leading to a delay in the G2/M transition. This delay might be caused by altered levels of HDAC2-mediated H4K12ac and H3K4me2-modulated H3K9me2 in nonsurrounded nucleolus (NSN)-type GV oocytes, which decreased transcription activity. Additionally, TRIM28-depleted oocytes exhibited elevated γ-H2A.X expression, accompanied by aberrant expression of CHK1 and CHK2, as well as dysregulated expression of RAD51, which collectively contributed to GVBD failure in mouse oocytes. In conclusion, our findings indicate that TRIM28 participates in the regulation of the G2/M transition during mouse oocyte meiotic maturation, acting through the modulation of histone modifications and DNA damage repair.

Animals↗

PubMed1989

Base and conformational specificity of an amine modification of DNA.

We have investigated the site and conformational preference of the reaction of a formaldehyde/amine reagent with DNA. Previous investigations of this laboratory have established that this reagent will react with native DNA, placing a positively charged amine moiety on the duplex that will survive exhaustive dialysis. The resulting adduct is duplex and base stacked in character, possessing B backbone geometry with a higher average winding angle and exhibiting remarkable stability with respect to the A-form, Z-form, or the single-strand denaturated species. In this current investigation, we have found that the stability of the adduct is dramatically reduced if the DNA is converted to mononucleotides, thus obviating the usual approach of nuclease digestion and chromatography for the identification of the modified nucleotides. Using indirect approaches, we have established that the reactive site that survives removal of the equilibrium concentrations of CH2O and amine is the exocyclic amino group of the guanine bases. This conclusion is based on (1) the positive correlation between GC content and the extent of adduct formation under standard reaction conditions (27 degrees C, 0.63M CH2O, 0.007M n-butylamine, pH 7); (2) decreases in the level of substitution of amine in DNA, which has this site blocked by trinitrobenzene modification; and (3) failure of poly(dI-dC) to retain amine upon dialysis. Raman spectra of the derivatized poly(dG-dC) show enhanced 2'-endo B character, with no marked shifts in the position of any of the lines, indicating the absence of any ring structures involving the N7 and the 06 of G. In standard reaction mixtures, other sites may react but this phenomenon appears to be minimal under conditions that do not favor fluctuational opening of base pairs. In the latter case, excess loading of amine on high GC content polymers produces a CD spectrum that is similar to one produced by poly(dA-dT) in the "X"-form [M. Vorlickova, E. Minyat, and J. Kypr (1984) Biopolymers 23, 1-4]. This conformation is lost, however, upon removal of excess reagents by dialysis and cannot be reestablished, in the absence of unbound amine and formaldehyde. The reaction is specific for the B-form of polynucleotides as demonstrated by the failure of poly(dG-m5dC) in the stable Z-form to exhibit substantial reaction. The B-form of this polymer will react readily with the retention of 0.23 moles amine/mole nucleotide under our standard reaction conditions.(ABSTRACT TRUNCATED AT 400 WORDS)

Amines↗

PubMed2006

Roles of PriA protein and double-strand DNA break repair functions in UV-induced restriction alleviation in Escherichia coli.

It has been widely considered that DNA modification protects the chromosome of bacteria E. coli K-12 against their own restriction-modification systems. Chromosomal DNA is protected from degradation by methylation of target sequences. However, when unmethylated target sequences are generated in the host chromosome, the endonuclease activity of the EcoKI restriction-modification enzyme is inactivated by the ClpXP protease and DNA is protected. This process is known as restriction alleviation (RA) and it can be induced by UV irradiation (UV-induced RA). It has been proposed that chromosomal unmethylated target sequences, a signal for the cell to protect its own DNA, can be generated by homologous recombination during the repair of damaged DNA. In this study, we wanted to further investigate the genetic requirements for recombination proteins involved in the generation of unmethylated target sequences. For this purpose, we monitored the alleviation of EcoKI restriction by measuring the survival of unmodified lambda in UV-irradiated cells. Our genetic analysis showed that UV-induced RA is dependent on the excision repair protein UvrA, the RecA-loading activity of the RecBCD enzyme, and the primosome assembly activity of the PriA helicase and is partially dependent on RecFOR proteins. On the basis of our results, we propose that unmethylated target sequences are generated at the D-loop by the strand exchange of two hemi-methylated duplex DNAs and subsequent initiation of DNA replication.

Chromosomes, Bacterial↗

PubMed1991

Cloning the BstVI restriction-modification system in Escherichia coli.

A standard DNA modification methyltransferase (MTase) selection protocol was followed to clone the BstVI restriction and modification system from Bacillus stearothermophilus in Escherichia coli. Both genes were contained in a 4.4-kb EcoRI fragment from B. stearothermophilus V chromosomal DNA. The heterologous expression of these genes did not depend on their orientation in the vector, suggesting that the genes are expressed in E. coli under the control of promoters located on the cloned fragment. Subcloning experiments demonstrated that the bstVIR gene was expressed in the absence of its cognate MTase.

Cloning, Molecular↗

PubMed1991

Molecular dosimetry of sister chromatid exchange induction in 9L cells treated with 6-thioguanine.

The induction of sister chromatid exchanges (SCE) in 9L cells treated with 6-thioguanine (6-TG) has been investigated. A 24 h treatment with 0.2 microM 6-TG induced approximately 28 SCE/metaphase. The dose-response curve was linear at doses below 0.2 microM and had a slope of 139 SCE/metaphase/microM 6-TG. At concentrations of 0.023 to 1 microM, incorporation of 6-TG in DNA was linear with dose. The slope of the dose-response curve was 4135 mumol 6-TG/mol DNA/microM 6-TG. Comparison of these results with those obtained in our previous studies of the monofunctional alkylating agent ethylnitrosourea and the bifunctional alkylating agent 3-(4-amino-2-methyl-5-pyrimidinyl)methyl-1-(2-chloroethyl)-1-nitrosourea suggest that to accurately estimate the effectiveness of particular DNA modifications at inducing SCE, the extent of formation of these DNA modifications must be known.

Alkylating Agents↗

PubMed1984

Use of short DNA oligonucleotides for determination of DNA sequence modifications induced by benzo[a]pyrene diol epoxide.

Various organic agents that alkylate DNA are known to induce mutations in bacterial and animal cells. The precise nature and location of modified DNA sequences in such mutants are often difficult to ascertain. In this report, a 10-base-pair oligomer (BamHI linker) is treated with (+/-)-trans-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide and inserted into replicative form DNA of phage M13 by ligation at a specific restriction site. Escherichia coli are transfected with the recombinant DNA containing the alkylated target, progeny viral plaques are selected, and their DNAs are subjected to DNA sequence analysis at the region of oligomer insertion. For the alkylated inserts used in this study, the DNA sequence analysis of progeny viral DNA showed that nucleotide deletions were present in every clone examined. These deletions occurred primarily, but not exclusively, at G-C cluster regions, varied from 1 to 24 base pairs in length, and included both target and nontarget nucleotides. A second type of repair, which restores most of the original nucleotide bases in the alkylated insert, is also implied by the DNA sequence data obtained.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed1998

High levels of endogenous DNA adducts (I-compounds) in pig liver. Modulation by high cholesterol/high fat diet.

I (indigenous)-compounds are bulky endogenous DNA adducts which are detected by 32P-postlabeling in unexposed animals. I-compound levels in rodents depend on age, species, strain, gender, tissue, diet, and chemical exposure. There are two classes of I-compounds, type I and type II. While many type I I-compounds may not reflect DNA damage, type II I-compounds have been identified as oxidative DNA lesions some of which can be produced in vitro under Fenton reaction conditions. In rats, caloric restriction (CR) increases the levels of many type I I-compounds compared with ad libitum fed animals, while high fat diet has the opposite effect. Here, we have tested whether hepatic DNA of a non-rodent mammal, the pig, contains I-compounds and whether feeding a high cholesterol/high fat (HC/HF) diet modulates their levels, assuming this would affect the formation of lipid-related precursors and cause oxidative stress. Male Yorkshire pigs aged 2 months old, were fed either control or HC/HF diet (control diet supplemented with 2% cholesterol and 19% lard) for 2 months. Pig liver DNA contained at least 19 type I and five type II I-compounds. Among the former, only five matched corresponding spots in rat liver DNA, while all the latter DNA lesions were detected in both species. The levels of both types of DNA modifications were six to eight-fold higher in pig DNA. HC/HF diet reduced levels of many type I I-compounds up to several fold but had little effect on the oxidative lesions. Several type I I-compounds showed negative linear correlations with serum cholesterol levels, while this association was positive for total type II I-compounds. The substantially elevated steady-state levels of bulky endogenous DNA adducts in the species with the longer life expectancy were surprising. Thus, for the first time, an intimate link between nutritional status and endogenous DNA modifications has been established in a non-rodent system. We propose that in order to explain our observations, differences in diet composition, antioxidant defenses, and DNA repair, as well as cytochrome P450 modulation of precursor levels and hormonal effects need to be considered.

Animals↗

PubMed1998

Duck hepatitis B virus inactivation and 8-methoxypsoralen photoadduct formation in human platelet concentrates.

Photochemical inactivation (PCI) of virus and bacteria in platelet concentrates (PC) has been demonstrated using 8-methoxypsoralen (8-MOP) and long-wavelength UV light (UVA). To study inactivation of blood-borne virus, we have employed duck hepatitis B virus (DHBV), a model for human hepatitis B virus. A specific hepatocyte culture infectivity assay, with PCR detection, could measure 5-6 log10 virus kill. The DHBV inactivation in PC was dependent on UVA dose, was enhanced when plasma was reduced from 100% to 20% and was limited by 8-MOP solubility in the reduced-plasma medium. Optimum conditions for PCI were 100 micrograms/mL 8-MOP in 20% plasma and 80% synthetic platelet storage medium. A radiolabeling assay for 8-MOP photoadducts in hepatocytes seeded into PC confirmed that DHBV inactivation reflected DNA modification and indicated that adduct formation was insensitive to minor variations in conditions. Kinetic modeling indicated that optimum adduct formation was a compromise between 8-MOP dark binding and optical transmittance and that plasma proteins competed for 8-MOP binding. The PCI results in various media correlated with corresponding DNA modification densities and were compared to statistical models incorporating DHBV characteristics and predictions of 8-MOP crosslink formation between DNA strands. Behavior was consistent with one or a small number of lethal modifications per DNA strand, including monoadducts, but probably not crosslinks alone. A minor subpopulation of DHBV was found to be somewhat more difficult to inactivate, consistent with three-fold lower modification, due possibly to single-stranded DNA character or host repair of photoadducts.

Blood Platelets↗

PubMed1985

Metabolism and specific benzopyrene metabolite modification of DNA in early S by human lung epithelial and fibroblast cells leading to the expression of an abnormal phenotype.

Examination of the high pressure liquid chromatographic profiles of ethyl acetate extractable benzo [a] pyrene (B(a)P)-metabolites from human lung fibroblast and type II epithelial cells after S phase entry indicated that B(a)P-7,8-diol and 9,10-diol species were produced following the oxygenation of B(a)P. These metabolites were detected intracellularly and in the extracellular growth medium. Both cell types appeared to release extracellularly, elevated amounts of the B(a)P-7,8-diol species. It was interesting to note of the 4 pmol of oxygenated metabolites localized intracellularly, in the fibroblast, that we identified two major metabolites, B(a)P-9,10 and -7,8-diol species. Lung epithelial cells metabolize intracellular B(a)P extensively, greater than or equal to 93% of the parent B(a)P. No tetrols were detected intracellularly or extracellularly in the treated fibroblast cells. The treated epithelial cells produced both tetrols and sulfate conjugates. The extent of observed modification of early S phase nuclear DNA of lung epithelial cells was 7.5 +/- 4.9 adducts per 10(6) bases and 4.2 +/- 2.7 adducts per 10(6) bases in lung fibroblasts. The major adduct formed in both cell types was 7 beta-BPDE-I-dG. Under conditions for transformation, both the B(a)P treated lung epithelial cells and lung fibroblasts treated in early S with either B(a)P or BPDE-I yielded populations that exhibited properties of anchorage independent growth and cellular invasiveness. Metabolism and the presence internally of metabolites did not correlate with the extent of modification of DNA in early S.

Benzo(a)pyrene↗

PubMed2004

Molecular diagnostic applications of DNA methylation technology.

Cancer arises due to the accumulation of DNA modifications that give cells a selective growth advantage. One common DNA modification is promoter hypermethylation associated with loss of expression of a tumor suppressor gene. The methylation status of a specific sequence or the pattern of methylation across the genome can be readily measured, and these sequences and analytical methods are being rapidly developed for molecular diagnostic applications. Detection of certain methylation events can be used for early detection of tumors, and analysis of patterns of methylation across the genome might provide information on disease subtype, aggressiveness, and treatment response. DNA methylation-based molecular diagnostic assays are particularly attractive because of the stability of the target analyte (DNA) and the potential sensitivity of the assays. As the field matures, methylation-based assays will make a major contribution to the field of molecular diagnostics, providing tools to fill unmet needs in current diagnostic and treatment plans for many types of cancer.

Biomarkers, Tumor↗

PubMed1976

Salmonella typhimurium SA host specificity system is based on deoxyribonucleic acid-adenine methylation.

We have determined the nature of the deoxyribonucleic acid (DNA) modification governed by the SA host specificity system of Salmonella typhimurium. Two lines of evidence indicate that SA modification is based on methylation of DNA-adenine residues. (i) The SA+ locus of Salmonella was transferred into Escherichia coli B, a strain that does not contain 5-methylcytosine in its DNA; although the hybrid strain was able to confer SA modification, its DNA still did not contain 5-methylcytosine. (ii) the N6-methyladenine content of phage L DNA was measured after growth in various host strains; phage lacking SA modification contained fewer N6-methyladenine residues per DNA. We also investigated the possibility, suggested by others (32), that SA modification protects phage DNA against restriction by the RII host specificity system. Phages lambda, P3, and L were grown in various SA+ and SA- hosts and tested for their relative plating ability on strains containing or lacking RII restriction; the presence or absence of SA modification had no effect on RII restriation. In vitro studies revealed, however, that Salmonella DNA is protected against cleavage by purified RII restriction endonuclease (R-EcoRII). This protection is not dependent on SA modification; rather, it appears to be due to methylation by a DNA-cytosine methylase which has overlapping specificity with the RII modification enzyme, but which is not involved in any other known host specificity system.

Adenine↗

PubMed1995

DNA base modifications and antioxidant enzyme activities in human benign prostatic hyperplasia.

The authors have studied DNA base damage and activities of antioxidant enzymes in human benign prostatic hyperplasia (BPH) tissues and surrounding disease-free tissues removed from prostate glands of 15 patients. In these tissues, endogenous levels of various typical hydroxyl radical-induced products of DNA bases and activities of catalase and superoxide dismutase were measured. The majority of patients had higher levels of DNA base lesions and lower activities of enzymes in BPH tissues than in normal prostate tissues. When activities of both enzymes were lower in BPH tissues than in normal tissues, the increases in the amounts of DNA base lesions over control levels were most prominent. In the case of similar enzyme activities in both BPH and normal tissues, no changes in levels of DNA base lesions were observed. These results suggest a possible association between antioxidant enzyme activities and levels of DNA base lesions in BPH tissues. Some of the identified DNA lesions are known to be premutagenic and may play a role in carcinogenesis. Although a possible link between BPH and prostate cancer is controversial, BPH patients with both decreased antioxidant enzyme activities and increased levels of DNA lesions may be at risk of developing prostate cancer.

Antioxidants↗

PubMed1995

DNA base modifications and membrane damage in cultured mammalian cells treated with iron ions.

We investigated DNA base damage in mammalian cells exposed to exogenous iron ions in culture. Murine hybridoma cells were treated with Fe(II) ions at concentrations of 10 microM, 100 microM, and 1 mM. Chromatin was isolated from treated and control cells and analyzed by gas chromatography/mass spectrometry for DNA base damage. Ten modified DNA bases were identified in both Fe(II)-treated and control cells. The quantification of modified bases was achieved by isotope-dilution mass spectrometry. In Fe(II)-treated cells, the amounts of modified bases were increased significantly above the background levels found in control cells. Dimethyl sulfoxide at concentrations up to 1 M in the culture medium did not significantly inhibit the formation of modified DNA bases. A mathematical simulation used to evaluate the plausibility of DNA damage upon Fe(II) treatment predicted a dose-dependent response, which agreed with the experimental results. In addition, Fe(II) treatment of cells increased the cell membrane permeability and caused production of lipid peroxides. The nature of DNA base lesions suggests the involvement of the hydroxyl radical in their formation. The failure of dimethyl sulfoxide to inhibit their formation indicates a site-specific mechanism for DNA damage with involvement of DNA-bound metal ions. Fe(II) treatment of cells may increase the intracellular iron ion concentration and/or cause oxidative stress releasing metal ions from their storage sites with subsequent binding to DNA. Identified DNA base lesions may be promutagenic and play a role in pathologic processes associated with iron ions.

Animals↗

PubMed1984

Modification of DNA by reducing sugars: a possible mechanism for nucleic acid aging and age-related dysfunction in gene expression.

Reducing sugars react nonenzymatically with protein amino groups to initiate a process called nonenzymatic browning. Long-lived proteins, such as collagen and the lens crystallins, accumulate sufficient modification in vivo that they acquire many of the chemical properties characteristic of aged proteins. We have obtained evidence that nucleic acids also can undergo nonenzymatic modification by sugars. Incubation of DNA or nucleotides with glucose 6-phosphate (Glc-6-P) produces spectral changes similar to those described for nonenzymatic browning proteins. The occurrence of chemical modification was verified by measuring the transfection efficiency of viral DNA after incubation with glucose and Glc-6-P. A loss of transfection potential occurred that was first order with respect to time and sugar concentration. The rate of inactivation by Glc-6-P was 25 times that of glucose; 8 days of incubation with 150 mM Glc-6-P decreased transfection by 4 orders of magnitude. Glc-6-P also produced strand scission in a time- and concentration-dependent manner. We conclude that glucose, Glc-6-P, and possibly other sugars can react with DNA to produce significant structural and biological alterations. Since nucleic acids are long-lived molecules in the resting cell, the accumulation of these addition products might be a mechanism for the decreased genetic viability characteristic of the aged organism.

Aging↗

PubMed2006

Surface modification for DNA and protein microarrays.

Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.

Manufactured Materials↗