Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA Modifications”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,675 records · Page 93Linked to original sources
PubMed1990

Modification of bases in DNA by copper ion-1,10-phenanthroline complexes.

Damage to the bases in DNA by the cupric ion-1,10-phenanthroline complex was investigated. Ten base products in DNA were identified and quantitated by the use of gas chromatography/mass spectrometry with selected-ion monitoring. DNA damage by the cupric ion-1,10-phenanthroline complex required the presence of a reducing agent such as ascorbic acid or mercaptoethanol. Products identified were typical hydroxyl radical induced products from the pyrimidines and purines in DNA, well-known from previous studies using various hydroxyl radical producing systems such as ionizing radiation, hypoxanthine/xanthine oxidase, or hydrogen peroxide in the presence of transition metal ions. Product formation was not significantly inhibited by typical scavengers of hydroxyl radical such as mannitol and sodium formate, but there was partial inhibition by dimethyl sulfoxide. Catalase substantially decreased formation of base products, and added hydrogen peroxide stimulated it, indicating the hydrogen peroxide dependency of DNA base damage. Superoxide dismutase afforded only a partial reduction in product yields in systems containing ascorbic acid. On the basis of the types of base products formed, the hydrogen peroxide dependency of product formation, and a previous report suggesting that DNA damage is due to a diffusible species [Williams, L. D., Thivierge, J., & Goldberg, I. H. (1988) Nucleic Acids Res. 16, 11607-11615], we propose that DNA base damage is caused by hydroxyl radical.

Catalase↗
PubMed2005

[How to localize epigenetics in the landscape of biological research?].

Today, epigenetics is a very fashionable field of research. Modification of DNA by methylation, and of chromatin by histone modification or substitution represents a major fraction of the studies; but this special issue shows that epigenetic studies are very diverse, and not limited to the study of chromatin. What is common behind these different uses of the word epigenetics? A brief historical survey shows that epigenetics was invented twice, with different meanings: in the 1940s, by Conrad Waddington, as the study of the relations between the genotype and the phenotype; in the 1960s, as the global mechanisms of gene regulation involved in differentiation and development; what is common is that an approach distinct from genetics was in both cases considered as necessary because genetic models were incapable to address these problems. A good way to appreciate the relations between genetics and epigenetics is to realize that the main aim of organisms is to reproduce, and to consider the way organisms perform this task. Genetics is the precise means organisms have invented to reproduce the structure of their macromolecular components; the genome is also used to control the level and place of this reproduction. All the other means organisms have used to reproduce were more or less the result of tinkering, and constitute the field of epigenetics, with its diversity and richness.

Epigenesis, Genetic↗
PubMed1986

Spermine-DNA interactions: a theoretical study.

Models for the interaction of spermine and DNA were studied by performing conformational energy calculations on spermine and molecular mechanics calculations on major and minor groove complexes of spermine and oligomers of DNA. Docked into the major groove of B-DNA, spermine stabilizes the complex by maximizing interactions between proton acceptors on the oligomer and proton donors on spermine. This is achieved by bending the major groove of DNA over spermine and altering oligomer sugar puckering and interstrand phosphate distances. By comparison, Liquori's minor groove model appears to be less stable than the major groove model. This evidence favors a preferential binding of spermine to certain sites in DNA, which provides a powerful force for the modification of DNA conformation.

DNA↗
PubMed2000

Modification of survival by DNA repair modifiers: a probable explanation for the phenomenon of increased radioresistance.

PURPOSE: The low dose (<1 Gy) survival curve of mammalian cells is characterized by a region of hypersensitivity (HRS) followed by increased resistance (IRR). Above 1 Gy, the survival response can be described with a smooth downward-bending curve. Indirect evidence has indicated that the IRR response might reflect an induced radioresistance triggered by DNA damage. The work reported here provides experimental evidence that consolidates this hypothesis. MATERIALS AND METHODS: Clonogenic survival of V79-379A cells was measured using automated microscopy (DMIPS cell analyser) in the presence or absence of three known modifiers of DNA repair processes over the X-ray dose range 0-1 Gy. RESULTS: 3-Aminobenzamide (5 microM), a potent inhibitor of poly(ADP ribose)-polymerase, inhibited the development of increased radioresistance as indicated by a statistically significant reduction in an RBE from 3.537 (+/-SEM (0.139)) to 2.168 (+/-0.191) at an X-ray dose of 1 Gy, implying an involvement of DNA repair pathways that require poly(ADP ribose)-polymerase in the IRR response. In contrast, novobiocin (350 microM), an inhibitor of topoisomerase II, did not inhibit the development of increased radioresistance (RBE 3.650 (+/-0.192) to 3.322+/-(0.156)) but eliminated low-dose hypersensitivity as measured by an increase in RBE from 2.508 (+/-0.536) to 1.135 (+/-0.057) at 0.04 Gy. Ara-A (120 microM), an inhibitor of DNA polymerase, sensitized cells at all doses. CONCLUSION: These data support the hypothesis that DNA repair processes are likely to be involved in the development of increased radioresistance and provide further evidence against a sensitive subpopulation explanation for the biphasic low-dose survival response.

Animals↗
PubMed1997

Induction and repair inhibition of oxidative DNA damage by nickel(II) and cadmium(II) in mammalian cells.

Compounds of nickel(II) and cadmium(II) are carcinogenic to humans and to experimental animals. One frequently discussed mechanism involved in tumor formation is an increase in reactive oxygen species by both metals with the subsequent generation of oxidative DNA damage. In the present study we used human HeLa cells to investigate the potential of nickel(II) and cadmium(II) to induce DNA lesions typical for oxygen free radicals in intact cells and the effect on their repair. As indicators of oxidative DNA damage, we determined the frequencies of DNA strand breaks and of lesions recognized by the bacterial formamidopyrimidine-DNA glycosylase (Fpg protein), including 7,8-dihydro-8-oxoguanine (8-hydroxyguanine), a pre-mutagenic DNA base modification. Nickel(II) caused a slight increase in DNA strand breaks at 250 microM and higher, while the frequency of Fpg-sensitive sites was enhanced only at the cytotoxic concentration of 750 microM. The repair of oxidative DNA lesions induced by visible light was reduced at 50 microM and at 100 microM nickel(II) for Fpg-sensitive sites and DNA strand breaks, respectively; the removal of both types of lesions was blocked nearly completely at 250 microM nickel(II). In the case of cadmium(II), DNA strand breaks occurred at 10 microM and no Fpg-sensitive sites were detected. However, the repair of Fpg-sensitive DNA lesions induced by visible light was reduced at 0.5 microM cadmium(II) and higher, while the closure of DNA strand breaks was not affected. Since oxidative DNA damage is continuously induced during aerobic metabolism, an impaired repair of these lesions might well explain the carcinogenic action of nickel(II) and cadmium(II).

Cadmium↗
PubMed1977

Modification of human DNA-dependent RNA polymerase activity by cyclic GMP.

The effect of low concentrations of cyclic GMP (guanosine 3':5'-cyclic monophosphate) on the in vitro enzymatic activities of DNA-dependent RNA polymerases isolated from human peripheral blood lymphocytes has been investigated. In agreement with earlier studies which employed isolated nuclei as the enzyme source, an increase in the activity of partially purified RNA polymerase I is observed in the presence of cyclic GMP (10(-8) to 10(-10)M). RNA polymerase II activity is inhibited by the presence of cyclic GMP at concentrations between 10(-4) and 10(-10)M. RNA polymerase III activity is stimulated in a bimodal fashion by the presence of cyclic GMP with maximal activity noted at 10(-8) to 10(-10) M and 10(-5)M. In addition, [3H]cyclic GMP binds specifically to chromatographic fractions which are known to contain RNA polymerases I, II and III. This binding to RNA polymerases II and III is apprarently less tenacious as demonstrated by dissociation studies. The observations provide additional evidence for a role for cyclic GMP in the regulation of RNA synthesis.

Cyclic AMP↗
PubMed2006

Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones.

By determining spatial-temporal expression patterns, reporter constructs provide significant insights into gene function. Although additionally providing information on subcellular distribution, translational reporters, where the reporter is fused to the gene coding sequence, are used less frequently than simpler constructs containing only putative promoter sequences. Because these latter constructs may not contain all necessary regulatory elements, resulting expression patterns must be interpreted cautiously. To ensure inclusion of all such elements and provide details of subcellular localization, construction of translational reporters would, preferably, utilize genomic clones, containing the complete locus plus flanking regions and permit seamless insertion of the reporter anywhere within the gene. We have developed such a method based upon lambda Red-mediated recombineering coupled to a robust two-step counter-selection protocol. We have inserted either gfp or cfp precisely at the C-termini of three Caenorhabditis elegans target genes, each located within different fosmid clones, and examined previously with conventional reporter approaches. Resulting transgenic lines revealed reporter expression consistent with previously published data for the tagged genes and also provided additional information including subcellular distributions. This simple and straightforward method generates reporters highly likely to recapitulate endogenous gene expression and thus represents an important addition to the functional genomics toolbox.

3' Flanking Region↗
PubMed2003

Interaction of 5-aza-2'-deoxycytidine and depsipeptide on antineoplastic activity and activation of 14-3-3sigma, E-cadherin and tissue inhibitor of metalloproteinase 3 expression in human breast carcinoma cells.

Genes that suppress tumorigenesis can be silenced by epigenetic events, such as aberrant DNA methylation and modification of chromatin structure. Inhibitors of DNA methylase and histone deacetylase (HDAC) can potentially reverse these events. The aim of this study was to determine the in vitro antineoplastic activity of 5-aza-2'-deoxycytidine (5-AZA-CdR), a potent inhibitor of DNA methylase, in combination with depsipeptide (depsi), an inhibitor of HDAC, on human breast carcinoma cells. We observed a synergistic antineoplastic interaction between 5-AZA-CdR and depsi in their capacity to inhibit colony formation of Hs578T and MCF-7 breast carcinoma cells. In order to understand the molecular mechanism of this interaction, we investigated the effect of these drugs on the activation of the 14-3-3sigma, E-cadherin and tissue inhibitor of metalloproteinase 3 (TIMP3) cancer-related genes, which were reported to be silenced by aberrant methylation in many breast tumor cell lines. 14-3-3sigma was reported to produce G cell cycle arrest following DNA damage. E-cadherin and TIMP3 function as suppressors of tumor metastasis. Semi-quantitative RT-PCR was used to determine the effect of the co-administration of 5-AZA-CdR and depsi on four breast carcinoma cell lines for the reactivation of these genes. We observed a synergistic activation of E-cadherin by the combination in Hs578T, MDA-MB-231 and MDA-MB-435 tumor cells. For 14-3-3sigma, we demonstrated an additive to synergistic activation by the combination for Hs578T and MDA-MB-435 tumor cells, respectively. In the MCF-7 tumor cells, the drug combination produced a synergistic activation of TIMP3. The association between the synergistic antineoplastic activity and the synergistic activation of the target genes in this study suggests that the mechanism of anticancer activity of 5-AZA-CdR, in combination with depsi, is probably related to their enhanced activation of different types of tumor suppressor genes that have been silenced by epigenetic events.(2)

14-3-3 Proteins↗
PubMed1981

Restriction and modification of bacteriophage SP10 DNA by Bacillus subtilis Marburg 168: stabilization of SP10 DNA in restricting hosts preinfected with a heterologous phage, SP18.

SP10 phage cannot propagate in Bacillus subtilis Marburg 168 containing the wild-type allele of either gene nonA or gene nonB. The latter gene codes for the intrinsic cellular restriction activity. SP10 DNA was degraded in nonB+ derivatives of Marburg 168. The degree of degradation depended upon the previous host in which SP10 was propagated. In the case of SP10 grown in B. subtilis W23 (a nonrestricting, nonmodifying bacterium), 90% of the phage DNA was hydrolyzed to acid solubles, and the residual acid-precipitable material was recovered as 0.5- to 1-megadalton fragments. In contrast, if SP10 was propagated in B. subtilis PS9W7 (a nonA nonB derivative of Marburg 168 that retains modifying activity), 40 to 50% of the input DNA was degraded to acid solubles, and most of the remainder was recovered as 15- to 20-megadalton fragments. In nonA+ nonB cells, SP10 DNA was conserved as unit-length molecules (ca. 80 megadalton). Prior infection of nonB+ cells with SP18 protected superinfecting SP10 DNA, even when rifampin or chloramphenicol was added before the primary infection. The data are discussed in terms of the following conclusions. (i) The nonB gene product of B. subtilis Marburg 168 is required for restriction of SP10 DNA. (ii) Some sites on SP10 DNA are sensitive to both the restricting and modifying activities, whereas other sites are nonmodifiable even though they are sensitive to the restriction enzyme. (iii) In some manner, SP18 antagonizes the action of the nonB gene product.

Bacillus subtilis↗
PubMed1983

Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SP beta, phi 3T, and rho 11.

The DNA methylation capacity and some other properties of the related temperate Bacillus subtilis phages Z, SPR, SP beta, phi 3T, and rho 11 are compared. With phage mutants affected in their methylation potential, we show that phage-coded methyltransferase genes are interchangeable among the phages studied. DNA/DNA hybridization experiments indicate that phage methyltransferase genes are structurally related, whereas no such relationship is observed to a bacterial gene, specifying a methyltransferase with the same specificity.

Bacillus subtilis↗
PubMed1992

[Analysis of cellular DNA content by flow cytometry in epidermoid carcinoma of the esophagus].

Flow cytometric DNA analysis was performed in 35 patients with squamous cell carcinoma of the esophagus. The aim of this study was a) to establish a tumoral DNA pattern, b) to determine an objective parameter correlating with tumoral response to chemotherapy (5 FU-cisplatin). DNA analysis was performed in perendoscopic ranged tumoral biopsy specimens to determine the DNA ploidy (DNA index) and S phase fraction. Tumor diameter and length were evaluated by computed tomography (CT) before and after chemotherapy in 24 patients. The relative variation of this product determined a CT index. Before chemotherapy, 82 percent (76/93) of the specimens were available for assessment; 72 percent (26/36) of the tumors were aneuploid. In these tumors, the DNA index ranged from 1.23 to 2.80. Five tumors had two distinct and simultaneous aneuploid populations. CT index values were not significantly different according to the ploidy (diploid, aneuploid), the S phase fraction (low, high), the DNA content modification after chemotherapy (absent, present). In this study, DNA analysis did not allow to select patients with higher response to chemotherapy. The inter- and intratumoral phenotypic heterogeneity may be one of the responsible factors.

Adult↗
PubMed1976

Modification of Escherichia coli DNA ligase by cleavage with trypsin.

Limited treatment of Escherichia coli DNA ligase with trypsin results in rapid loss of DNA joining activity. However, the ability to react with DPN to form the covalent enzyme-AMP intermediate is unaffected. The cleaved enzyme is also unable to catalyze the formation of DNA-adenylate, the second covalent intermediate in the ligase-catalyzed reaction. These findings demonstrate that portions of the DNA ligase molecule that are required for phosphodiester bond formation are not required for at least one of the partial reactions catalyzed by this enzyme.

Escherichia coli↗
PubMed1991

[DNA intercalators: their interaction with DNA and other cell components and their use in biological research].

DNA intercalators include aromatic heterocyclic compounds of various chemical classes with profound biological activities. The flat molecules of these ligands intercalate between base pairs of DNA right-handed helix, lengthening and unwinding this structure at the intercalation sites. Lerman first postulated the intercalation model for complexes of native DNA with acridine derivatives. The structures of intercalative complexes were further confirmed by the X-ray diffraction method. Besides, other physico-chemical criteria of DNA intercalation are as following: the increase in the contour length of duplex DNA; unwinding of supercoils from natural supercoiled covalently closed duplex DNA; the increase in Tm of DNA in the complexes with ligands. The changes of spectral properties of bounded ligands are also observed for DNA-intercalating agents. Various experimental methods are based on changes in the properties of nucleic acid structures and ligands due to DNA intercalation, including the fluorescent determination of nucleic acid structures and quantities; fluorescent assays of activities of various enzymes involved in nucleic acid metabolism; chromosome identification according to their fluorescent banding patterns; separation of nucleic acid topological forms, and many other methods. The inhibition of reactions of DNA replication, transcription, topoisomerization and of enzymatic degradation by DNA intercalators represents an important consequence of DNA structure modification due to intercalation. Besides, as hydrophobic cations DNA intercalators uncouple the oxidative phosphorylation in mammalian cell mitochondria. There are some other protein and phospholipid targets for DNA-intercalators in vivo. The intracellular distribution of these agents appear to be a very complicated selective process. These data point to the importance of application of DNA intercalators in pharmacology.

Animals↗
PubMed1985

Influence of ethidium bromide on hyperthermic modification of bleomycin-DNA interaction.

The effect of hyperthermic treatment on the binding of 59Fe-labeled bleomycin to DNA has been studied. Enhanced binding was observed at elevated temperatures. The influence of the DNA-intercalating agent, ethidium bromide, on bleomycin-DNA interaction was also studied and revealed a considerable decrease in this interaction at ethidium bromide levels below 1 microgram/ml. Ethidium bromide was observed to remove the enhanced bleomycin-DNA interaction recorded previously following incubation at hyperthermic temperatures. Synergistic action of bleomycin and hyperthermia on loss of clonogenic ability of HT29R cells is reported. Incubation of cells under hyperthermic conditions with bleomycin in the presence of ethidium bromide removes this synergism, producing a less than additive effect for the action of bleomycin and heat after ethidium bromide effects are taken into account.

Adenocarcinoma↗