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PubMed1999

Diet modification affects DNA oxidative damage in healthy humans.

DNA 8-hydroxy-2'-deoxyguanosine (8-OHdG) is a promising biomarker for oxidative damage. We assessed its responsiveness to diet in 32 nonsmoking, healthy subjects (12 male, 20 female) aged 31+/-7.6 years. They consumed two liquid formula diets (Ensures) as the sole source of nutrition for 10-d in a randomized crossover design, with 5-d control solid food diets as washout before each liquid diet period. Reformulated Ensure (Re-En) had a vitamin E/ PUFA of 3.5 compared to standard Ensure (En) of 1.1. We hypothesized that subjects would have lower leukocyte 8-OHdG/deoxyguanosine (dG) ratios while consuming Re-En compared to En. But 8-OHdG/dG ratios did not change with the consumption of either Re-En or En. The mean ratios of 8-OHdG/dG after 10 days of Re-En and En consumption were (2.12+/-0.68)x10(-5) and (2.16+/-0.63)x10(-5), respectively. However, there was a 22% decrease in 8-OHdG/dG by the end of the study and a significant downward trend of leukocyte 8-OHdG among all subjects throughout all nutrient-rich diet phases as the study progressed (Test for trend: p = .04; paired t-test: p = .07). Because all the experimental diets provided antioxidant nutrients at higher quantities than typically consumed by a U.S. age-matched population, this study adds to the few in vivo studies that show a decrease in DNA damage in healthy nonsmoking subjects through dietary intervention.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1999

Cisplatin-modification of DNA repair and ionizing radiation lethality in yeast, Saccharomyces cerevisiae.

Cis-diamminedichloroplatinum II (cisplatin) is a DNA inter- and intrastrand crosslinking agent which can sensitize prokaryotic and eukaryotic cells to killing by ionizing radiation. The mechanism of radiosensitization is unknown but may involve cisplatin inhibition of repair of DNA damage caused by radiation. Repair proficient wild type and repair deficient (rad52, recombinational repair or rad3, excision repair) strains of the yeast Saccharomyces cerevisiae were used to determine whether defects in DNA repair mechanisms would modify the radiosensitizing effect of cisplatin. We report that cisplatin exposure could sensitize yeast cells with a competent recombinational repair mechanism (wild type or rad3), but could not sensitize cells defective in recombinational repair (rad52), indicating that the radiosensitizing effect of cisplatin was due to inhibition of DNA repair processes involving error free RAD52-dependent recombinational repair. The presence or absence of oxygen during irradiation did not alter this radiosensitization. Consistent with this result, cisplatin did not sensitize cells to mutation that results from lesion processing by an error prone DNA repair system. However, under certain circumstances, cisplatin exposure did not cause radiosensitization to killing by radiation in repair competent wild type cells. Within 2 h after a sublethal cisplatin treatment, wild type yeast cells became both thermally tolerant and radiation resistant. Cisplatin pretreatment also suppressed mutations caused by exposure to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), a response previously shown in wild type yeast cells following radiation pretreatment. Like radiation, the cisplatin-induced stress response did not confer radiation resistance or suppress MNNG mutations in a recombinational repair deficient mutant (rad52), although thermal tolerance was still induced. These results support the idea that cisplatin adducts in DNA interfere with RAD52-dependent recombinational repair and thereby sensitize cells to killing by radiation. However, the lesions can subsequently induce a general stress response, part of which is induction of RAD52-dependent error free recombinational repair. This stress response confers radiation resistance, thermal tolerance, and mutation resistance in yeast.

Cisplatin↗
PubMed1988

Modification of DNA dynamics by platinum drug binding: a time-dependent fluorescence depolarization study of the interaction of cis- and trans-diamminedichloroplatinum(II) with DNA.

The interaction of calf thymus DNA with the antitumor drug cis-diamminedichloroplatinum(II), and with the clinically ineffective trans isomer, is studied by time-dependent fluorescence depolarization spectroscopy of intercalated ethidium. The effect of the platinum compounds on the rapid torsional motions of DNA in solution is observed via depolarization of the ethidium fluorescence. The depolarization data are successfully analyzed with an elastic model of DNA dynamics and yield a value for the product of the torsional rigidity of the DNA and the friction factor for DNA twisting. The dependence of this quantity on the degree of platination of the DNA is determined for each isomer. At low levels of platination, the cis isomer increases the solute-solvent friction acting on the DNA torsional motions, which we attribute to local kinking of the helix axis at the sites of platination. At high levels of platination, the cis isomer decreases the torsional rigidity of the DNA, indicating that disruption of DNA duplex structure occurs under these conditions. The binding of the trans isomer to DNA has no effect on the torsional rigidity or the friction. The present results are compared with other findings on the interaction of these platinum compounds with DNA.

Cisplatin↗
PubMed1999

Orientation of DNA replication establishes mating-type switching pattern in S. pombe.

The fission yeast Schizosaccharomyces pombe normally has haploid cells of two mating types, which differ at the chromosomal locus mat1. After two consecutive asymmetric cell divisions, only one in four 'grand-daughter' cells undergoes a 'mating-type switch', in which genetic information is transferred to mat1 from the mat2-P or mat3-M donor loci. This switching pattern probably results from an imprinting event at mat1 that marks one sister chromatid in a strand-specific manner, and is related to a site-specific, double-stranded DNA break at mat1. Here we show that the genetic imprint is a strand-specific, alkali-labile DNA modification at mat1. The DNA break is an artefact, created from the imprint during DNA purification. We also propose and test the model that mat1 is preferentially replicated by a centromere-distal origin(s), so that the strand-specific imprint occurs only during lagging-strand synthesis. Altering the origin of replication, by inverting mat1 or introducing an origin of replication, affects the imprinting and switching efficiencies in predicted ways. Two-dimensional gel analysis confirmed that mat1 is preferentially replicated by a centromere-distal origin(s). Thus, the DNA replication machinery may confer different developmental potential to sister cells.

Artifacts↗
PubMed1977

Chemical modification of DNA polymerase phosphoprotein from avian myeloblastosis virus.

Fractionation of purified avian myeloblastosis virus DNA polymerase, after phosphorylation in vitro, revealed the presence of a small acidic proten, a phosphate acceptor polypeptide with high specific activity. Its presence in the phosphorylated form with the polymerase resulted in as much as a 10-fold increase in the rate of DNA synthesis. Its presence in the dephosphorylated form with the polymerase had no effect in the rate of DNA synthesis.

Avian Leukosis Virus↗
PubMed1985

Modification of DNA by glucose 6-phosphate induces DNA rearrangements in an Escherichia coli plasmid.

Reducing sugars such as glucose or glucose 6-phosphate (Glc-6-P) have been shown previously to modify the amino groups of nucleotides and single-stranded DNA. We have examined the mutagenic effect of Glc-6-P-induced lesions in the double-stranded DNA plasmid pBR322. Seventeen mutants of the Ampr Tets phenotype were isolated from plasmid preparations whose transforming capacity had been decreased by incubation with Glc-6-P. A number of the mutant plasmids were found to have undergone gross DNA alterations, including insertions and deletions, as well as the development of multiple species originating from a single cell. The ability of an endogenous reducing sugar to induce extensive DNA rearrangements suggests that these lesions may be significant contributors to cellular mutation.

Chromosome Deletion↗
PubMed1994

Immunochemical detection of sequence-specific modifications to DNA induced by UV light.

Sequence specificity of antibodies to UV-damaged DNA has not been described previously. The antisera investigated here were specific for UV-modified DNA and were absolutely dependent upon the presence of thymine residues. Using a series of oligonucleotides in competition ELISA, increased inhibition was observed with increasing chain length of UV-polythymidylate. A minimum of three adjacent thymines was required for effective inhibition; alone, dimers of thymine were poor antigens. Although UV-irradiated poly(dC) was not antigenic, cytosines could partially replace thymines within the smallest effective epitope (T-T-T) with a high degree of sequence specificity, not previously described. The main epitope induced by UV was formed from adjacent thymines and either a 3' or a 5' pyrimidine.

Animals↗
PubMed1988

Site-directed modification of DNA duplexes by chemical ligation.

The efficiency of chemical ligation method have been demonstrated by assembling a number of DNA duplexes with modified sugar phosphate backbone. Condensation on a tetradecanucleotide template of hexa(penta)- and undecanucleotides differing only in the terminal nucleoside residue have been performed using water-soluble carbodiimide as a condensing agent. As was shown by comparing the efficiency of chemical ligation of single-strand breaks in those duplexes, the reaction rate rises 70 or 45 times if the 3'-OH group is substituted with an amino or phosphate group (the yield of products with a phosphoramidate or pyrophosphate bond is 96-100% in 6 d). Changes in the conformation of reacting groups caused by mismatched base pairs (A.A, A.C) as well as the hybrid rU.dA pair or an unpaired base make the template-directed condensation less effective. The thermal stability of DNA duplexes was assayed before and after the chemical ligation. Among all of the modified duplexes, only the duplex containing 3'-rU in the nick was found to be a substrate of T4 DNA ligase.

Base Composition↗
PubMed1997

Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei.

African trypanosomes such as Trypanosoma brucei undergo antigenic variation in the bloodstream of their mammalian hosts by regularly changing the variant surface glycoprotein (VSG) gene expressed. The transcribed VSG gene is invariably located in a telomeric expression site. There are multiple expression sites and one way to change the VSG gene expressed is by activating a new site and inactivating the previously active one. The mechanisms that control expression site switching are unknown, but have been suggested to involve epigenetic regulation. We have found previously that VSG genes in silent (but not active) expression sites contain modified restriction endonuclease cleavage sites, and we have presented circumstantial evidence indicating that this is attributable to the presence of a novel modified base beta-D-glucosyl-hydroxymethyluracil, or J. To directly test this, we have generated antisera that specifically recognize J-containing DNA and have used these to determine the precise location of this modified thymine in the telomeric VSG expression sites. By anti J-DNA immunoprecipitations, we found that J is present in telomeric VSG genes in silenced expression sites and not in actively transcribed telomeric VSG genes. J was absent from inactive chromosome-internal VSG genes. DNA modification was also found at the boundaries of expression sites. In the long 50-bp repeat arrays upstream of the promoter and in the telomeric repeat arrays downstream of the VSG gene, J was found both in silent and active expression sites. This suggests that silencing results in a gradient of modification spreading from repetitive DNA flanks into the neighboring expression site sequences. In this paper, we discuss the possible role of J in silencing of expression sites.

Animals↗
PubMed1988

Benzo[a]pyrene diol epoxide I modification of DNA in human skin xenografts.

Human skin xenografts were established on the subscapular area of skin of nude (nu/nu NIH-Swiss background) mice. When treated with benzo[a]pyrene diol epoxide I (BPDE I), specific carcinogen-DNA adducts were formed. Separation and identification of these adducts by the 32P-postlabeling technique indicated that the 7R- and 7S-BPDE I-dpGp adducts were the major adducts. Xenografts pretreated with either allantoin or anthralin showed an increase in the major 7R- and 7S-BPDE I adducts compared to only BPDE I treatment. Likewise, we observed an increase in the quantity of different minor adducts. The ratios between the minor and major adducts in the pretreated grafts remained consistent with the ratio in the grafts treated with BPDE I only. We conclude that these modulators induce cells in the xenograft to enter S phase of the cell cycle. Moreover, we observed that these compounds altered the quantity of the minor carcinogen-DNA adducts without altering the overall ratios between the major 7R- and 7S-BPDE I-dpGp adducts and the minor carcinogen-DNA adducts.

Allantoin↗
PubMed1985

Type III 5-methylcytosine modification of DNA in Neisseria gonorrhoeae.

We present here the first report of a type III methyltransferase that modifies a cytosine. Neisseria gonorrhoeae 82409/55 (pJD1) modifies the first cytosine on only one strand from the 5' end of the nonpalindromic sequence: (Formula; see text). We have called this modifying activity M X NgoVIII.

5-Methylcytosine↗
PubMed2006

Five repair pathways in one context: chromatin modification during DNA repair.

The eukaryotic cell is faced with more than 10 000 various kinds of DNA lesions per day. Failure to repair such lesions can lead to mutations, genomic instability, or cell death. Therefore, cells have developed 5 major repair pathways in which different kinds of DNA damage can be detected and repaired: homologous recombination, nonhomologous end joining, nucleotide excision repair, base excision repair, and mismatch repair. However, the efficient repair of DNA damage is complicated by the fact that the genomic DNA is packaged through histone and nonhistone proteins into chromatin, a highly condensed structure that hinders DNA accessibility and its subsequent repair. Therefore, the cellular repair machinery has to circumvent this natural barrier to gain access to the damaged site in a timely manner. Repair of DNA lesions in the context of chromatin occurs with the assistance of ATP-dependent chromatin-remodeling enzymes and histone-modifying enzymes, which allow access of the necessary repair factors to the lesion. Here we review recent studies that elucidate the interplay between chromatin modifiers / remodelers and the major DNA repair pathways.

Base Pairing↗
PubMed1993

Modification of DNA topoisomerase II activity via direct interactions with the cyclic adenosine-3',5'-monophosphate response element-binding protein and related transcription factors.

DNA topoisomerase II (topo II) is an essential nuclear enzyme which catalyzes the interconversions of various forms of DNA. As predicted from the human topo II cDNA, the enzyme contains a potential leucine zipper protein dimerization motif. We therefore tested whether topo II could enter protein-protein interactions with other better characterized leucine zipper-containing proteins and determined if these interactions could modify topo II enzymatic activity in vitro. By far Western analyses, a large C-terminal fragment of human topo II was shown to interact with the DNA binding and dimerization regions of either cAMP response element binding protein (CREB) or the activating transcription factor-2. The C-terminal topo II fragment also interacted with full-length c-Jun, but not with full-length c-Fos. Using CREB as a prototype, the effect of this interaction on various topo II catalytic activities was assessed in vitro. CREB, at a 1- to 10-fold molar excess relative to topo II, inhibited site-specific DNA cleavage activity on a 242-base pair fragment of the human alpha-glycoprotein hormone subunit gene promoter. Very high CREB concentrations (400-fold excess) apparently inhibited topo II DNA relaxation activity, but this result was likely a direct effect of CREB on the topology of the DNA substrate. More interestingly, a 10-fold molar excess of CREB stimulated topo II decatenation activity, the essential function of this enzyme in cell division. This stimulatory effect could also be elicited by c-Jun, which interacts with topo II, but not by c-Fos, which does not bind topo II in our in vitro assay. Since similar amounts of CREB reduced the abundance of topo II DNA cleavage products from the human alpha-CG promoter yet also stimulated decatenation activity, it can be concluded that either: 1) CREB stimulated the religation rate of topo II; or 2) CREB directed topo II to a new cleavage site present on the decatenation substrate but not present on the limited alpha-CG promoter. The structural requirements for topo II protein-protein interactions were also investigated. Site-directed mutations which destroyed the putative topo II leucine zipper did not disrupt topo II protein-protein interactions. Since the putative leucine zipper in topo II does not appear to mediate protein-protein interactions, we propose that an alternate as yet uncharacterized structure is involved in the association of topo II with itself and other regulatory proteins.

Amino Acid Sequence↗
PubMed1985

Chemical modification of DNA with muta-carcinogens. I. 3-Amino-1-methyl-5H-pyrido[4,3-b]indole and 2-amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole: metabolic activation and structure of the DNA adducts.

3-Amino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2) and 2-amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1) are potent mutagen/carcinogens isolated from pyrolyzates of tryptophan and glutamic acid, respectively, and they have been found to exist in many cooked foods. Trp-P-2 and Glu-P-1 bind to DNA covalently after metabolic activations. The compounds are oxidized to the corresponding hydroxylamines (N-OH-Trp-P-2 and N-OH-Glu-P-1) by microsomes. N-OH-Trp-P-2 and N-OH-Glu-P-1 are the proximate forms of Trp-P-2 and Glu-P-1, respectively. They are further activated by cytosol to the O-acyl derivatives, which bind covalently with DNA. The structures of the modified nucleic acid bases were identified as 3-(C8-guanyl)amino-1-methyl-5H-pyrido[4,3-b]indole (Gua-Trp-P-2) and 2-(C8-guanyl)amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Gua-Glu-P-1). These initial events caused by Trp-P-2 and Glu-P-1 were established chemically, both in vitro and in vivo.

Animals↗
PubMed1985

Chemical modification of DNA with muta-carcinogens. II. Base sequence-specific binding to DNA of 2-amino-6-methyl-dipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1).

2-Amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1) binds covalently to DNA after metabolic activation to give 2-(C8-guanyl)amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Gua-Glu-P-1). The importance of the intercalative ability of the Glu-P-1 skeleton into DNA base pairs for this reaction is emphasized. The reactive form of Glu-P-1, N-acetoxy-Glu-P-1 (N-OAc-Glu-P-1), reacts preferentially at the C8 position of guanine residues in G-C-rich regions of DNA.

Base Sequence↗
PubMed1985

Chemical modification of DNA with muta-carcinogens. III. Reductive alkylation of DNA with mitomycin C.

Mitomycin C (MMC) binds to DNA after its reductive activation by catalytic hydrogenation with Pd on charcoal. Three modified nucleotides, named MG-1, MG-2, and MA, were isolated from the modified DNA after enzymatic hydrolysis to 5'-nucleotides. The structures of these modified nucleotides were deduced from their 1H-NMR and UV spectra, and from studies of the chemically transformed derivatives (hydrolysis, methylation, diazotization, and thioketonization). These three modified nucleotides were concluded to be 1,2-trans-2,7-diamino-1-(N2-deoxyguanylyl)mitosene (MG-1), 2,7-diamino-1-(O6-deoxyguanylyl)mitosene (MG-2) and 2,7-diamino-1-(N6-deoxyadenylyl)mitosene (MA). The same modified nucleotides were identified in DNA extracted from the livers of rats treated with MMC.

Alkylation↗