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PubMed1990

Quantitation of ultraviolet radiation-induced cyclobutyl pyrimidine dimers in DNA by video and photographic densitometry.

We have compared video and photographic methods for calculating the number of ultraviolet radiation (uv)-induced pyrimidine dimers in DNA from the bacteriophage T7 exposed to uv (0 to 800 J/m2) from an FS40 sunlamp. DNA was incubated with a pyrimidine dimer-specific Micrococcus luteus uv endonuclease, subjected to alkaline agarose gel electrophoresis, neutralized, and stained with ethidium bromide, and the DNA fluorescence was recorded either with a video camera or on photographic film. The slopes of the dose-response curves for the number of uv-endonuclease-sensitive sites per 10(3) bases (pyrimidine dimers) was 1.2 (+/- 0.1) X 10(-4) uv-endonuclease-sensitive sites per J/m2 for the video analysis and 1.3 (+/- 0.04) X 10(-4) uv-endonuclease-sensitive sites per J/m2 for the photographic analysis. Results for pyrimidine dimer determination by either method were statistically comparable.

Analog-Digital Conversion↗

PubMed1986

Biosynthesis of thiamine: origin of the methyl carbon atom of the pyrimidine moiety in Salmonella typhimurium.

Two biosynthetic, unevenly labeled samples of 5-aminoimidazole riboside were prepared. The incorporation of radioactivity from these labeled samples was studied in a Salmonella typhimurium strain able to use this riboside as precursor of the pyrimidine moiety of thiamine. In one sample, the ribose part was labeled almost equally at C-1' and C-2' and threefold more at C-3' but unlabeled at C-4' and C-5'. The pyrimidine moiety of thiamine derived from it was found almost inactive at C-5, C-7; the specific activity of the methyl carbon atom was found close to that of C-1' or C-2' of ribose in the precursor. On the other hand, only a poor incorporation of radioactivity occurred from a sample in which the ribose part was labeled mainly at C-1'. We conclude that C-5, C-7 of the pyrimidine moiety of thiamine derive from C-4', C-5' and the methyl carbon atom of the pyrimidine derives from C-2' of the ribose part of 5-aminoimidazole ribotide.

Binding Sites↗

PubMed1977

Electrophoretic characterization of pyrimidine 5'-nucleotidase of human erythrocytes and its distinction from acid phosphatase.

Electrophoresis of red cell pyrimidine 5'-nucleotidase was carried out on cellulose acetate strips. One major band of activity was found in preparations from human erythrocytes. This enzyme showed a specificity for the pyrimidine nucleotides UMP and CMP. No activity was detected with AMP. Pyrimidine 5'-nucleotidase activity could be separated from that of acid phosphatase with the use of alpha-glycerophosphate. This method may be useful in the study of pyrimidine 5'-nucleotidase deficiency in red cells.

Acid Phosphatase↗

PubMed1980

Urinary purines and pyrimidines in patients with hyperammonemia of various origins.

Excretion patterns of pyrimidines and purines in patients with various types of hyperammonemia have been investigated by 2-dimensional thin-layer chromatography and high pressure liquid chromatography (HPLC). For the quantitative analysis of pseudouridine, uracil and uridine a new procedure has been developed, consisting of pre-fractionation with Dowex 1 X 8, followed by dual column HPLC on a strong anion-exchanger and a reverse phase column. Thymine has also been analyzed in the pre-fractionated urine by a new HPLC method using the reverse phase column in combination with a strong cation-exchange column. Quantitative data for urinary pyrimidines and uric acid in hyperammonemia are given. In patients with a defect in one of the urea cycle enzymes, the level of pyrimidine excretion was found to depend on plasma ammonia concentrations. In other hyperammonemic patients, an increased excretion of orotic acid, uracil and uridine has only been found in one of the two patients with lysinuric protein intolerance, all other patients showing normal excretion patterns. Elevated uric acid excretions have been found frequently in our patients with hyperammonemia, but they did not always coincide with high plasma ammonia levels. A possible explanation for the difference in the excretion levels of the various pyrimidines is discussed.

Amino Acid Metabolism, Inborn Errors↗

PubMed1987

Tissue-specific gene expression results from a purine- and pyrimidine-free diet and 6-mercaptopurine in the rat small intestine and colon.

Dietary purines and pyrimidines are not considered to have a nutritional role, much less a direct effect on the functioning of the gastrointestinal tract. We found that a dramatic decrease in adult rat small intestinal and colonic total ribonucleic acid (RNA) results from the removal of dietary purines and pyrimidines or the administration of 6-mercaptopurine. Ribonucleic acid hybridization analysis indicated specific decrease of the messenger ribonucleic acid (mRNA) for the purine salvage enzymes hypoxanthine-guanine phosphoribosyl transferase and adenine phosphoribosyl transferase in the small intestine and proximal colon but not in the liver of animals fed a diet lacking purines and pyrimidines. Levels of intestinal and hepatic beta-actin mRNA transcripts were generally not depressed by either diet or by the administration of 6-mercaptopurine. Liver hypoxanthine-guanine phosphoribosyl transferase and adenine phosphoribosyl transferase mRNAs were unaffected by the change in diet but were lowered by the administration of 6-mercaptopurine. These data indicate that nutrition and 6-mercaptopurine affect both total RNA, and individual mRNA concentrations at specific sites in the gastrointestinal tract. These findings are of potentially great significance because the regulation of intestinal total RNA levels and purine salvage mRNAs by both 6-mercaptopurine and a purine- and pyrimidine-free diet suggests a potential mechanism by which dietary components differentially control specific proteins synthesized in the body. These findings may be related to the efficacy of 6-mercaptopurine as well as so-called elemental diets as therapeutic agents in chronic inflammatory bowel disease (i.e., Crohn's disease).

Adenine Phosphoribosyltransferase↗

PubMed1985

Pyrimidine dimers are not the principal pre-mutagenic lesions induced in lambda phage DNA by ultraviolet light.

Experiments were performed to examine the role of cyclobutyl pyrimidine dimers in the process of mutagenesis by ultraviolet (u.v.) light. Lambda phage DNA was irradiated with u.v. and then incubated with an Escherichia coli photoreactivating enzyme, which monomerizes cyclobutyl pyrimidine dimers upon exposure to visible light. The photoreactivated DNA was packaged into lambda phage particles, which were used to infect E. coli uvr- host cells that had been induced for SOS functions by ultraviolet irradiation. Photoreactivation removed most toxic lesions from irradiated phage, but did not change the frequency of induction of mutations to the clear-plaque phenotype. This implies that cyclobutyl pyrimidine dimers can be lethal, but usually do not serve as sites of mutations in the phage. The DNA sequences of mutants derived from photoreactivated DNA showed that almost two-thirds (16/28) were transitions, the same fraction found for u.v. mutagenesis without photoreactivation. These results show that in this system, the lesion inducing transitions (the major type of u.v.-induced mutation) is not the cyclobutyl pyrimidine dimer; a strong candidate for a mutagenic lesion is the Pyr(6-4)Pyo photoproduct. On the other hand, photoreactivation of SOS-induced host cells before infection with u.v.-irradiated phage reduced mutagenesis substantially. In this case, photoreversal of cyclobutyl dimers serves to reduce expression of the SOS functions that are required in the process of targeted u.v. mutagenesis.

Bacteriophage lambda↗

PubMed1985

Mutagenesis in UV-irradiated simian virus 40 occurs predominantly at pyrimidine doublets.

Phenotypic wild-type revertants from a UV-irradiated temperature-sensitive late mutant (ts BC245) of simian virus 40 (SV40) were isolated after replication in monkey cells at the nonpermissive temperature. The mutations occurring in 7 revertants were identified by DNA sequence analysis of the entire gene involved. All 10 mutations identified constituted single base substitutions, 7 of which occurred opposite pyrimidine doublets. Transitions were 3 times more abundant than transversions. Three base changes did not occur opposite pyrimidine-pyrimidine sequences. Exchange of a DNA fragment harbouring the altered base from a revertant with the corresponding fragment from the parental virus, showed that the base substitution was indeed responsible for the reversions to the wild-type phenotype (growth at the restrictive temperature). The data suggest that most base substitutions in highly UV-irradiated simian virus 40 are targeted at sites comprising two adjacent pyrimidines.

Animals↗

PubMed1982

Enzymes of purine and pyrimidine metabolism from the human malaria parasite, Plasmodium falciparum.

Plasmodium falciparum trophozoites were isolated by mechanical rupture of infected human erythrocytes followed by a series of differential centrifugation steps. After lysis with sonication, the 100 000 x g supernatant of parasites and uninfected host cells was used to determine the specific activities of a number of enzymes involved in purine and pyrimidine metabolism. P. falciparum possessed the purine salvage enzymes: adenosine deaminase, purine nucleoside phosphorylase, hypoxanthine-guanine phosphoribosyltransferase (PRTase), xanthine PRTase, adenine PRTase, adenosine kinase. The last two enzymes, however, were present at much lower activity levels. Hypoxanthine was converted (presumably via IMP) into adenine and guanine nucleotides only in the presence both of supernatant and membrane fractions of P. falciparum. Two enzymes involved in the de novo synthesis of pyrimidines, orotic acid PRTase, and orotidine 5'-phosphate decarboxylase, were present in parasite extracts as were the enzymes for pyrimidine nucleotide phosphorylation: UMP-CMP kinase, dTMP kinase, nucleoside diphosphate kinase. Xanthine oxidase, CTP synthetase, cytidine deaminase and several kinases for the salvage of pyrimidine nucleosides were not detected in the parasites. Both phosphoribosyl pyrophosphate synthetase and uracil PRTase were present but at low activity levels. Human erythrocytes displayed similar but not identical enzyme patterns. Enzyme specific activities, however, were generally much lower than those of the corresponding parasite enzymes.

Adenosine Deaminase↗

PubMed1985

Inhibition of pyrimidine biosynthesis de novo in Plasmodium falciparum by 2-(4-t-butylcyclohexyl)-3-hydroxy-1,4-naphthoquinone in vitro.

The effects of the hydroxynaphthoquinone BW58C on some metabolite levels and the flux of H14CO3 through the de novo pyrimidine biosynthetic pathway of intact Plasmodium falciparum have been studied in vitro using HPLC techniques. 800 nM BW58C appeared to have no significant effect on the energy status of isolated P. falciparum, but at 0.1 nM it caused a dramatic decrease in the concentrations of pyrimidine nucleotides, specifically UTP, during 256 min of incubation. Although about one hour was required to achieve a significant decrease in pyrimidine nucleotide concentrations, a much more rapid inhibition of the flux of H14CO3 through the de novo pathway was found upon addition of 0.1 nM BW58C. This inhibition caused about a 10 fold increase in the radioactivity of carbamoyl-aspartate over a 64 min period, and an overall increase in the concentration of this metabolite of about 3 fold during 256 min of incubation. These effects of BW58C against P. falciparum in vitro are discussed in terms of inhibition of de novo pyrimidine biosynthesis at the site of dihydroorotate dehydrogenase.

Adenosine Triphosphate↗

PubMed1986

A sensitive, enzymatic assay for the detection of closely opposed cyclobutyl pyrimidine dimers induced in human diploid fibroblasts.

A sensitive, enzymatic assay has been developed for the detection of closely opposed cyclobutyl pyrimidine dimers induced in UV-irradiated human diploid fibroblasts. In this assay closely opposed dimers are detected as bifilar enzyme-sensitive sites. Single-strand incisions are made at the positions of individual pyrimidine dimers through the action of M. luteus pyrimidine dimer-DNA glycosylase. Incisions at closely opposed dimers, effectively expressed as double-strand breaks, are quantified from the resulting reduction in DNA double-strand molecular weight as determined by velocity sedimentation through neutral sucrose density gradients. The stability of the bacteriophage lambda cos site under our reaction conditions indicates that opposed incisions must be relatively close to be expressed as a double-strand break. The dose response for the induction of bifilar enzyme-sensitive sites in mammalian cells was found to be complex but can be approximated by a function that increases as the 1.2-1.4 power of UV dose. The frequency of bifilar enzyme-sensitive sites observed decreased during postirradiation incubation of excision-repair-proficient human diploid fibroblasts with less than 20% still detectable at 24 h after irradiation with 5 J/m2 (254 nm). By comparison, over 80% of the bifilar enzyme-sensitive sites induced in fibroblasts assigned to xeroderma pigmentosum complementation group A remained detectable 24 h after irradiation. The implications of these results for models addressing the induction and repair of closely opposed pyrimidine dimers are discussed.

Cells, Cultured↗

PubMed1988

Photorepair of ultraviolet radiation-induced pyrimidine dimers in corneal DNA.

The induction and photorepair of pyrimidine dimers in DNA have been measured in the ultraviolet-irradiated, corneal epithelium of the marsupial, Monodelphis domestica, using damage-specific nucleases from Micrococcus luteus in conjunction with agarose gel electrophoresis. We observed that FS-40 sunlamps (280-400 nm) induced 7.2 +/- 1.0 X 10(-5) pyrimidine dimers per kilobase (kb) of DNA per J/m2. Following 100 J/m2, 50% and greater than 90% of the dimers were photorepaired during a 10- and 30-min exposure to photoreactivating light (320-400 nm), respectively. In addition, approximately 70% and approximately 60% of the dimers induced by 300 and 500 J/m2, respectively, were repaired by a 60-min exposure to photoreactivating light. The capacity of the corneal epithelium of M. domestica to photorepair pyrimidine dimers identifies this animal as a potentially useful model with which to determine whether pyrimidine dimers are involved in pathological changes of the irradiated eye.

Animals↗

PubMed1983

Different biosynthetic pathways of the pyrimidine moiety of thiamin in procaryotes and eucaryotes.

[14C]Formate is incorporated into the C-2 of the pyrimidine moiety of thiamin by Escherichia coli and Salmonella typhimurium. In Saccharomyces cerevisiae, it is incorporated into C-4. Radioactive carbons of [1-14C]glycine and [2-14C]glycine are incorporated by S. typhimurium into the C-4 and C-6 of the pyrimidine, respectively, but not by S. cerevisiae. These facts suggest that procaryotes and eucaryotes have different biosynthetic pathways for pyrimidine. In this study, the procaryotes tested incorporated [14C]formate into the C-2 and the eucaryotes incorporated it into the C-4 of the pyrimidine.

Aspergillus nidulans↗

PubMed1988

Isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma pyrimidine nucleosides and bases: concentration and radioactivity measurements.

A rapid and efficient isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma cytosine, uracil, thymine, cytidine, deoxycytidine and uridine has been elaborated. For each compound this method can measure concentrations in the range 0.5-200 microM and determine radioactivity. All the pyrimidine compounds can be eluted in less than 18 min, and the total time elapsed between collection of the blood and completion of the analysis need not exceed 3 h. All measurements can be performed on 0.025-ml blood samples. Blood plasma pyrimidine concentrations were determined for the rat, the rabbit, the guinea pig, the dog and the healthy human. This method could be well applied to experimentation on small animals using radiolabelled pyrimidine derivatives, in order to study the metabolic pathways of nucleotides and nucleic acids. It could also be used to characterize certain illnesses or cases of toxicity created by a chemotherapy affecting the plasma level of pyrimidine bases or nucleosides.

Animals↗

PubMedDate not supplied

Role of various carbon and nitrogen sources in the regulation of enzymes of pyrimidine biosynthesis in Mycobacterium smegmatis TMC 1546.

Pyrimidine biosynthesis and its regulation in the presence of different carbon and nitrogen sources in the growth medium of Mycobacterium smegmatis were studied. M. smegmatis TMC 1546 cells grown in shake culture were found to have marginally higher pyrimidine enzyme biosynthesis activities than cells grown in static culture. The activity was highest at the mid-log phase of growth during both surface and shake cultures, suggesting that the cells were metabolically most active at this stage of growth. Replacement of glycerol by glucose and fructose slightly increased the activities of carbamyl phosphate synthetase and aspartate transcarbamylase. The enzyme activities involved in pyrimidine biosynthesis decreased when citrate was replaced by succinate, fumarate, pyruvate or acetate in the growth medium. The activities of the enzymes in pyrimidine biosynthesis were found to decrease when asparagine as a nitrogen source in the medium was replaced by glutamate, glutamine or ammonium chloride. The presence of ornithine in place of asparagine in the growth medium increased these enzyme activities, while the presence of arginine instead of asparagine in the growth medium decreased these enzyme activities, though the differences in activity were small. The activity of aspartate transcarbamylase in vitro was inhibited by arginine. In the case of cells grown in the presence of ornithine, the activity of aspartate transcarbamylase was induced by ornithine, but inhibited by arginine.

Amino Acids↗

PubMed1989

Mitomycin C-induced postmitotic fibroblasts retain the capacity to repair pyrimidine photodimers formed after UV-irradiation.

The formation and excision of UV-C light-induced cyclobutane-type pyrimidine photodimers were determined in cultures of human skin fibroblasts at time zero and several weeks following treatment with mitomycin C (MMC). Characteristic morphological changes of the fibroblasts and specific shifts in the [35S]methionine polypeptide pattern of total cellular proteins support the notion that MMC accelerates the differentiation pathway from mitotic (MF) to post-mitotic fibroblasts (PMF). No discernible difference could be detected between the fluence-response curves of pyrimidine dimers for untreated and MMC-treated repair-deficient xeroderma pigmentosum cells of group A. Furthermore we investigated the removal of pyrimidine dimers in 3 normal human skin fibroblast strains frequently used in mutation, transformation and aging research. We were able to demonstrate that no significant difference exists in the rate and extent of the excision-repair response to thymine-containing pyrimidine dimers following UV-irradiation shortly after MMC treatment of fibroblasts and in the MMC-induced PMF stage of these cells.

Cell Differentiation↗

PubMed2003

Antiangiogenic and antitumor agents. Design, synthesis, and evaluation of novel 2-amino-4-(3-bromoanilino)-6-benzylsubstituted pyrrolo[2,3-d]pyrimidines as inhibitors of receptor tyrosine kinases.

Several different classes of growth factor receptors containing tyrosine kinases (RTK) are directly or indirectly involved in angiogenesis. Inhibition of these RTKs has provided a new paradigm in the treatment of tumors by restricting their growth and metastasis. We have designed, synthesized and evaluated eleven novel 2-amino-4-(3-bromoanilino)-6-substituted benzyl pyrrolo[2,3-d]pyrimidines as the first in a series of RTK inhibitors. These analogues were synthesized from appropriate alpha-bromomethylbenzyl ketones by cyclocondensation with 2,6-diamino-4-pyrimidone to afford the 2-amino-4-oxo-6-substituted benzyl pyrrolo[2,3-d]pyrimidines. Chlorination of the 4-position followed by displacement with 3-bromoaniline afforded the target compounds. In some instances, the 2-amino moiety of the pyrrolo[2,3-d]pyrimidines was protected prior to the chlorination and displacement followed by deprotection. The compounds were evaluated as inhibitors of vascular endothelial growth factor receptors VEGFR-2 (Flk-1, KDR) and VEGFR-1 (Flt-1); epidermal growth factor receptor (EGFR); and platelet-derived growth factor receptor-beta (PDGFR-beta). Selected compounds were also evaluated against the growth of A431 cells (which overexpress EGFR) in culture and as inhibitors of angiogenesis in the chicken embryo chorioallantonic membrane (CAM) assay. In each evaluation, a known standard compound was used as a comparison. Of the 11 analogues, five were more potent or equipotent as compared to standard compounds against the growth factor receptors. Two analogues showed superior inhibition of A431 cells in culture compared to the standard compounds. Three analogues were equipotent with the standard compound in the CAM assay and four of the analogues were dual inhibitors of RTKs. The structure-activity relationship for inhibition of different RTKs was quite distinct and different, and for VEGFR-2 and EGFR diametrically opposite. The inhibitory data against the RTKs in this study demonstrates that variation of the substituent(s) in the benzyl ring of these 2-amino-4-anilino 6-benzyl pyrrolo[2,3-d]pyrimidines does indeed control both the potency and specificity of inhibitory activity against RTKs.

Adenosine Triphosphate↗

PubMed2006

Organoiodine(III) mediated synthesis of 3,9-diaryl- and 3,9-difuryl-bis-1,2,4-triazolo[4,3-a][4,3-c]pyrimidines as antibacterial agents.

Nine 3,9-diaryl- and 3,9-difuryl-bis-1,2,4-triazolo[4,3-a][4,3-c]pyrimidines (3a-i) have been synthesized by the oxidation of bis-2,4-pyrimidinylhydrazones of various araldehydes and furfural with 2equiv of iodobenzene diacetate (IBD) in dichloromethane and tested in vitro for their antibacterial activity. Three compounds, namely 3,9-di-(4'-fluorophenyl)-bis-1,2,4-triazolo[4,3-a][4,3-c]pyrimidine (3f), 3,9-di-(4'-nitrophenyl)-bis-1,2,4-triazolo[4,3-a][4,3-c]pyrimidine (3g) and 3,9-di-(5'-nitro-2'-furyl)-bis-1,2,4-triazolo[4,3-a][4,3-c]pyrimidine (3i), were associated with substantially higher antibacterial activity than some commercial antibiotics against Gram-positive bacteria namely Staphylococcus aureus, Staphylococcus epidermidis and Bacillus subtilis; two Gram-negative bacteria namely Salmonella typhi and Escherichia coli at MIC (minimum inhibitory concentration) 10microg/ml.

Anti-Bacterial Agents↗

PubMed2006

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.

The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5' to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of approximately 20 degrees, twist angles of approximately 17 degrees). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, approximately 46 degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.

Base Sequence↗