Selective inhibition of the polymerase activity of DNA polymerase. I. Further evidence for separate active sites for polymerase and 3' to 5' exonuclease activities

4 Final Report on the Safety Assessment of Captan

Captan is used in cosmetic products as a bacteriostat. Captan is not appreciably absorbed through the skin of mice. When administered orally to rats and absorbed, it is eliminated in the urine and feces. The compound is considered to be practically nontoxic to rats when orally administered. It is considered to be both a human irritant and sensitizer. Although teratogenic and reproductive studies indicated that Captan produced adverse effects in rats, mice, rabbits, and dogs, the ingredient was not teratogenic. Captan in the diet increased the incidence of intestinal neoplasms in mice.

Because Captan is mutagenic in vitro, produces intestinal neoplasms in mice following oral administration, and upon degradation becomes an elec-trophile, it is concluded that an 18-month skin carcinogenicity bioassay in mice must be conducted before a conclusion on the safety of Captan can be reached.

Mechanism of copper surface toxicity in Escherichia coli O157:H7 and Salmonella involves immediate membrane depolarization followed by slower rate of DNA destruction which differs from that observed for Gram-positive bacteria

We have reported previously that copper I and II ionic species, and superoxide but not Fenton reaction generated hydroxyl radicals, are important in the killing mechanism of pathogenic enterococci on copper surfaces. In this new work we determined if the mechanism was the same in non-pathogenic ancestral (K12) and laboratory (DH5α) strains, and a pathogenic strain (O157), of Escherichia coli. The pathogenic strain exhibited prolonged survival on stainless steel surfaces compared with the other E. coli strains but all died within 10 min on copper surfaces using a 'dry' inoculum protocol (with approximately 10(7)  cfu cm(-2) ) to mimic dry touch contamination. We observed immediate cytoplasmic membrane depolarization, not seen with enterococci or methicillin resistant Staphylococcus aureus, and loss of outer membrane integrity, inhibition of respiration and in situ generation of reactive oxygen species on copper and copper alloy surfaces that did not occur on stainless steel. Chelation of copper (I) and (II) ionic species still had the most significant impact on bacterial survival but protection by d-mannitol suggests hydroxyl radicals are involved in the killing mechanism. We also observed a much slower rate of DNA destruction on copper surfaces compared with previous results for enterococci. This may be due to protection of the nucleic acid by the periplasm and the extensive cell aggregation that we observed on copper surfaces. Similar results were obtained for Salmonella species but partial quenching by d-mannitol suggests radicals other than hydroxyl may be involved. The results indicate that copper biocidal surfaces are effective for Gram-positive and Gram-negative bacteria but bacterial morphology affects the mechanism of toxicity. These surfaces could not only help to prevent infection spread but also prevent horizontal gene transmission which is responsible for the evolution of virulent toxin producing and antibiotic resistant bacteria.

Age-associated changes in the template-reading fidelity of DNA polymerase alpha from regenerating rat liver

DNA polymerases (deoxynucleosidetriphosphate: DNA deoxynucleotidyltransferase EC 2.7.7.7.) were extracted from regenerating livers from young and aged rats. DNA polymerase alpha was separated and partially purified by DEAE-cellulose column chromatography, polyethyleneglycol precipitation, and phosphocellulose column chromatography, and fidelity levels were then monitored with the synthetic template-primer poly (dG-dC). The fidelity level of the DNA polymerase from regenerating liver a 4-month-old rat was very high, while that of the DNA polymerase from a 24-month-old rat was significantly decreased. To confirm this result, DNA was synthesized on poly (dG-dC) in a reaction mixture containing [32P]dTTP, and the synthetic polynucleotide was purified and digested with HhaI restriction endonuclease. After hydrolysis, the oligonucleotides were developed by two dimensional thin layer chromatography on PEI cellulose plates. Spots containing [32P]dTMP were observed when DNA polymerase from a 24 month-old rat was used, but none was found in polynucleotides synthesized using DNA polymerase from a 4 month-old rat. Nearest neighbor analysis suggested that dG-dT and dC-dT pairs were constructed by mis-incorporation due to DNA polymerase alpha.

Structure-function analysis of mononucleotides and short oligonucleotides in the priming of enzymatic DNA synthesis

The reversed-phase chromatography technique was employed in the measurement of DNA synthesis at the primers d(pT)n, r(pU)n, d(pA)n, and r(pA)n (n = 1-16) in the presence of template poly(dA) or poly(dT). DNA synthesis was catalyzed by Escherichia coli DNA polymerase I Klenow fragment, Physarum polycephalum DNA polymerase beta-like, P. polycephalum DNA polymerase alpha, and human placenta DNA polymerase alpha. Values of Km and Vmax were measured as functions of the primer chain lengths. It was found that all mononucleotides and small oligonucleotides served as primers of DNA synthesis. Values of the logarithm of both Km and Vmax increased linearly until primers had attained a chain length of 9-12 nucleotides, where a break was observed. The incremental as well as the absolute values of Km were interpreted in terms of free binding energies. These together with other data indicate that the 3'-ultimate nucleotide of the primer contributes a decisive amount of free energy of binding to DNA polymerase both from the nucleoside and from the phosphate moiety. The incremental increase is due to a complementary interaction between bases of primer and template buried in the binding cleft of the polymerase. It is also the ultimate nucleotide that determines whether the ribonucleotide or the deoxyribonucleotide is an efficient primer. It is of interest that the major results seem preserved for all four DNA polymerases. An energetic model for the binding of the template-primer was proposed and compared with available crystallographic data.

Raised cerebrospinal-fluid copper concentration in Parkinson's disease

The cerebrospinal-fluid copper concentration, measured by electrothermal atomisation/atomic absorption spectrophotometry, was significantly higher in 24 patients with untreated, idiopathic Parkinson's disease than in a control population of 34 patients (p less than 0.001). The difference in the in-vitro capacity of copper to damage DNA, measured by the phenanthroline assay was even greater. The high phenanthroline-copper concentration correlated with disease severity (p = 0.02) and with the rate of progression of disease (p less than 0.05). A possible role is suggested for copper-catalysed oxidative mechanisms in the pathogenesis of Parkinson's disease.

Alteration of the exonuclease activities of DNA polymerase I by captan

DNA polymerase I is a multifaceted enzyme with one polymerizing and two exonuclease activities. Captan was previously shown to be an inhibitor of this enzyme's polymerizing activity and this report measures the effects of captan on the two exonuclease activities. When the holoenzyme was tested, captan enhanced the degradation of poly(dA-dT), T7 DNA and, to a significantly lesser extent, heat-denatured DNA. However, when the effects of captan were tested as a function of substrate concentration, the stimulatory influence was measured only at high substrate concentrations. At low concentrations of DNA, captan was inhibitory. Inhibition and enhancement each showed an ED50 of the same value (approx. 100 microM). By assaying the two exonuclease activities separately it was shown that the differential effect on the holoenzyme by captan was the result of a combined inhibition of the 3'----5' exonuclease and enhancement of the 5'----3' exonuclease. Klenow fragment with poly(dA-dT) as substrate was used to assay for 3'----5' exonuclease activity. Captan inhibited this exonuclease and the inhibition could be prevented by the addition of greater concentrations of substrate. Holoenzyme and poly(rA)-poly(dT) were used to assay for 5'----3' exonucleolysis, which was enhanced at higher concentrations of substrate in the presence of captan.

Molecular mechanisms of manganese mutagenesis

The mechanism by which DNA polymerase discriminates between complementary and noncomplementary nucleotides for insertion into a primer terminus has been investigated. Apparent kinetic constants for the insertion of dGTP and dATP into the hook polymer d(C)194-d(G)12 with Escherichia coli DNA polymerase I (large fragment) were determined. The results suggest that the high specificity of base selection by DNA polymerase I is achieved by utilization of both Km and Vmax differences between complementary and noncomplementary nucleotides. The molecular basis for the increased error frequency observed with DNA polymerase I in the presence of Mn2+ has also been investigated. Our studies demonstrate that when Mn2+ is substituted for Mg2+, there is a higher ratio of insertion of incorrect to correct dNTP by the polymerase activity, accompanied by a decreased hydrolysis of a mismatched dNMP relative to a matched dNMP at the primer terminus by the 3',5' exonuclease activity. Kinetic analysis revealed that in the presence of Mn2+, the kcat for insertion of a complementary dNTP is reduced, whereas the catalytic rate for the insertion of a mismatched nucleotide is increased. The apparent Km values for either complementary or noncomplementary nucleotide substrates are not significantly altered when Mg2+ is replaced by Mn2+. The rate of hydrolysis of a mismatched dNMP at the primer terminus is greater in the presence of Mg2+ vs. Mn2+, whereas the rate of hydrolysis of a properly base-paired terminal nucleotide is greater in Mn2+ vs. Mg2+. These studies demonstrate that both the accuracy of base selection by the polymerase activity and the specificity of hydrolysis by the 3',5' exonuclease activity are altered by the substitution of Mn2+ for Mg2+.

Activated cyclophosphamide: an enzyme-mechanism-based suicide inactivator of DNA polymerase/3'-5' exonuclease

DNA polymerase I from E. coli can toxify activated cyclophosphamide (CP) by means of the 3'-5' exonuclease activity associated with the enzyme. Acrolein and an alkylating moiety are released in the process. Preincubation of DNA polymerase I with activated CP for 15-60 min leads to an increasing inhibition of DNA polymerase activity, which can be prevented when preincubation of DNA polymerase I with activated CP is carried out in the presence of 5' AMP, a competitive inhibitor of the 3'-5' exonuclease subsite of the enzyme. This demonstrates that toxification of activated CP by the 3'-5' exonuclease subsite of DNA polymerase is a prerequisite for the inhibition of DNA polymerase activity. The kinetics and the degree of DNA polymerase inhibition suggest that the alkylating moiety rather than acrolein released from activated CP during toxification is responsible for the inhibition of DNA polymerase. DNA polymerase with associated 3'-5' exonuclease activity has also been isolated from eukaryotic cells, and toxification of activated CP by such an enzyme (DNA polymerase delta from rabbit bone marrow) has been shown previously. Thus we suggest that toxification of activated CP by DNA polymerases/3'-5' exonucleases present mainly in proliferating cells might lead to the specific alkylation of macromolecules involved in the cell proliferation process, such as the DNA polymerase subsite of these enzymes and probably also the DNA bound to the enzymes. The relatively high cancerotoxic selectivity and cytotoxic specificity of activated CP could be based on this specific enzyme-mediated alkylation.

Degradation of deoxyribonucleic acid by a 1,10-phenanthroline-copper complex: the role of hydroxyl radicals

Degradation of deoxyribonucleic acid (DNA) by 1,10-phenanthroline has been shown to require Cu(II), a reducing agent, and O2. Other metal ions do not substitute for Cu(II), and degradation of DNA is inhibited by metal ions that can form stable complexes with 1,10-phenanthroline, such as Co(II), Cd(II), Ni(II), or Zn(II), as well as by chelators that can bind copper, such as triethyltetraamine, neocuproine, or ethylenediaminetetraacetic acid (EDTA). Neocuproine, a specific copper chelator, is more effective than EDTA in inhibiting the breakdown of DNA. The degradation of DNA shows a requirement for a reducing agent which can be satisfied by either ascorbate or a thiol. A free radical generating system, e.g., xanthine oxidase-hypoxanthine, can substitute for the reducing agent. DNA degradation, in the presence of either an organic reducing agent or xanthine oxidase-hypoxanthine, is inhibited by hydroxyl radical scavengers and by catalase, suggesting that hydroxyl radical is the reactive species in DNA degradation and that hydrogen peroxide is an intermediate in hydroxyl radical generation.