Degradation Of Deoxyribonucleic Acid Research Articles

Dynamics of the degradation of tritium-substituted deoxyribonucleic acid in aqueous solution from dielectric relaxation and viscosity measurements

The molecular degradation of deoxyribonucleic acid substituted by tritium at medium and low radioactivity levels has been studied in aqueous solution by means of dielectric dispersion measurements in the frequency range 50–8000 Hz, and the mean molecular weight has been determined. From the results obtained we have been able to deduce that one effect of the β-radiation from the tritium incorporated in the DNA is that of the breaking of a double-strand to form lower-molecular-weight fragments. The degree of degradation is proportional to the radioactivity of the specimens. These results are in good agreement with those obtained from viscosity measurements.

Studies on a new antibiotic M-92 produced by micromonospora. V. Mechanism of action of the component VA-2.

Effects of VA-2, a component of quinoid antibiotic M-92, on the incorporation of radioisotope-labeled compounds into the cells of Staphylococcus aureus were studied. Deoxyribonucleic acid (DNA) synthesis was immediately inhibited by the addition of VA-2. Significant inhibitions of ribonucleic acid and protein syntheses and minor reduction of peptidoglycan synthesis were observed after a short delay. VA-2 immediately induced the degradation of DNA prelabelled with [14C]thymidine in the cells of S. aureus. In the examinations using E. coli enzyme and calf thymus DNA as a template, VA-2 prevented DNA-dependent DNA polymerase reaction. The inhibition of DNA polymerase I reaction was fairly reversed by increasing the concentration of template DNA, but slightly by that of the enzyme. Agarose gel electrophoresis showed that VA-2 elicited an extensive cleavage of PM2 cccDNA. VA-2 caused a primary conversion of the cccDNA to ocDNA at a low concentration (0.2 micrograms/ml), while at high concentrations (2.0 and 20 micrograms/ml) it cleaved the cccDNA to ocDNA and linear DNA progressively. These cleavages were observed even at 0 degrees C as well as at 37 degrees C, and were enhanced with the addition of a reducing agent such as 2-mercaptoethanol or sodium borohydride.

The effects of lexA101, recB21, recF143 and uvrD3 mutations on liquid-holding recovery in ultraviolet-irradiated Escherichia coli K12 rcA56

Using an Escherichia coli K12 recA strain, we have tested the effects of incorporating additional mutations affecting deoxyribonucleic acid (DNA) repair on ultraviolet-radiation sensitivity and on the expression of liquid-holding recovery (LHR). (This laboratory had previously shown that a mutation at uvrA, uvrB or uvrC blocked LHR in a recA strain). In the recA56 background, an additional lexA101 mutation had no effect on UV-radiation sensitivity or LHR. The addition of a recB21 mutation to recA56 did not alter UV-radiation sensitivity, but greatly increased the rate of LHR. The recB gene product (exonuclease V) appears to act as a competitive inhibitor both of excision repair and of photoreactivation under liquid-holding (LH) conditions. The uvrD3 mutation increased the radiation sensitivity of a recA strain, and almost completely blocked LHR. The recA uvrD strain showed more DNA degradation and DNA double-strand breaks during LH than did the reca strain. The recF143 mutation increased both UV-radiation senstivity and LHR in a recA strain, suggesting that the recF gene product may also function in recA-independent pathways of DNA repair.

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.

Synthesis of recA protein and induction of bacteriophage lambda in single-strand deoxyribonucleic acid-binding protein mutants of Escherichia coli.

We investigated the capacity of Escherichia coli mutants defective in the single-strand deoxyribonucleic acid (DNA)-binding protein to amplify the synthesis of the recA protein, induce prophage lambda, and degrade their DNA after treatment with ultraviolet radiation, mitomycin C, or bleomycin. The thermosensitive ssbA1 strain induced recA protein and lambda phage normally at 30 degrees C, but no induction was observed at 42 degrees C when ultraviolet radiation or mitomycin C was used. The lexC113 mutant did not amplify recA protein synthesis or induce phage lambda at either 30 or 42 degrees C with those agents. Bleomycin was able to elicit induction of recA and phage lambda in both mutants at any temperature. After induction with ultraviolet radiation at the elevated temperature, no DNA degradation was observed for 40 min, but at later times there was increased degradation in the lexC113 strain, compared with the wild type, and even greater degradation in the ssbA1 mutant. We discuss the role of single-strand DNA-binding protein in induction and the possibility that the lexC product may exert its influence on recA and lambda induction at the level of the single-strand DNA gap.

Apurinic/apyrimidinic endonuclease sensitive sites as intermediates in the in vitro degradation of deoxyribonucleic acid by neocarzinostatin.

Neocarzinostatin (NCS) induces alkali-labile sites in DNA which are stabilized by NaBH4 reduction. The stabilized sites are sensitive to an AP endonuclease from human lymphoma cells. NCS-induced degradation of supercoiled Col E1 DNA proceeds in stepwise fashion with apurinic/apyrimidinic (AP) sites as intermediates. Degradation is increased when reaction occurs in the presence of AP endonuclease, and DNA reacted with NCS can be shown to have numerous AP endonuclease sensitive sites.

Recombination-deficient mutant of Streptococcus faecalis.

An ultraviolet radiation-sensitive derivative of Streptococcus faecalis strain JH2-2 was isolated and found to be deficient in recombination, using a plasmid-plasmid recombination system. The strain was sensitive to chemical agents which interact with deoxyribonucleic acid and also underwent deoxyribonucleic acid degradation after ultraviolet irradiation. Thus, the mutant has properties similar to those of recA strains of Escherichia coli.

Ultraviolet light induction of recA protein in a recB uvrB mutant of Escherichia coli.

Full and persistent ultraviolet light induction of recA protein with minimal bacterial deoxyribonucleic acid degradation implicates blocked replication sites rather than degradation products as the inducing signals.

Influence of chromosome integrity on Escherichia coli cell division.

The antitumor agent cis-platinum(II)diamminodichloride (PDD) caused wild-type and recA+ deoxyribonucleic acid (DNA) repair-deficient mutant cells of Escherichia coli K-12 to grow as long, multinucleated filaments. At 5 micrograms/ml, the times required for reduction of viability to 37% for wild-type, polA, recB,C, uvrA, and recA organisms were > 200, 200, 120, 25, and 5 min, respectively. Only recA cells exhibited @reckless" degradation of DNA at this concentration of PDD. As shown by sedimentation in alkaline sucrose gradients, generation of single-strand breaks in DNA of the remaining organisms was a major consequence of growth in PDD. Upon incubation in fresh medium after removal of the compound and storage for 4 h at 4 degrees C, a respective lag of 3, 4, 6, and 9 h occurred before filaments of wild-type, polA, recB,C, and uvrA cells commenced cell division. Maintenance at 4 degrees C, which evidently delayed postshift initiation of chromosome replication, was only essential for fragmentation of uvrA filaments. In all cases, these periods of division delay corresponded to those required for restoration of normal chromosomal molecular weight as determined in alkaline sucrose gradients.

Mode of action of pesticin: N-acetylglucosaminidase activity

Homogeneous preparations of pesticin, a bacteriocin produced by Yersinia pestis, neither significantly inhibited net synthesis of deoxyribonucleic acid, ribonucleic acid, or protein in Escherichia coli phi nor caused detectable degradation of deoxyribonucleic acid in vivo. Accordingly, its mode of action does not resemble that of colicin E2 as suggested by others. However, incorporation of cell wall-specific label ([14C]diaminopimelic acid) into trichloroacetic acid-insoluble material of growing cells was inhibited by pesticin which also promoted release of such radioactivity from both resting cells and purified mureinlipoprotein. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of reaction mixtures containing appropriately labeled mureinlipoprotein showed that [3H]N-acetylglucosamine comigrated either with [14C]diaminopimelic acid in the murein peptide or with [14C]isoleucine of the Braun lipoprotein. As judged by these findings and pesticin-dependent release of reducing equivalents but not 4-hydroxy-2-acetamido sugars, the bacteriocin possesses N-acetylglucosaminidase activity. Hydrolysis of murein-lipoprotein occurred over a broad pH, with an optimum of 4.7. Mureinlipoproteins from a variety of pesticin-sensitive and -resistant organisms were hydrolyzed by the bacteriocin, indicating that its antibacterial specificity resides at the level of absorption.

Novel acriflavin resistance genes, acrC and acrD, in Escherichia coli K-12

Acriflavine-resistant mutants were isolated from an acriflavine-sensitive (acrA) strain of Escherichia coli K-12 and then tested for temperature sensitivity of cell division. Genetic analysis characterized two new genetic loci, acrC and acrD. The former was mapped between tonA and proA, and the latter between the origin of genetic transfer of HfrH and serB. acrC and acrD mutants could divide but did not initiate a new round of deoxyribonucleic acid (DNA) replication at 43 degrees C. DNA synthesis of the acrC mutant cells ceased after a period of time following temperature shift-up, and thereafter DNA degradation occurred. However, cell mass continued to increase for a long time at the nonpermissive temperature. On the other hand, DNA synthesis of the acrD mutant cells ceased soon after the shift-up, and the cell mass did not appreciably increase during the prolonged incubation.

Role of exonucleases V and VIII in adenosine 5'-triphosphate- and deoxynucleotide triphosphate-dependent strand break repair in toluenized Escherichia coli cells treated with X-rays

The repair of X-ray-induced strand breaks was studied in permeabilized Escherichia coli recBC cells deficient for the adenosine 5'-triphosphate (ATP)-dependent exonuclease V and in recBC sbcA cells that possess the ATP-independent exonuclease VIII. It is shown that repair induced by additon of ATP does not take place in recBC and recBC sbcB cells and is limited in recBC sbcA cells. ATP-dependent repair is nevertheless observable if together with ATP a mixture of deoxynucleotide monophosphates is supplied to the cells. These data fit with the assumption that in wild-type cells ATP-dependent repair involves exonuclease V-induced deoxyribonucleic acid degradation and rephosphorylation of the degradation products which are reused for deoxyribonucleic acid polymerase I-dependent break closure. Repair in the presence of deoxynucleotide triphosphates rejoins a similar fraction of breaks in all strains tested irrespective of the amount of postirradiation degradation resulting from exonuclease V and exonuclease VIII activities. Thus, exonuclease V is dispensable for deoxynucleotide triphosphate-dependent repair, i.e., does not "clean" the ends of breaks produced by X-irradiation. ATP- and deoxynucleotide triphosphate-dependent repair are not additive and seem to repair the same population of deoxyribonucleic acid molecules damaged by X-irradiation.

Enzymatic degradation of uracil-containing deoxyribonucleic acid. V. Survival of Escherichia coli and coliphages treated with sodium bisulfite

A number of mutants of Escherichia coli defective in the ung gene (structural gene for uracil-deoxyribonucleic acid [ura-DNA] glycosylase) are shown to be abnormally sensitive to treatment with sodium bisulfite when compared with congenic ung+ strains. These results provide further evidence that sodium bisulfite causes the deamination of cytosine to uracil in DNA and that ura-DNA glycosylase is required for the repair of U-G mispairs. The effect of the chemical is apparently selective with respect to base damage; coliphages containing cytosine in their DNA are inactivated by treatment with sodium bisulfite, whereas those containing hydroxymethylcytosine are not. ura-DNA glycosylase and the major apurinic-apyrimidinic endonuclease of E. coli may function in the same repair pathway, since the extent of inactivation of a congenic set of strains which are ung xth (structural gene for the major apurinic-apyrimidinic endonuclease of E. coli) or ung xth+ is the same.

Induction of deoxyribonucleic acid degradation inEscherichia coli by ozone

Cell survival and deoxyribonucleic acid (DNA) degradation wave measured for wild-type Escherichia coli B251 cells after exposure to different concentrations of ozone. The results show that extensive breakdown of DNA occurs after ozonation and that the extent of ozone-induced DNA degradation generally correlates with the colony-forming ability of the cells.

Mode of Action of Quindoxin and Substituted Quinoxaline-di- N -Oxides on Escherichia coli

The effect of quindoxin on the synthesis of deoxyribonucleic acid (DNA), ribonucleic acid, and protein in Escherichia coli KL 399 was examined under aerobic and anaerobic conditions. In the absence of oxygen the synthesis of DNA was completely inhibited by 10 ppm of quindoxin, whereas the syntheses of ribonucleic acid and protein were not affected. Quinoxalin-di-N-oxides (QdNO) induce degradation of DNA in both proliferating and non-proliferating cells. polA, recA, recB, recC, exrA, and uvrA mutants were more susceptible than the corresponding repair-proficient strains. All strains were more resistant in the presence of oxygen. Quindoxin was reduced to quinoxalin-N-oxide by intact E. coli cells or by a cell-free E. coli extract. Electron spin resonance measurements demonstrated the generation of free radicals during the reduction of quindoxin. Oxygen or deficiency of energy sources impaired the antibiotic activity and the reduction of QdNO. The QdNO reductase activity was demonstrated to be lower in QdNO-resistant mutants than in the susceptible parent strain. Based on these results it is concluded that an intermediate of reduction, probably a free radical, is responsible for the lethal effect of quindoxin. With three independent techniques no evidence has been found for binding of quindoxin to DNA.

Mode of action of the Haemophilus bactericidal factor

Haemocin, a bacteriocin produced by Haemophilus influenzae b, caused pronounced cell elongation of the sensitive strains H. influenzae Rd and Escherichia coli CR34 thyA. In the sensitive strains, haemocin markedly inhibited the synthesis of deoxyribonucleic acid (DNA) but did not affect either ribonucleic acid or protein synthesis. The observed inhibition in synthesis of DNA was not due to degradation of preexisting DNA. The data suggest that haemocin may specifically inhibit DNA synthesis.

Absence of strand breaks in deoxyribonucleic acid treated with metronidazole.

The deoxyribonucleic acid (DNA)-degrading potential of metronidazole was evaluated in vitro by three techniques: determination of melting curve, measurement of viscosity, and centrifugation in neutral or alkaline sucrose gradients. Studies were performed on calf thymus DNA and on (3)H-labeled or unlabeled pneumococcal and T7 phage DNA after treatment with metronidazole alone or metronidazole reduced by sodium dithionite in the presence of DNA. This latter process is known to elicit covalent binding of metronidazole to DNA. Reduced or unreduced metronidazole had no effect on the melting properties, viscosity, or sedimentation velocity of the nucleic acids studied. Sodium dithionite alone, however, caused a 25% decrease in the intrinsic viscosity of pneumococcal DNA, and decreased the sedimentation velocity of pneumococcal and T7 phage DNA in both neutral and alkaline sucrose gradients. These data suggest that degradation of DNA is not important in the interaction of metronidazole with nucleic acids, an interaction assumed relevant to the cytotoxic, radiosensitizing, and mutagenic activities of this compound.

Isolation and Characterization of a Bacillus subtilis Mutant with a Defective N -Glycosidase Activity for Uracil-Containing Deoxyribonucleic Acid

Crude cell extracts of Bacillus subtilis 168T exhibit enzyme activity capable of releasing free uracil from phage PBS1 deoxyribonucleic acid (DNA) in the presence of ethylenediaminetetraacetate. By measuring the enzyme activity in 300 clones that emanated from mutagenized cells, we obtained a mutant strain that did not show this N-glycosidase activity. The mutant strain, designated as TKJ6901 (urg-1) exhibited no physiological abnormalities. We observed the intracellular action of the enzyme by following the fate of uracil-containing DNA in cells from wild-type and mutant cultures. When infection with phage PBS1 was allowed in the presence of chloramphenicol, extensive degradation of phage DNA was observed only in the wild-type cells. When bromouracil residues were converted to uracil residues by ultraviolet light irradiation in the presence of cysteamine, the DNA was extensively fragmented in the wild-type cells. These single-strand breaks were rejoined upon postirradiation incubation. In contrast, such fragmentation of the DNA was not observed in the mutant cells, indicating that the uracil residues were not removed from the DNA. This demonstrated that the N-glycosidase activity was involved in the excision of uracil in DNA. A transformation assay with four types of recipient strains with combinations of N-glycosidase and DNA polymerase I deficiencies indicated that DNA polymerase I was involved in the later steps of this base excision repair pathway initiated by the action of the N-glycosidase.

Deoxyribonucleic acid repair in Escherichia coli mutants deficient in the 5'----3' exonuclease activity of deoxyribonucleic acid polymerase I and exonuclease VII

A series of Escherichia coli strains deficient in the 5'----3' exonuclease activity associated with deoxyribonucleic acid (DNA) polymerase I (exonuclease VI) and exonuclease VII has been constructed. Both of these enzymes are capable of pyrimidine dimer excision in vitro. These strains were examined for conditional lethality, sensitivity to ultraviolet (UV) and X-irradiation, postirradiation DNA degradation, and ability to excise pyrimidine dimers. It was found that strains deficient in both exonuclease VI (polAex-) and exonuclease VII (xseA-) are significantly reduced in their ability to survive incubation at elevated temperature (43 degrees C) beyond the reduction previously observed for the polAex single mutants. The UV and X-ray sensitivity of the exonuclease VI-deficient strains was not increased by the addition of the xseA7 mutation. Mutants deficient in both enzymes are about as efficient as wild-type strains at excising dimers produced by up to 40 J/m2 UV. At higher doses strains containing only polAex- mutations show reduced ability to excise dimers; however, the interpretation of dimer excision data at these doses is complicated by extreme postirradiation DNA degradation in these strains. The additional deficiency in the polAex xseA7 double-mutant strains has no significant effect on either postirradiation DNA degradation or the apparent deficiency in dimer excision at high UV doses observed in polAex single mutants.

Regulation of ribonucleoside diphosphate reductase synthesis in Escherichia coli: increased enzyme synthesis as a result of inhibition of deoxyribonucleic acid synthesis.

Inhibition of deoxyribonucleic acid (DNA) synthesis in Escherichia coli by chemical inhibitors or by shifting cultures of temperature-sensitive elongation (dnaE and dnaB) or initiation (dnaA) mutants to nonpermissive conditions led to greatly increased synthesis of the enzyme ribonucleoside diphosphate reductase, which catalyzes the first reaction unique to the pathway leading to DNA replication. In contrast to the Gudas and Pardee proposed model for control of the synthesis of DNA repair enzymes, in which both DNA inhibition and DNA degradation are involved, DNA synthesis inhibition in recA, recB, recC, or lex strains results in increased synthesis of ribonucleotide reductase, which suggests that DNA degradation is not required. We propose that inhibition of DNA synthesis causes a cell to accumulate an unknown compound that stimulates the initiation of a new round of DNA replication, and that this same signal is used to induce ribonucleotide reductase synthesis.