Effect of phosphatidylcholine vesicles on the activity of DNA polymerase-α

Summary Phosphatidylcholine vesicles stimulate the activity of the DNA polymerase- from calf thymus. This effect is dependent upon the way of addition of the Mg ions, and the extent of the ³H-dTTP incorporation is closely related to the concentration of the vesicles. A role of phospholipids on the activity of the DNA-related enzymes is suggested.     

Effect of Oxidized Polyamines on the Infectivity of φX174 DNA

Oxidized spermine and oxidized spermidine inhibited markedly the infectivity of the 6 m-urea treated φX174 particle, whereas they did not inactivate the infectivity of the untreated phage particle. They also markedly inhibited the infectivity of φX174 DNA, while φX174 RF I DNA was less sensitive to these reagents. These facts suggested that oxidized polyamines could react with phage DNA.

The possible reasons of the insensitivity of phage φX174 particle and less sensitivity of φX174 RF I DNA to these reagents were discussed.     

Effect of Chloramphenicol on the DNA Synthesis of Bacteriophage ϕX174

In bacteriophage ?X174 infection, the net synthesis of replicative form DNA ceased between 15 and 20 min after infection. When 30 μg of chloramphenicol/ml was added, net RF synthesis, however, continued beyond the normal time and level of turn-off. Experiments with ?X174 mutants unable to synthesize single-stranded DNA showed that a protein synthesis was required for the cessation of net RF synthesis and the protein was synthesized between 10 and 15 min after infection.     

Effects of glutathione on chromium‐induced DNA. Crosslinking and DNA polymerase arrest

Hexavalent chromium (Cr (VI)) is reduced intracellularly to Cr (V), Cr (IV) and Cr (III) by ascorbate (Asc), cysteine and glutathione (GSH). These metabolites induce a spectrum of genomic DNA damage resulting in the inhibition of DNA replication. Our previous studies have shown that treatment of DNA with Cr (III) or Cr (VI) plus Asc results in the formation of DNACrDNA crosslinks (CrDDC) and guaninespecific arrests of both prokaryotic and mammalian DNA polymerases. GSH not only acts as a reductant of Cr (VI) but also becomes crosslinked to DNA by Cr, thus, the focus of the present study was to examine the role of GSH in Crinduced DNA damage and polymerase arrests. Coincubation of Cr (III) with plasmid DNA in the presence of GSH led to the crosslinking of GSH to DNA. GSH cotreatment with Cr (III) also led to a decrease in the degree of Crinduced DNA interstrand crosslinks relative to Cr (III) alone, without affecting total Cr DNA binding. DNA polymerase arrests were observed following treatment of DNA with Cr (III) alone, but were markedly reduced when GSH was added to the reaction mixture. Preformed polymerasearresting lesions (CrDDC) were not removed by subsequent addition of GSH. Treatment of DNA with Cr (VI), in the presence of GSH, resulted in crosslinking of GSH to DNA, but failed to produce detectable DNA interstrand crosslinks or polymerase arrests. The inhibitory effect of GSH on Crinduced polymerase arrest was further confirmed in human genomic DNA using quantitative PCR (QPCR) analysis. Treatment of genomic DNA with Cr (III) resulted in a marked inhibition of the amplification of a 1.6 kb target fragment of the p53 gene by Taq polymerase. This was almost completely prevented by cotreatment with GSH and Cr (III). These results indicate that Crinduced DNA interstrand crosslinks, and not DNACrGSH crosslinks, are the principal lesions responsible for blocking DNA replication. Moreover, the formation of DNACrGSH crosslinks may actually preclude the formation of the polymerase arresting lesions.     

Organization of the variant domains of α satellite DNA on human chromosome 21

The de novo creation of long, homogeneous, satellite DNA domains was postulated previously to occur by saltatory amplification. In this paper, pulsed field gel electrophoresis analysis of the α satellite DNA block organization of the human chromosome 21 supports this hypothesis. Double-dimension electrophoresis indicated that the variant copies of the basic α satellite repeat of chromosome 21 are organized in a single 3,150 Kblong domain. It was also established that the other satellite DNAs found in man (β, II, and III) are organized independently of the α satellite DNA block of the same chromosome. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

The effects ofγ-irradiation on the hydration characteristics of DNA and polynucleotides

Summary The effects of-irradiation and changes in the macromolecular structure on the water proton resonance spectra observed in frozen and liquid solutions have been compared for the DNA and polynucleotide solutions, using H₂O or mixed H₂O/D₂O solvents. The results indicate that in order to obtain information concerning the role of hydration water in mediating the overall radiation damage, the NMR studies must be performed in the frozen state.Member of the Euratom biology division     

The effect of temperature on the electrochemical properties of copper—DNA membranes

The influence of temperature, electrode plate metals and protamine on the membrane potential of an electrochemically prepared copper—DNA (Cu-DNA) membrane (size, 2.5×6cm; thickness, 80μm; Cu/P molar ratio, 0.4) was investigated. The results obtained showed that the membrane potential increased with temperature as well as with increasing order of ionization tendency of the divalent metals used, and decreased with an increase of protamine bound to the membrane. These results indicated that electrons accumulated on the anode side, and positive holes formed on the cathode side, of a Cu-DNA membrane prepared by electrolysis.     

Lack of DNA polymerase μ affects the kinetics of DNA double-strand break repair and impacts on cellular senescence

The specialised DNA polymerase μ (pol μ) affects a sub-class of immunoglobulin genes rearrangements and haematopoietic development in vivo. These effects appear linked to double-strand breaks (DSBs) repair, but it is still unclear how and to what extent pol μ intervenes in this process. Using high-resolution quantitative imaging of DNA damage in irradiated wild-type and pol μ^?/? mouse embryonic fibroblasts (MEFs) we show that lack of pol μ results in delayed DSB repair kinetics and in persistent DNA damage. DNA damage triggers cellular senescence, and this response is thought to suppress cancer. Independent investigations either report or not a proliferative decline for MEFs lacking pol μ. Here we show pronounced senescence in pol μ^?/? MEFs, associated with high levels of the tumor-suppressor p16^INK4A and the DNA damage response kinase CHK2. Importantly, cellular senescence is induced by culture stress and exacerbated by low doses of irradiation in pol μ^?/? MEFs. We also found that low doses of irradiation provoke delayed immortalisation in MEFs lacking pol μ. Pol μ^?/? MEFs thus exhibit a robust anti-proliferative defence in response to irreparable DNA damage. These findings indicate that sub-optimal DSB repair, due to the absence of an auxiliary DNA damage repair factor, can impact on cell fitness and thereby on cell fate.     

A Study on the Mechanism of DNA Excretion from P. aeruginosa KYU-1—Effect of Mitomycin C on Extracellular DNA Production—

The mechanism of excretion of DNA was investigated using strain KYU-1. This strain produced a considerable amount of DNA extracellularly (7.8mg/ml), and the amount of extracellular DNA per ml of the culture was scores of times more compared to that of intracellular DNA per ml of the culture. DNA synthesis was repressed by the addition of inhibitors (nalidixic acid, 5-fluoro uracil or mitomycin C), their inhibition rates were 35 to 54%. With the addition of 100 μg/ml of mitomycin C at the middle of the logarithmic growth phase, only 0.89 mg of extracellular DNA per ml of the culture was obtained, the inhibition rate was 95%. However, the amount of organic phosphate synthesized in the culture was almost the same no matter whether with or without an inhibitor.

Furthermore, the excretion of DNA from the cell surface of strain KYU-1 was observed with on electron microscope and the DNA molecules excreted were found to be double-stranded.     

Effect of spermine on interaction of DNA polymerase α from the loach (Misgurnus fossilis) eggs with DNA

Polyamines (putrescine, spermidine and spermine) cause a marked increase in the activity of the loach Misgurnus fossilis DNA polymerase α on activated (gapped) DNA. The stimulatory effect increases in the order: putrescine, spermidine, spermine. Kinetic analysis shows that spermine does not change the affinity of the polymerase for dTTP, but it decreases the enzyme affinity for DNA. The apparent K_m of the polymerase for activated DNA progressively increases from 14 to 1200 μM (nucleotide), if the concentration of spermine rises up to 2 mM, while V_max reaches a maximum at 0.5 mM spermine and then drops at higher polyamine concentrations. Native calf thymus DNA and especially single-stranded DNA from phage M13 appear to be inhibitors of α-polymerase activity on gapped DNA. Dixon plots suggest simple competitive inhibition of the polymerase activity by single- or double-stranded DNA and absence of cooperativity in the interaction of the polymerase with DNA. Hill-plot analysis is compatible with the interpretation that there is only one DNA binding site on each DNA polymerase α molecule. Spermine, even at low concentrations, decreases sharply the affinity of the enzyme for double-stranded DNA, while the enzyme affinity for single-stranded DNA changes insignificantly. Another result of spermine action is the destabilization of the polymerase-DNA complex. The ratio of the ‘static affinity’ of the enzyme to its ‘kinetic affinity’ decreases 2.2-fold in the presence of 0.5 mM spermine. As a result, the sensitivity of DNA synthesis to 3′-deoxy-3′-aminothymidine 5′-triphosphate and to 1-β-d-arabinofuranosylcytidine 5′-triphosphate decreases in the presence of the polyamine. Both spermine effects, the decrease in the ‘nonproductive binding’ of the polymerase to double-stranded regions in DNA and the destabilization of the polymerase-DNA complex, presumably account for the increase in the activity of the loach α-polymerase on activated DNA.     

Effect of Supporting Substrates on the Structure of DNA and DNA–Trivaline Complexes Studied by Atomic Force Microscopy

Linear DNA, circular DNA, and circular DNA complexes with trivaline (TV), a synthetic oligopeptide, were imaged by atomic force microscopy (AFM) using mica as a conventional supporting substrate and modified highly ordered pyrolytic graphite (HOPG) as an alternative substrate. A method of modifying the HOPG surface was developed that enabled the adsorption of DNA and DNA–TV complexes onto this surface. On mica, both purified DNA and DNA–TV complexes were shown to undergo significant structural distortions: DNA molecules decrease in height and DNA–TV displays substantial changes in the shape of its circular compact structures. Use of the HOPG support helps preserve the structural integrity of the complexes and increase the measured height of DNA molecules up to 2 nm. AFM with the HOPG support was shown to efficiently reveal the particular points of the complexes where, according to known models of their organization, a great number of bent DNA fibers meet. These results provide additional information on DNA organization in its complexes with TV and are also of methodological interest, since the use of the modified HOPG may widen the possibilities of AFM in studying DNA and its complexes with various ligands.     

The impact of the C-terminal domain on the interaction of human DNA topoisomerase II α and β with DNA

Background

Type II DNA topoisomerases are essential, ubiquitous enzymes that act to relieve topological problems arising in DNA from normal cellular activity. Their mechanism of action involves the ATP-dependent transport of one DNA duplex through a transient break in a second DNA duplex; metal ions are essential for strand passage. Humans have two isoforms, topoisomerase IIα and topoisomerase IIβ, that have distinct roles in the cell. The C-terminal domain has been linked to isoform specific differences in activity and DNA interaction.

Methodology/Principal Findings

We have investigated the role of the C-terminal domain in the binding of human topoisomerase IIα and topoisomerase IIβ to DNA in fluorescence anisotropy assays using full length and C-terminally truncated enzymes. We find that the C-terminal domain of topoisomerase IIβ but not topoisomerase IIα affects the binding of the enzyme to the DNA. The presence of metal ions has no effect on DNA binding. Additionally, we have examined strand passage of the full length and truncated enzymes in the presence of a number of supporting metal ions and find that there is no difference in relative decatenation between isoforms. We find that calcium and manganese, in addition to magnesium, can support strand passage by the human topoisomerase II enzymes.

Conclusions/Significance

The C-terminal domain of topoisomerase IIβ, but not that of topoisomerase IIα, alters the enzyme''s K_D for DNA binding. This is consistent with previous data and may be related to the differential modes of action of the two isoforms in vivo. We also show strand passage with different supporting metal ions for human topoisomerase IIα or topoisomerase IIβ, either full length or C-terminally truncated. They all show the same preferences, whereby Mg > Ca > Mn.     

Dependence ofγ-irradiated Y-peak and melting of DNA on concentration and ionic environment

Summary Y-peak is found to be a function of ionic strength and concentrations of DNA. The Y-peak reveals close dynamic interaction between DNA and solvent system. Electronic transitions responsible for Y-peak are not the same transitions that are responsible for X-peak. Y-peak's electronic transitions are indicative of charge transfer complex formation between DNA and solvent system.-irradiation induces hyperchromicity due to strand separation at lower doses. A-T base pairs are first to undergo coiled state as shown byTm spread. Strand chopping and saturation of double bonds of the exposed bases by free radicals (H° and OH°) give rise to hypochromic regions at X-peak. Rise in ionic strength and the concentration of DNA has protective effect against-damage. Y-peak is found to be a function of solvent, whereas, X-peak is independent of solvent nature.     

Effects of 2＇-O-methyl nucleotide on ligation capability of T4 DNA ligase

To further understand the ligation mechanism, effects of 2＇-O-methyl nucleotide （2＇-OMeN） on the T4 DNA ligation efficiency were investigated. Fluorescence resonance energy transfer assay was used to monitor the nick-joining process by T4 DNA ligase. Results showed that substitutions at 5＇- and 3＇-ends of the nick decreased the ligation efficiency by 48.7% ± 6.7% and 70.6% ±4.0%, respectively. Substitutions at both 5＇- and 3＇-ends decreased the ligation efficiency by 76.6%±1.3%. Corresponding kinetic para- meters, Vmax, Kin, and kcat, have been determined in each case by using the Michaelis-Menten equation. The kinetic data showed that the 2＇-OMeN substitutions reduced the maximal initial velocity and increased the Michaelis constant of T4 DNA ligase. Mismatches at 5＇- and 3＇-ends of the nick have also shown different influences on the ligation. Results here showed that the sugar pucker conformation at 3＇-end impairs the ligation efficiency more profoundly than that at 5＇-end. Different concentrations of Mg2＋, Ca2＋, K＋, Na＋, and ATP were also demonstrated to affect the T4 DNA ligase activ- ity. These results enriched our knowledge about the effects of 2＇-OMEN substitutions on the T4 DNA ligase.     

Effects of different extenders on DNA integrity of boar spermatozoa following freezing–thawing

The sperm-rich fraction, collected from eight mature Yorkshire boars, was frozen in an extender containing 9% LDL (w/v), 100 mM trehalose, or 20% yolk (v/v), respectively. Sperm DNA integrity was assessed using the single-cell gel electrophoresis (SCGE). Other sperm quality characteristics such as motility, acrosome and membrane integrity were also monitored. The results showed that freezing–thawing caused an increase in sperm DNA fragmentation, and extender containing 9% LDL could significantly protect sperm DNA integrity (P < 0.05) from the damage caused by cryopreservation and decrease DNA damages compared with extender containing 100 mM trehalose and 20% yolk (v/v). No significant difference in damaged DNA was detected between frozen and unfrozen semen samples for extender of 9% LDL and 100 mM trehalose, but cryopreservation could increase the degree of DNA damage (P < 0.05), the percentage of damaged DNA degree of grade 2 and 3 was significantly increased. The deterioration in post-thaw sperm DNA integrity was concurrent with reduced sperm characteristics. The data here demonstrated that the cryoprotectant played a fundamental role in reducing boar sperm DNA damage and protecting DNA integrity. It can be suggested that evaluation of sperm DNA integrity, coupled with correlative and basic characteristics such as motility, acrosome integrity and membrane integrity, may aid in determining the quality of frozen boar semen.     

Effect of α-difluoromethylornithine on polyamine and DNA synthesis in regenerating rat liver: Reversal of inhibition of DNA synthesis by putrescine

The possibility that α-difluoromethylornithine, a specific, irreversible inhibitor of ornithine decarboxylase could be used to prevent the rise in hepatic putrescine and spermidine content following partial hepatectomy was tested. Administration of α-difluoromethylornithine at a dose of 400 mg/kg every 4 h reduced hepatic putrescine to <2 nmol/g, but had only a small effect on the rise in spermidine seen at 28 h after partial hepatectomy. Such treatment also reduced the rise in DNA synthesis produced by partial hepatectomy by up to 70%. The inhibitory effect towards DNA synthesis could be reversed by administration of putrescine which increased the hepatic putrescine content to about 30–40% of that in the regenerating control livers. These results suggest that accumulation of putrescine rather than spermidine is needed for DNA synthesis after partial hepatectomy. They also suggest that part, but not all of the rise in putrescine normally seen in the liver after partial hepatectomy is needed for the enhanced DNA synthesis associated with liver regeneration. Experiments with lower doses of α-difluoromethylornithine showed that a substantial part of the rise in hepatic ornithine decarboxylase activity could be abolished without affecting either the rise in spermidine content or the increase in DNA synthesis after partial hepatectomy.     

The effects of DNA intercalators on chromatin of chicken red blood cells——differential extraction on nonhistone proteins

Taking advantage of the effects on DNA secondary structure of two DNA-intercalators,ethidium bromide and chloroquine,we used each of them to treat nuclei from both mature erythrocytes and reticulocytes of chicken,as an alternative approach to study the relationships between DNA secondary structure,nuclear proteins and chromatin structure.We presented results of differential extraction of nuclear proteins from nuclei with DNA-intercalators,as well as preliminary characterization of these proteins.A 45kd protein is the major component in fractions extracted by both intercalators from nuclei from either mature erythrocytes or reticulocytes and seems to be a DNA-binding protein.Furthermore,from current concepts of functional aspects of DNA conformation and structural heterogeneity in chromatin and nuclear proteins,we have discussed both the significance of our results as well as technical aspects of this approach.