Kinetic behavior of the reaction between hydroxyl radical and the SV40 minichromosome.

Aqueous solutions containing the minichromosomal form of the virus SV40 and the radical scavenger DMSO were subjected to gamma-irradiation, and the resulting formation of single strand breaks (SSB) was quantified. Under the irradiation conditions, most SSBs were produced as a consequence of hydroxyl radical ((•)OH) reactions. By controlling the competition between DMSO and the viral DNA substrate for (•)OH, we are able to estimate the rate coefficient for the reaction of (•)OH with the SV40 minichromosome. The results cannot be described adequately by homogeneous competition kinetics, but it is possible to describe the rate coefficient for the reaction as a function of the scavenging capacity of the solution. The experimentally determined rate coefficient lies in the range 1×10(9) - 2×10(9) L mol(-1) s(-1) at 10(7) s(-1), and increases with increasing scavenging capacity.

Repair of oxidative DNA damage by amino acids.

Guanyl radicals, the product of the removal of a single electron from guanine, are produced in DNA by the direct effect of ionizing radiation. We have produced guanyl radicals in DNA by using the single electron oxidizing agent (SCN)2-, itself derived from the indirect effect of ionizing radiation via thiocyanate scavenging of OH. We have examined the reactivity of guanyl radicals in plasmid DNA with the six most easily oxidized amino acids cysteine, cystine, histidine, methionine, tryptophan and tyrosine and also simple ester and amide derivatives of them. Cystine and histidine derivatives are unreactive. Cysteine, methionine, tyrosine and particularly tryptophan derivatives react to repair guanyl radicals in plasmid DNA with rate constants in the region of approximately 10(5), 10(5), 10(6) and 10(7) dm3 mol(-1) s(-1), respectively. The implication is that amino acid residues in DNA binding proteins such as histones might be able to repair by an electron transfer reaction the DNA damage produced by the direct effect of ionizing radiation or by other oxidative insults.

Evaluation of lesion clustering in irradiated plasmid DNA.

PURPOSE: To measure the yield of DNA strand breaks and clustered lesions in plasmid DNA irradiated with protons, helium nuclei, and y-rays. MATERIALS AND METHODS: Plasmid DNA was irradiated with 1.03, 19.3 and 249 MeV protons (linear energy transfer = 25.5, 2.7, and 0.39 keV microm(-1) respectively), 26 MeV helium nuclei (25.5 keV microm) and gamma-rays (137Cs or 60Co) in phosphate buffer containing 2 mM or 200 mM glycerol. Single-and double-strand breaks (SSB and DSB) were measured by gel electrophoresis, and clustered lesions containing base lesions were quantified by converting them into irreparable DSB in transformed bacteria. RESULTS: For protons, SSB yield decreased with increasing LET (linear energy transfer). The yield of DSB and all clustered lesions seemed to reach a minimum around 3 keV microm(-1). There was a higher yield of SSB, DSB and total clustered lesions for protons compared to helium nuclei at 25.5 keV microm(-1). A difference in the yields between 137Cs and 60Co gamma-rays was also observed, especially for SSB. CONCLUSION: In this work we have demonstrated the complex LET dependence of clustered-lesion yields, governed by interplay of the radical recombination and change in track structure. As expected, there was also a significant difference in clustered lesion yields between various radiation fields, having the same or similar LET values, but differing in nanometric track structure.

Yield of single-strand breaks due to attack on DNA by scavenger-derived radicals.

We have measured the yield of single-strand breaks (SSBs) in plasmid DNA after 137Cs gamma irradiation, in the presence of dimethyl sulfoxide (DMSO). In the presence of oxygen, the formation of SSBs is due to hydroxyl radical attack. As the DMSO concentration is increased from 10(-4) mol dm-3 to 1 mol dm-3, the SSB yield in the presence and absence of oxygen decreases by over 100-fold and less than 10-fold, respectively. From the DMSO and DNA concentration dependencies of the SSB yield in the absence of oxygen, the second-order rate constant for the reaction of the methyl radical (derived from DMSO) and DNA can be estimated as k2 = 8.8 x 10(4) dm3 mol-1 s-1. Several other scavengers were compared with DMSO under anoxia. Radicals derived from isopropyl alcohol and glycerol also caused SSB formation in DNA, while those from 2-deoxyribose, thymine, 1,3-dimethylthymine and 1,3-dimethyluracil did not. In the case of the scavenger tert-butyl alcohol, it is unclear whether the hydrogen atom (H.) or an organic radical is responsible for the higher SSB yield under anoxic conditions.

The effect of superhelical density on the yield of single-strand breaks in gamma-irradiated plasmid DNA.

Using agarose gel electrophoresis, the formation of DNA single-strand breaks (SSBs) by 137Cs gamma irradiation was quantified in negatively supercoiled topological isomers of plasmid pUC18. The G value for SSB formation falls slightly from 1 x 10(8) to 8 x 10(-9) SSB Gy-1 Da-1 as the superhelical density varies from 0.00 to -0.08. This result is not in agreement with recent observations by others which suggest that increasing the negative superhelical density of plasmid DNA increases its sensitivity to X irradiation.

Variation of single-strand break yield with scavenger concentration for plasmid DNA irradiated in aqueous solution.

We have measured the yield of single-strand breaks (SSBs), induced by 137Cs gamma radiation as assayed by agarose gel electrophoresis, for three plasmids and SV40 DNA irradiated in aerobic aqueous solution. DNA SSBs are caused mainly by the hydroxyl radical under these conditions. To characterize the reactivity of DNA with the hydroxyl radical, we investigated the variation of the G value for SSBs [G(SSB)] with the concentration of added hydroxyl radical scavengers. We find that simple competition kinetics does not describe our results, but that a nonhomogeneous kinetics model is in good agreement. At a DNA concentration of 50 micrograms cm-3, G(SSB) for the direct effect is about 1 x 10(-5) mumol J-1 for the DNA substrates studied. This is equivalent to 2 x 10(-10) SSB Gy-1 Da-1. Estimates of the efficiency of SSB induction per OH. radical interaction with DNA (0.32-0.44) reveal that all plasmids are essentially equal in reactivity.

Variation of single-strand break yield with scavenger concentration for the SV40 minichromosome irradiated in aqueous solution.

We have measured the yield of single-strand breaks (SSBs) induced in aerobic aqueous solution by 137Cs gamma irradiation for the SV40 minichromosome as measured by agarose gel electrophoresis. Under these conditions, DNA SSBs are caused mainly by the hydroxyl radical. To characterize the reactivity of the SV40 minichromosome with the hydroxyl radical and to compare its behavior with that of naked DNA, we examined the variation of the G value for SSB formation, G(SSB), with the concentration of added hydroxyl radical scavengers. We find that simple competition kinetics is not applicable, but that a nonhomogeneous kinetics model is in much better agreement. Estimates of the efficiency of SSB induction per OH radical interaction with the SV40 minichromosome (0.04-0.05) indicate that this substrate is about five times more radioresistant than naked DNA at scavenging capacities < 10(8) s-1. At a DNA concentration of 50 micrograms ml-1, G(SSB) for the direct effect in the minichromosome is about 1 x 10(-5) mumol J-1 (2 x 10(-10) SSB Gy-1 Da-1), essentially equal to that for naked DNA.

Critical target and dose and dose-rate responses for the induction of chromosomal instability by ionizing radiation.

To investigate the critical target, dose response and dose-rate response for the induction of chromosomal instability by ionizing radiation, bromodeoxyuridine (BrdU)-substituted and unsubstituted GM10115 cells were exposed to a range of doses (0.1-10 Gy) and different dose rates (0.092-17.45 Gy min(-1)). The status of chromosomal stability was determined by fluorescence in situ hybridization approximately 20 generations after irradiation in clonal populations derived from single progenitor cells surviving acute exposure. Overall, nearly 700 individual clones representing over 140,000 metaphases were analyzed. In cells unsubstituted with BrdU, a dose response was found, where the probability of observing delayed chromosomal instability in any given clone was 3% per gray of X rays. For cells substituted with 25-66% BrdU, however, a dose response was observed only at low doses (<1.0 Gy); at higher doses (>1.0 Gy), the incidence of chromosomal instability leveled off. There was an increase in the frequency and complexity of chromosomal instability per unit dose compared to cells unsubstituted with BrdU. The frequency of chromosomal instability appeared to saturate around approximately 30%, an effect which occurred at much lower doses in the presence of BrdU. Changing the gamma-ray dose rate by a factor of 190 (0.092 to 17.45 Gy min(-1)) produced no significant differences in the frequency of chromosomal instability. The enhancement of chromosomal instability promoted by the presence of the BrdU argues that DNA comprises at least one of the critical targets important for the induction of this end point of genomic instability.

Characterization of the reaction rate coefficient of DNA with the hydroxyl radical.

Using agarose gel electrophoresis, we have measured the yield of single-strand breaks (SSBs) induced by 137Cs gamma irradiation in a variety of plasmid DNA substrates ranging in size from 2.7 kb to 38 kb irradiated in aerobic aqueous solution in the presence of the hydroxyl radical scavenger dimethyl sulfoxide (DMSO). Under these conditions DNA SSBs are caused mainly by the hydroxyl radical. Using the competition between DMSO and DNA for the hydroxyl radical, we have estimated the rate coefficient for the reaction of the hydroxyl radical with DNA. The results cannot be characterized by conventional steady-state competition kinetics. However, it is possible to describe the second-order rate constant for the reaction as a function of the scavenging capacity of the solution. The second-order rate constant increases with increasing scavenging capacity, rising from about 5 x 10(8) dm3 mol-1 s-1 at 10(5) s-1 to about 10(10) dm3 mol-1 s-1 at 10(10) s-1. This dependence of the second-order rate constant on the scavenging capacity appears to be more pronounced for larger plasmids.

Yield of strand breaks as a function of scavenger concentration and LET for SV40 irradiated with 4He ions.

We have measured by gel electrophoresis the yields of single- and double-strand breaks (SSBs and DSBs) induced in aqueous solutions of SV40 DNA and the SV40 minichromosome by 137Cs gamma rays (mean LET 0.3 keV micron-1) and 4He ions (mean LETs 85, 102, and 152 keV microns-1). DNA SSBs are caused mainly by the hydroxyl radicals under these conditions and are reduced in yield as either the hydroxyl radical scavenger concentration or the LET is increased (over the range studied). The G(SSB) for 4He ion irradiation is less by a factor of up to 10 than the G(SSB) for gamma irradiation, depending upon the scavenger concentration. The difference in the yields of SSBs agrees well with the difference in the yields of hydroxyl radicals for the radiations in question. In contrast, the yields of DSBs are similar for gamma and 4He ion irradiation over much of the range of scavenging capacity studied. However, at the highest scavenger concentrations the yields of DSBs are greater for 4He ion irradiation. In addition, the yields of DSBs remain almost constant with increasing LET (over the range studied). Therefore the relative yield of DSBs per SSB increases with increasing LET, supporting the hypothesis that increasing LET leads to an increased clustering of damage in DNA.

The difference that linear energy transfer makes to precursors of DNA strand breaks.

Using agarose gel electrophoresis, we have measured the yields of DN A single- and double-strand breaks (SSBs and DSBs) for plasmid DNA irradiated in aerobic aqueous solution with either 137Cs gamma rays or 4He ions with a mean LET of 94 or 150 keV micron-1. The presence of dimethyl sulfoxide (DMSO) resulted in a decrease in the yields of both SSBs and DSBs, with a greater decrease being apparent for gamma irradiation than for 4He-ion irradiation. Irradiation by 4He ions in the presence of N-(2-thioethyl)- 1,3-diaminopropane (WR-1065) resulted in a decrease in the yield of SSBs and a slightly larger decrease in the yield of DSBs. Together with results obtained previously, these observations suggest a substantial contribution to the formation of SSBs and DSBs by 4He ions by species containing at least two radicals and more than two radicals, respectively.

Effect of hydroxyl radical scavenging capacity on clustering of DNA damage.

We have shown previously that the thiol N-(2'-mercaptoethyl)-1,3-diaminopropane (WR-1065) can attenuate the formation of strand breaks associated with ionizing radiation. The mechanism of this protection is predominantly the reduction of DNA radical species which otherwise would attenuate the chemical repair of DNA radical species which are strand break precursors. We had observed that the presence of a hydroxyl radical scavenger during irradiation resulted in a decrease in the ability of WR-1065 to attenuate the formation of strand breaks. Since ionic compounds are known to affect the binding of the dicationic WR-1065 with the polyanion DNA, the effect of the scavenger was initially attributed to its polar nature having a similar effect on the interaction of WR-1065 with DNA, and not as a consequence of its ability to scavenge hydroxyl radicals. After examining additional scavengers, we now conclude that an increased hydroxyl radical scavenging capacity does attenuate the repair of strand break precursors to some extent. The probable explanation for this observation is that an increased scavenging capacity results in a greater degree of radical clustering on the DNA, and that these clusters of multiple radicals are repaired more slowly than are single radical species.

Methylperoxyl radicals as intermediates in the damage to DNA irradiated in aqueous dimethyl sulfoxide with gamma rays.

Using agarose gel electrophoresis, we have measured the yields of DNA single-strand breaks (SSBs) for plasmid DNA gamma-irradiated in aerobic aqueous solution. Incubation after irradiation with the base damage repair endonucleases formamidopyrimidine-DNA N-glycosylase (FPG) or endonuclease III (endo III) results in an increase in the yield of SSBs. In the absence of dimethyl sulfoxide (DMSO) during irradiation, this increase is consistent with the yields of known substrates for FPG and endo III as determined by gas chromatography/mass spectrometry. After irradiation in the presence of 1 mol dm-3 DMSO, the increase in the yield of SSBs after enzyme incubation was further enhanced by a factor of about 5 to 7. The magnitude of this effect, the inability of acrylamide or oxygen to suppress it, and its attenuation by N,N,N',N'-tetramethylphenylenediamine (TMPD) or glycerol all suggest that the methylperoxyl radical (derived from DMSO) is involved as an intermediate. Reactions of the methylperoxyl radical (or some other species derived from it) do not result in strand break damage, but are responsible for DNA base damages which are recognized by FPG and endo III.

DNA repair by thiols in air shows two radicals make a double-strand break.

Using agarose gel electrophoresis, we have measured the yields of DNA single- and double-strand breaks (SSBs and DSBs) for plasmid DNA gamma-irradiated in aerobic aqueous solution. The presence during irradiation of either of the thiols cysteamine or N-(2-thioethyl)-1,3-diaminopropane (WR-1065) resulted in a concentration-dependent decrease in the yield of SSBs and a much greater decrease in the yield of DSBs. This large differential protective effect was not produced by thioethers or an alcohol of structural similarity to the two thiols, suggesting that repair of DSB radical precursors by thiols is more efficient than for SSB precursors. These observations suggest the existence of a diradical intermediate in the formation of DSBs. The results argue against a major contribution by a single radical mechanism involving interstrand radical transfer via hydrogen abstraction by a peroxyl intermediate, since the half-life of this radical transfer reaction appears to be significantly greater than the lifetime of the intermediate.

Yield of DNA strand breaks after base oxidation of plasmid DNA.

We have irradiated aerobic aqueous solutions of plasmid DNA with 137Cs gamma rays in the presence of inorganic radical scavengers including nitrite, iodide, azide, thiocyanate and bromide. These scavengers react with the strongly oxidizing hydroxyl radical (*OH) to produce less powerful oxidants. Of these scavengers, only thiocyanate and bromide result in the formation of oxidizing species [(SCN)2*- and Br2*-, respectively] which are capable of reacting with the bases in DNA. The oxidized bases were detected after incubation of the irradiated plasmid with the two E. coli DNA base excision repair endonucleases, formamidopyrimidine-DNA N-glycosylase and endonuclease III. Depending on the experimental conditions, the intermediate base radicals may ultimately form stable oxidized bases in very high yields (within an order of magnitude of the *OH yield), and possibly also single-strand breaks (SSBs) in much lower yield (between 0.1 and 1% of the total yield of base damage). By competing for (SCN)2*- with an additional species (nitrite), it was possible to estimate the second-order rate constant for the reaction of (SCN)2*- with DNA as 1.6 x 10(4) dm3 mol(-1) s(-1), and also to demonstrate a correlation between the large yield of damaged bases and the much smaller increase in the yield of SSBs over background levels due to *OH. The efficiency of transfer of damage from oxidized base to sugar is estimated as about 0.5% or 5%, depending on whether purine or pyrimidine base radicals are responsible for the base to sugar damage transfer.

Redox equilibrium between guanyl radicals and thiocyanate influences base damage yields in gamma irradiated plasmid DNA. Estimation of the reduction potential of guanyl radicals in plasmid DNA in aqueous solution at physiological ionic strength.

PURPOSE: Gamma irradiation of an aqueous solution containing thiocyanate ions produces the strongly oxidizing intermediate (SCN)2*-. Reaction of this species with plasmid DNA produces damage that is revealed as strand breaks after incubation with the Escherichia coli base excision repair endonuclease formamidopyrimidine-DNA N-glycosylase (FPG). It has been previously reported that the yield of damage is highly sensitive to the experimental conditions, leading to the suspicion that electron transfer between DNA and (SCN)2*- is reversible. In principle this makes it possible to determine the oxidation potential for plasmid DNA (more formally the reduction potential of one-electron oxidized plasmid DNA), a fundamental parameter describing the reactivity of DNA towards electron transfer reactions. MATERIALS AND METHODS: Aqueous solutions of plasmid DNA and thiocyanate ions were subjected to 137Cs gamma-irradiation. After irradiation, the plasmid was incubated with the E. coli base excision repair endonuclease formamidopyrimidine-DNA N-glycosylase (FPG). The yield of this damage was quantified by using agarose gel electrophoresis to identify the fraction of the plasmid population that contains strand breaks. RESULTS: The yield of FPG-sensitive sites decreases with increasing thiocyanate concentration, decreasing DNA concentration, and increasing dose rate. By making some simple assumptions about the chemical reactions that produce DNA damage, it is possible to derive a quantitative mathematical model for the yield of FPG-sensitive sites. A good agreement was found between this model and the experimental observations over a wide range of conditions (thiocyanate concentrations, DNA concentrations, and dose rates that vary by 20-, 40-, and 150-fold respectively). CONCLUSIONS: It was possible to assign a value to the equilibrium constant for the one electron transfer reaction between the two radical species (SCN)2*- and DNA-G*+. This leads to an estimate of the reduction potential at pH 7 for the couple DNA G*+/DNA of E7 = +1.39+/-0.01V.

Radioprotection of plasmid DNA by oligolysines.

PURPOSE: To define ionic conditions under which oligolysines condense DNA as assayed by radioprotection of a plasmid substrate. And to compare these conditions with those required by the well-characterized ligands spermidine and hexammine cobalt (III). This will enable a reversible compaction model for plasmid DNA to be devised that models more closely mammalian chromatin than those based on polyamines. MATERIALS AND METHODS: Aqueous solutions containing plasmid DNA, sodium perchlorate and one of the five ligands trilysine, tetralysine, pentalysine, spermidine, or hexammine cobalt (III) were subjected to gamma-irradiation. The yields of the resulting single-strand breaks were quantified by gel electrophoresis. The effects of tetralysine and pentalysine were also examined by light scattering. RESULTS: The combination of low concentrations of the ligand and high concentrations of sodium perchlorate produced a relatively high yield of single-strand breaks. In contrast, the combination of high concentrations of the ligand and low concentrations of sodium perchlorate resulted in an approximately 25-fold lower single-strand break yield. The transition between these two break yields took place over very narrow concentration ranges of the ligand. A large change in light scattering occurred at the same concentration. The radioprotective ability of the ligands decreased in the order pentalysine > tetralysine > hexammine cobalt (III) > spermidine > trilysine. CONCLUSIONS: The effect of the oligolysines is qualitatively very similar to the previously reported radioprotection produced under similar conditions by the polyamines spermidine and spermine. It is caused by condensation of the DNA into a highly compacted form. As peptides, oligolysines are structurally more closely related than other ligands to naturally occurring DNA condensing agents such as histone proteins. Therefore, they may form the basis of a model system suitable for studying DNA damage produced by the direct effect of ionizing radiation (ionization of the DNA itself).

Reaction of guanyl radicals in plasmid DNA with biological reductants: chemical repair of DNA damage produced by the direct effect of ionizing radiation.

PURPOSE: It has been previously argued that the use of the one-electron oxidants (SCN)2(*-) and Br2(*-) with plasmid DNA leads to the formation of DNA guanyl radicals. These guanyl radical species are intermediates in the DNA damage produced by processes such as photo-ionization and ionizing irradiation. The present paper evaluates the use of thallium(II) ions (Tl(II)OH(+)) as the one-electron oxidant, and also determines rate constants for the reduction (repair) of guanyl radicals in plasmid DNA by a variety of reducing agents including the biologically important compounds ascorbate and glutathione. MATERIALS AND METHODS: Aqueous solutions of plasmid DNA containing 10(-3) mol dm(-3) thiocyanate or thallous ions and a reducing agent (azide, nitrite, ferrocyanide, hexachloroiridate(III), iodide, ascorbate, glutathione, glutathione disulphide, methionine, tyrosine, 5-hydroxyindole-3-acetic acid, 10(-7)-10(-4) mol dm(-3)) were irradiated with 137Cs gamma-rays (662 keV). After irradiation, the plasmid was incubated with the E. coli base excision repair endonuclease formamidopyrimidine-DNA N-glycosylase (FPG). Strand break yields after incubation were quantified by means of agarose gel electrophoresis. RESULTS: High yields of FPG-sensitive sites produced by the oxidants (SCN)2(*-) and Tl(II)OH(+) were strongly attenuated by the presence of the reducing agents. CONCLUSIONS: From the results, it is possible to arrive at estimates of the rate constants for the reduction of the DNA guanyl radical by the reducing agents. Values lie in the range 10(4)-10(7) dm(3) mol(-1) s(-1). Using the values for ascorbate and glutathione, it is possible to estimate an upper limit on the order of milliseconds for the lifetime of DNA guanyl radicals under cellular conditions. The implication is that there may well be a significant chemical repair of DNA base damage by the direct effect of ionizing radiation.

A comparison of DNA damages produced under conditions of direct and indirect action of radiation.

Studies using a 32P-postlabelling assay reveal that at both low and high concentrations of hydroxyl radical scavenger, DNA damage from alpha-irradiation is similar to that from gamma-irradiation. At low concentrations of scavenger the identified damages are predominantly thymine glycol (Tg) and phosphoglycolate (pg) lesions, indicative of indirect hydroxyl radical (.OH) action. However, at high concentrations of scavenger (i.e. where direct effects are expected to dominate) a somewhat different pattern of damage is observed after alpha- and gamma-irradiation, with several novel lesions detected. Further experiments, in which the results of DMSO scavenging of irradiated DNA solutions are compared with glycerol scavenging and irradiation of 'dry' solid DNA, demonstrate that both direct effects and scavenger-derived secondary radicals contribute to the different spectra of lesions observed upon irradiation of highly scavenged DNA systems. Generally, irradiation under conditions that favour direct damage result in a lower relative yield of pg, whilst for the highly scavenged systems Tg damages persist. To account for this we propose that Tg are efficiently produced by direct action in these systems. Differences seen upon irradiation of the 'dry' system, compared with those of dilute aqueous solution, suggest that direct action yields a distinct spectrum of lesions.

DNA strand-break yields after post-irradiation incubation with base excision repair endonucleases implicate hydroxyl radical pairs in double-strand break formation.

PURPOSE: To determine the increases in SSB and DSB yields after post gamma-irradiation incubation of plasmid DNA with the Escherichia coli base excision repair endonucleases formamidopyrimidine-DNA N-glycosylase (FPG) and endonuclease III (endo III). MATERIALS AND METHODS: Aqueous solutions of plasmid DNA were irradiated with 137Cs gamma-rays in the presence of 10(-4) - 10(-1) mol dm(-3) formate. After irradiation, aliquots were treated with FPG and/or endo III. SSB and DSB yields were then determined using gel electrophoresis. RESULTS: Both SSB and DSB yields were found to increase after enzyme incubation, with the increase in the DSB yield being approximately equal to the square of the increase in the SSB yield. The correlation between the increases in the SSB and DSB yields was unaffected by the scavenger concentration during irradiation. CONCLUSION: Under the conditions used, the majority of DSB appear to be formed from two hydroxyl radical attacks.