Reactivity of thymine to gamma rays in HeLa chromatin and nucleoprotein preparations

Influence of Chromatin Structure and Radical Scavengers on Yields of Radiation-Induced 8-oxo-dG and DNA Strand Breaks in Cellular Model Systems

Radiation-induced formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG) and DNA strand breaks was studied in cultured cells with normal or modified chromatin structure. Human fibroblasts were irradiated as cellular monolayers (intact cells), nuclear monolayers (permeabilized cells with intact chromatin structure), and nucleoid monolayers (permeabilized and salt-treated cells with histone-free DNA). 8-oxo-dG was assayed with reverse-phase HPLC coupled to an electrochemical detector and strand breaks with the alkali unwinding assay. Depletion of low-molecular-weight nuclear components increased the radiation-induced formation of 8-oxo-dG fivefold compared to twofold for the formation of strand breaks. Removal of both low-molecular-weight components and histones increased the yield of 8-oxo-dG 46-fold and the yield of strand breaks 43-fold. Removal of only the histones thus leads to a two times greater increase in the yield of strand breaks compared to 8-oxo-dG. Addition of radical scavengers to nuclear and nucleoid monolayers provided a significantly better protection against the formation of 8-oxo-dG relative to the formation of strand breaks. These results suggest that in intact cells, 8-oxo-dG is preferentially formed in histone-free structures of chromatin, indicating a larger role for the indirect effect of radiation in the formation of 8-oxo-dG than in the formation of strand breaks.

Chromatin structure and radiation-induced DNA strand breaks in human cells: soluble scavengers and DNA-bound proteins offer a better protection against single- than double-strand breaks

In the present investigation we have studied the formation of DNA double-strand breaks (dsbs) in different chromatin substrates and made a comparison with our previous results on radiation-induced single-strand breaks (ssb). Removal of soluble scavengers increased the number of ssbs by a factor of 2, but increased dsbs only 1.2 times. Decondensation of the chromatin increased ssbs and dsbs to the same extent, by a factor of 3-4. Removal of DNA-bound proteins gave an additional increase in ssbs and dsbs by a factor of 14 and 5 respectively. The increase in both ssbs and dsbs was caused by OH radicals. The differential effect on ssbs and dsbs can be explained by assuming that dsbs are formed mainly by multiple hits from clusters of ionizations close to the DNA. When the DNA-bound proteins are removed, more distant radicals can reach the DNA, which favours ssb formation. Under those conditions dsbs also induced by single OH radicals become important. DNA-bound proteins protect DNA only to a limited extent by acting as scavengers of OH radicals. The largest part of the protection depends on the fact that DNA in the chromatin is made up of large, compact aggregates, where the distance between separate aggregates exceeds the effective range of the OH radicals and the amount of water inside the aggregates is too small to give a maximal contribution of OH radicals compared with when DNA is more evenly distributed in a given volume.

Nuclear structure and the microdistribution of radiation damage in DNA

Evidence for the roles of proteins and metal ions in the microheterogeneity of DNA damage is reviewed. Decondensation of chromatin in hypotonic buffers markedly sensitizes the DNA to radiation, while treatment of nuclei with hypertonic buffers strips the DNA of histones and other nuclear proteins and enhances the radiosensitivity of the DNA with respect to double-strand break (dsb) formation. Addition of the radical scavenger DMSO reduces the yield of strand breaks, but dehistonized chromatin remains approximately 2.5 times more sensitive to radiation than does native chromatin at 0.1 M DMSO. DNA-protein crosslink (DPC) formation is relatively unaffected by the removal of the majority of histones from chromatin. Most DPC form at or near the nuclear matrix, and matrix is stabilized and radiosensitized by Cu++. To elucidate the role of Cu++, the induction of dsb and DPC by gamma-radiation has been compared with that by hydroxyl radical from Fe(++)-EDTA, or Cu++ catalysed Fenton reactions. Data comparing the size of DNA fragments produced, the effect of expanding or dehistonizing chromatin, and the effects of radical scavengers suggest that gamma-radiation and Fe(++)-EDTA produce dsb at open chromatin sites, whereas Cu(++)-generated dsb are similar to radiation-induced DPC in their location at the nuclear matrix. Both metal ions appeared to produce damage by site-specific generation of hydroxyl radicals. The nuclear matrix, the proteinaceous skeleton which anchors chromosomal loops and provides sites for DNA replication and transcription, binds metal ions and matrix-attachment DNA regions (MARs) consisting of 300 + bp of AT-rich DNA. The interaction of cloned MARs with isolated nuclear matrices has been found to be hypersensitive to crosslinking upon gamma-irradiation, in comparison with associations formed by similarly sized DNA fragments lacking MAR sequences. Thus, the non-random distribution of radiation damage is partially explained by the protection of DNA afforded by histones and chromatin structure and partially by the hypersensitivity of DNA-nuclear matrix associations.

Accessibility of nucleic acid-complexed biomolecules to hydroxyl radicals correlates with their conformation: a fluorescence polarization spectroscopy study

A fluorescence methodology has been developed to examine the relationship between the conformational state of specific biomolecules in simple chromatin models and their accessibility to hydroxyl radicals (OH). Polylysine and histone H1 were labelled with SECCA, the succinimidyl ester of coumarin-3-carboxylic acid, which generates the fluorescent derivative 7-OH-SECCA following its interaction with radiation-induced OH in aqueous solution. The fluorescence induced per unit gamma-ray dose reflecting the accessibility of OH to such SECCA-conjugated biomolecules was recorded. The biomolecules were also labelled with the fluorescent derivative 7-OH-SECCA in trace amounts to study their conformation under identical conditions via fluorescence polarization spectroscopy. When these biomolecules were complexed with a polynucleotide or DNA, a major increase in polarization anisotropy was recorded. Upon salt-induced dissociation of these biomolecules from the nucleic acids, the increase in anisotropy was reversed. The histone H1-DNA complexes also exhibited an initial increase in anisotropy with increasing NaCl concentration (maximum at 100 mmol dm-3) indicating the possible formation of a more compact conformation. The fluctuations in anisotropy were inversely proportional to the recorded fluorescence/Gy. The data indicate a direct correlation between the accessibility of OH to polylysine or histone H1 complexed with nucleic acids and the conformation of these biomolecules.

Role of protein thiols in intrinsic radiation protection of DNA and cells

Previous data have been consistent with the hypothesis that the thiol depleter dimethyl fumarate (DMF) increases radiation sensitivity of hypoxic mammalian cells by a combination of two actions: depletion of glutathione (GSH) which interferes with the chemical competition between damage fixation and repair and depletion of protein thiol (PSH) which causes inhibition of enzymatic repair processes. However, one cannot rule out the possibility that PSH also acts in the chemical competition to restitute damaged DNA. The studies presented here have addressed this question by studying the effects of ionizing radiation on isolated nuclei which contain very low levels of GSH, but substantial amounts of PSH, compared to intact cells. The results show that DNA damage, measured using the non-denaturing filter elution assay, is increased about 1.6-fold in isolated nuclei irradiated in air, compared to whole cells, and about 4.3-fold in nuclei irradiated in N2. Thus, the OER for DNA damage decreases from about 3 in whole cells to 1 in isolated nuclei. Also, although DMF increases radiation-induced DNA damage in whole cells irradiated in hypoxia about 2-fold, it does not increase DNA damage in isolated nuclei irradiated in hypoxia. These data do not support the idea that PSH can act in the chemical competition reaction to chemically repair radiation-induced DNA radicals. The data are discussed in relation to the effect that various procedures for nuclei isolation can have on radiation sensitivity of DNA and on the OER. We also address the question of whether radiation-induced DNA damage measured by non-denaturing elution correlates with cell killing.

Oxidative damage to DNA in mammalian chromatin

Efforts have been made to characterize and measure DNA modifications produced in mammalian chromatin in vitro and in vivo by a variety of free radical-producing systems. Methodologies incorporating the technique of gas chromatography/mass spectrometry have been used for this purpose. A number of products from all four DNA bases and several DNA-protein cross-links in isolated chromatin have been identified and quantitated. Product formation has been shown to depend on the free radical-producing system and the presence or absence of oxygen. A similar pattern of DNA modifications has also been observed in chromatin of cultured mammalian cells treated with ionizing radiation or H2O2 and in chromatin of organs of animals treated with carcinogenic metal salts.

DNA base damage in chromatin of gamma-irradiated cultured human cells

We report on the chemical characterization of DNA base damage in chromatin of gamma-irradiated cultured human cells. Chromatin was isolated from unirradiated and irradiated cells and analyzed by gas chromatography/mass spectrometry with selected-ion monitoring after acidic hydrolysis of chromatin and trimethylsilylation of hydrolysates. Prior to analysis of chromatin samples, experimental conditions for acidic hydrolysis were optimized by determining the relative molar response factors of modified bases under non-acidic and acidic conditions, and their release from DNA under various acidic conditions. A number of modified bases in chromatin isolated from irradiated cells were identified and quantitated. These were 5-hydroxy-5-methylhydantoin, 5-hydroxyhydantoin, 5-(hydroxymethyl)uracil, cytosine glycol, thymine glycol, 5,6-dihydroxycytosine, 4,6-diamino-5-formamidopyrimidine, 8-hydroxyadenine, 2-hydroxyadenine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 8-hydroxyguanine. Radiation doses ranging from 42 to 420 Gy (J.kg-1) were used. Background levels of all modified bases were observed in chromatin isolated from unirradiated cells. The radiation yields of a number of modified bases were increased significantly over their background levels at a dose as low as 42 Gy. In most cases, linear dose-yield relationships were obtained up to approximately 200 Gy. At radiation doses higher than 420 Gy, no additional increase in the yields of modified bases was observed. The yields of guanine-derived bases amounted to approximately 45% of the total net yield of modified bases measured, followed by almost equal yields of adenine-, cytosine- and thymine-derived bases. Modified bases identified were typical products of hydroxyl radical attack on DNA bases, indicating the involvement of hydroxyl radical, although their induction in part by the direct effect of ionizing radiation through ionization of DNA bases cannot be excluded. The yields of modified bases were lower than those previously measured after gamma-irradiation of fully expanded chromatin in aqueous buffer solutions.

Genetic effects of 5-hydroxymethyl-2'-deoxyuridine, a product of ionizing radiation

Ionizing radiation causes formation of heterogeneous types of damage to DNA. Among those, 5-hydroxymethyl-2'-deoxyuridine (HMdU) was identified as a major thymidine derivative in gamma-irradiated HeLa cells [G.W. Teebor, K. Frenkel and M.S. Goldstein (1984) Proc. Natl. Acad. Sci. (U.S.A.), 81, 318-321]. We report here that HMdU is a strong inducer of lambda prophage in Escherichia coli WP2s(lambda) and is highy mutagenic in Salmonella typhimurium. HMdU causes his+ revertants in strains TA100, which reverts predominantly by base-pair substitution at G-C sites, and TA97, which reverts mainly by frameshift mutation at G-C sites. It does not cause reversion in TA98, another frameshift-sensitive strain, nor in strains TA1535 and TA1537. Of those tested, only the last two strains do not contain pkM101, a plasmid which enhances mutagenic effects of ionizing radiation. HMdU also causes reversion in strains TA102 and TA104, which detect oxidative damage and can revert by base-pair substitution at A-T base pairs at the hisG428 site. We show that HMdU can be incorporated into DNA of TA100 and that, in addition to causing point mutations, it causes suppressor mutations as well. The ability of HMdU to induce lambda prophage and its strong mutagenicity in Salmonella typhimurium provide evidence that the presence of HMdU in DNA is biologically significant and may play a major role in the genetic consequences of ionizing radiation and other types of oxidative damage.

Nuclear medicine and the environment: radiation interactions

The effect of radiation interactions on the environment may be considered from the perspective of the purely physical phenomena occurring or from the effects the interactions produce in organized biological systems. The physical processes by which radiation interacts with the environment are quite well defined. Although these processes differ depending upon the nature (either electromagnetic or particulate) of the primary radiation, the ultimate result is the production in the medium of high-speed, secondary charged particles. Some of the energy of these particles is absorbed by the medium, while a portion may be lost as bremsstrahlung. The energy that is absorbed produces excitation and ionization, which can be disruptive to biological systems. The effects produced by ionizing radiations at the biochemical, cellular, and organ level are less well defined. Nevertheless, available data indicate that certain generalizations are possible. For example, given the ubiquitous nature of water in tissues, macromolecules, regardless of their structural types, tend to serve as acceptors of the energy and products of water radiolysis. However, a deeper insight into the consequences of irradiation requires an understanding of the interplay of such parameters as the type and energy of the radiation, and the dose and rate of its application. Furthermore, at the cellular level, the type and age of the irradiated cells, the concentration of oxygen in their environment, and their cell-cycle phase are all important factors in determining the consequences of irradiation.

The role of specific DNA base damages in the X-ray-induced inactivation of bacteriophage PM2

Two types of X-ray-induced base damages, alkali-labile sites and thymine ring saturation products, were quantitated in PM2 DNA irradiated in the phage capsid under oxic and anoxic conditions. The extent of formation of these base damages was compared with the number of single- and double-strand breaks and lethal hits produced under the same conditions. The individual inactivation efficiencies of alkali-labile sites and thymine ring saturation products were determined by selectively inducing each of these damages in isolated PM2 DNA by chemical means in vitro and determining the rate of biological inactivation of the treated DNA by transfection. For each lethal X-ray hit induced in oxic conditions there were 1.06 alkali-labile sites, 0.40 thymine ring saturation products, 2.09 singe-strand breaks and 0.11 double-strand breaks in the PM2 genome. In anoxic conditions, the respective number of lesions was 1.00, 0.19, 1.73 and 0.09. The individual inactivation efficiencies of thymine ring saturation products and alkali-labile sites were found to be essentially equal, 7-8 lesions per lethal event in the PM2 genome. Alkali-labile sites and thymine ring saturation products together accounted for 15-20% of the biological inactivation of X-irradiated bacteriophage PM2. The presence or absence of oxygen during irradiation did not affect the contribution to inactivation made by alkali-labile sites, but the contribution by thymine ring saturation products to inactivation was about 2-fold higher in oxic compared with anoxic conditions. With the 4 lesions measured, we have accounted for some 28-34% of the lethal events in X-irradiated PM2 phage, most of the remaining events being caused by as yet unidentified base damages.

Age associated alteration in DNA damage and repair capacity in Turbatrix aceti exposed to ionizing radiation

Excision repair capacity was measured in young and old Turbatrix aceti (phylum Nematoda) following exposure to ionizing radiation. Both repair synthesis and removal of 5,6-dihydroxydihydrothymine type (glycol) base damage were quantitated. At least two-fold higher glycol levels were produced in the DNA of young than of old nematodes for the same radiation dose. Young worms also excised glycol damage more rapidly and completely than old worms. Both peak repair synthesis activity and completion of repair synthesis occurred at earlier times during post-irradiation incubation in young nematodes. The data indicate there is a significant age-associated difference in both the incidence and removal of ionizing radiation damage in T. aceti which is used as a model of the ageing process.

Hypersensitivity of DNA in transcriptionally active chromatin to ionizing radiation

We have examined the size distribution of single-strand fragments of total 3H-labeled DNA and of DNA sequences complementary to specific probes in gamma-irradiated and unirradiated mouse L929 cells. Those DNA sequences which hybridize to rDNA or to poly(A+)RNA have lower number average molecular weights and sustain 5--6-times the number of single-strand breaks as do satellite DNA sequences or the bulk DNA. We therefore conclude that transcriptionally active DNA sequences are more susceptible to ionizing radiation-induced damage than are inactive sequences, and suggest that these differential susceptibilities are a likely consequence of differences in their chromatin organization.

Protein composition of cells, nuclei and chromatin from some radiosensitive and radioresistant mouse tissues

The radioresistant tissues, heart, liver, lung and kidney, contain 2 to 15 times more protein per cell, nucleus and chromatin compared with the radiosensitive tissues, spleen and thymus. As determined by polyacrylamide gel electrophoresis, in the nuclear fraction and chromatin of radiosensitive tissues there is a deficit of high molecular weight (Mw greater than 20 000) non-histone proteins. It is suggested that the radiosensitivity of lymphoid cells, which die of interphase death a few hours after exposure to small doses of radiation, is closely correlated with this deficit in non-histone proteins.

Radiolysis of chromatin extracted from cultured mammalian cells: formation of DNA-protein cross links

Chromatin extracted from Chinese hamster lung fibroblasts has been examined for the formation of radiation-induced DNA-protein cross links, using a membrane filter assay. The relative efficiencies of the aqueous radical intermediates, OH., eaq- and O2-, were investigated. Cross links were found in gamma-irradiated isolated chromatin and in chromatin irradiated in the cell before isolation. When isolated chromatin was irradiated under conditions in which the chromosomal proteins were dissociated from the DNA, no cross links were detectable. The most efficient radical for the production of cross links in irradiated, isolated chromatin was found to be the hydroxyl radical, whereas, the superoxide radical was essentially ineffective. For chromatin irradiated in the cell before isolation, the greatest effect was seen for cells irradiated in an atmosphere of nitrous oxide, suggesting the hydroxyl radical may be involved in the formation of cross links in intact cells also. The formation of cross links in chromatin irradiated in cells before isolation was considerable less efficient than in irradiated, isolated chromatin.

Radiolysis of chromatin extracted from cultured mammalian cells: production of alkali-labile strand damage in DNA

Chromatin has been isolated from cultured Chinese-hamster lung fibroblasts as an expanded aqueous gel. The DNA in isolated chromatin has been examined by sedimentation on alkaline sucrose gradients. The average molecular weight of the DNA has been determined to be 50 million. gamma-irradiation of isolated chromatin degrades the DNA to lower molecular weight. The yield of single-strand breaks in the DNA is 0.02 single-strand breaks per krad-10(6) dalton, calculated from a dose-range of &--400 krad and covering a DNA molecular weight range of 2 X 10(7)-1.4 X 10(5). There is a considerable difference in the efficiency of the formation of single-strand breaks in DNA irradiated as isolated chromatin compared with chromatin irradiated in whole cells before isolation. For isolated chromatin, values of 6 dV per break have been calculated compared with about 80 eV per break for chromatin irradiated in whole cells, which suggest a large contribution from indirect action by aqueous radicals in isolated chromatin.

Mode of chromatin reconstitution. Elements controlling globin gene transcription

The mode of reconstitution has been determined for the factors that control globin gene transcription in chicken reticulocyte chromatin. During chromatin reconstitution, elements in the nonhistone protein fraction that control the globin gene reassociate with the DNA before the histones. From our results, it appears that it is necessary for these elements to reassociate with the DNA before the histones for the globin gene to be transcribed.

Excision of gamma-ray induced thymine lesions by preparations from ataxia telangiectasia fibroblasts

The capacity of whole cell sonicates of skin fibroblasts of normal individuals and patients with the autosomal recessive disease Ataxia telangiectasia (AT) to remove aerobic gamma-ray products of the 5,6-dihydroxydihydrothymine type (tgamma02) from exogenous DNA substrates was investigated. All four AT strains (AT CRL 1312, AT CRL 1343, AT GM 367, AT 4BI) possessed normal capabilities to excise tgamma02 from irradiated bacteriophage DNA and irradiated chromatin isolated from normal and AT-skin fibroblasts.

Mode of reconstitution of chicken erythrocyte and reticulocyte chromatin

The mode of reconstitution of chicken erythrocyte and reticulocyte chromatin has been investigated. Chromatin was dissociated in 2 M NaCl, 5 M urea, and 0.01 M potassium phosphate (pH 7.2) and was dialyzed against various NaCl concentrations in 5 M urea and 0.01 M potassium phosphate (pH 7.2). Histone reassociation to DNA occurs with the binding of histone H5 at 0.5 M NaCl in 5 M urea, followed by histone H1 at 0.4 M NaCl in 5 M urea. All the classes of histones are reassociated with DNA at 0.2 M NaCl in 5 M urea and binding of all classes of histones is complete in 0.1 M NaCl and 5 M urea. Nonhistone proteins reassociate with DNA before and at the same time that histones reassociate with DNA. Binding of nonhistone proteins to DNA appears to be complete in 5 M urea and 0.01 M potassium phosphate (pH 7.2). There is also found in both erythrocyte and reticulocyte chromatin a nonhistone protein present in relatively high concentrations, which remains associated with DNA in 2 M NaCl and 5 M urea. This tightly bound protein appears as one major band when chromatographed on sodium dodecyl sulfate-polyacrylamide gels, with a molecular weight of 95 000. This protein is soluble in phenol and sodium dodecyl sulfate but is insoluble in 5 M urea or 4 M guanidine hydrochloride. A fraction of reticulocyte nonhistone proteins was found to bind to DNA-cellulose in 5 M urea. The majority of these proteins elute at 0.15 M NaCl in 5 M urea but a significant fraction elutes at NaCl concentrations at which the bulk of the histones do not bind to DNA. The proteins that bind to free DNA have low molecular weights and do not show species speciificity. Approximatley 50% of the reticulocyte nonhistone protein does not bind to a DNA-cellulose column in 5 M urea and may require histones for complete reassociation.

The effect of a mammalian repair endonuclease on x-irradiated DNA

DNA was extracted from rat liver of non-irradiated animals, and was irradiated in vitro, and from animals which received whole body doses of X-radiation. Sedimentation on neutral and alkaline sucrose gradients as well as measurements of 32P release after sequential treatment with endonuclease and alkaline phosphatase and determination of triphosphate incorporation after the sequential treatment with endonuclease, alkaline phosphatase and DNA polymerase indicated that DNA irradiated in vivo and in vitro were effective substrates for the mammalian repair endonuclease. The experiments suggest that in addition to strand breaks, X-radiation causes base damage and they have provided a plausible explanation for the formation of double strand breaks in DNA irradiated in vivo.