Direct measurement by pulsed-field gel electrophoresis of induction and rejoining of X-ray-induced double-strand breaks in cultured mouse cells

Repair of DNA strand breaks in a minichromosome in vivo: kinetics, modeling, and effects of inhibitors

To obtain an overall picture of the repair of DNA single and double strand breaks in a defined region of chromatin in vivo, we studied their repair in a ∼170 kb circular minichromosome whose length and topology are analogous to those of the closed loops in genomic chromatin. The rate of repair of single strand breaks in cells irradiated with γ photons was quantitated by determining the sensitivity of the minichromosome DNA to nuclease S1, and that of double strand breaks by assaying the reformation of supercoiled DNA using pulsed field electrophoresis. Reformation of supercoiled DNA, which requires that all single strand breaks have been repaired, was not slowed detectably by the inhibitors of poly(ADP-ribose) polymerase-1 NU1025 or 1,5-IQD. Repair of double strand breaks was slowed by 20–30% when homologous recombination was supressed by KU55933, caffeine, or siRNA-mediated depletion of Rad51 but was completely arrested by the inhibitors of nonhomologous end-joining wortmannin or NU7441, responses interpreted as reflecting competition between these repair pathways similar to that seen in genomic DNA. The reformation of supercoiled DNA was unaffected when topoisomerases I or II, whose participation in repair of strand breaks has been controversial, were inhibited by the catalytic inhibitors ICRF-193 or F11782. Modeling of the kinetics of repair provided rate constants and showed that repair of single strand breaks in minichromosome DNA proceeded independently of repair of double strand breaks. The simplicity of quantitating strand breaks in this minichromosome provides a usefull system for testing the efficiency of new inhibitors of their repair, and since the sequence and structural features of its DNA and its transcription pattern have been studied extensively it offers a good model for examining other aspects of DNA breakage and repair.

Oxygen Effect for DNA Double-strand Break Induction Determined by Pulsed-field Gel Electrophoresis

The induction of DNA double-strand breaks (dsb) following irradiation under oxygenated and hypoxic conditions with and without misonidazole was measured by pulsed-field gel electrophoresis (PFGE) in a human bladder carcinoma cell line. The dose-response curve for DNA dsb detection by PFGE was biphasic with an apparent reduction in rate of dsb induced with dose. Oxygen enhancement ratios (OER) for cell survival (at a surviving fraction of 0.1) and for DNA damage assessed by PFGE (at 80% retained) were 2.0 and 3.0 respectively. Dose-modifying factors for misonidazole (15 mM), of 1.9 (survival) and 2.4 (DNA damage) were found. Although the magnitude of the inter-experiment variations limit the precision with which cell survival and DNA electrophoresis can be compared, the data do support a simple correlation between these two measures of response. When DNA dsb induction frequency was assessed from the number average molecular weight, values of 2.7 (+/- 0.3), 0.7 (+/- 0.1) and 2.6 (+/- 0.5) x 10(-9) dsb/bp/Gy were found for irradiation under oxic, hypoxic alone and hypoxic + misonidazole conditions respectively. This gives an OER of 3.9 and a DMF of 3.7.

Bleomycin-induced DNA damage and repair inXenopus laevis andXenopus tropicalis

Microgel cell electrophoresis has been used with various species to measure breakage of DNA and DNA repair following exposure to the radiomimetic antibiotic, bleomycin. With humans, a high degree of DNA damage is considered to be predictive of cancer susceptibility. Non-isogeneic Xenopus laevis, the South African clawed toad, rarely develop spontaneous or induced cancers. Here, we investigate bleomycin-induced DNA damage and repair in splenic lymphocytes of this species to test consistency with cancer predictability. As X. laevis is pseudotetraploid in nature, while Xenopus tropicalis is diploid, we additionally explore the effect of polyploidy on DNA damage and repair in these vertebrates. The results show that higher doses of bleomycin are required to induce comparable levels of DNA damage in both Xenopus species, than in humans. X. tropicalis, the diploid, is more bleomycin-sensitive than is X. laevis. Additionally, repair rates of damaged DNA of X. laevis lymphocytes are more rapid than those of X. tropicalis, although both are hours slower than human leukocytes. While no data exist on cancer susceptibility in X. tropicalis, the results suggest greater susceptibility to cancer than X. laevis, but less than in humans. Thus, polyploidy serves as a protection against DNA damage and allows more rapid repair.

Repair kinetics of DNA-DSB induced by X-rays or carbon ions under oxic and hypoxic conditions

We studied the relation between initial DNA double-strand breaks (DNA-DSB) and the rejoining kinetics of the strand breaks, as well as the OER (oxygen enhancement ratio) after low- and high-LET (linear energy transfer) radiations. CHO cells were exposed to 200 kVp X-rays or 80 keV/microm carbon ions under oxic and hypoxic conditions. DNA-DSB in the cells were analyzed by a static-field gel electrophoresis (SFGE). The kinetics of the rejoining could be described by a sum of fast and slow components. The initial released DNA after X-ray irradiation was higher for cells irradiated under an oxic condition than that under a hypoxic condition. The OER of DNA-DSB after X-ray irradiation was 5.7. This value decreased rapidly to be 3.4 with the fast component by 15 minutes. On the other hand, the OER of DNA-DSB after carbon ion irradiation was 2.2, and this value was not changed by rejoining incubation. The OER values for cell killing were 2.8 and 1.8 after X-ray and carbon ion irradiations, respectively. These values matched to the OER for DNA-DSB with complete rejoining. We conclude that the rejoining of DNA-DSB is an important factor in the mechanism of the oxygen effect.

Role of DNA-dependent protein kinase in recognition of radiation-induced DNA damage in human peripheral blood mononuclear cells

The DNA-dependent protein kinase (DNA-PK) complex plays a crucial role in radiation-induced DNA damage recognition. The complex includes the ku heterodimer, which comprises ku 70 and ku 80 subunits, that binds DNA termini of breaks without sequence specificity, and the catalytic subunit DNA-PKCS: The activation of the DNA-PK complex was studied in X-irradiated peripheral blood mononuclear cells (PBMC) from subjects of different ages. Radiation-induced changes in the DNA-binding activity of the ku heterodimer, and in the concentrations of ku 70, ku 80, DNA-PKcs and phosphorylated ku 80 were determined in nuclear and cytoplasmic extracts. DNA-binding activity was increased by irradiation only in the nuclear extract of PBMC from young, but not from elderly subjects, whereas it was found unchanged in cytoplasmic extracts regardless of age. The radiation-induced activation of the DNA-PK complex may result from the increased concentrations of ku 80 and DNA-PKcs in the cytoplasm of PBMC from young, but not from elderly subjects, leading to a higher concentration of phosphorylated ku 80 which readily migrates to the nucleus where, after dimerization with ku 70, binds to DNA breaks. These findings suggest major steps involved in DNA-PK activation, and the intracellular and molecular changes that may account for the age-dependent impairment of DNA repair capacity in irradiated mammalian cells.

Hydroxyurea accelerates the loss of epidermal growth factor receptor genes amplified as double-minute chromosomes in human glioblastoma multiforme

OBJECTIVE

We sought to determine whether hydroxyurea could accelerate the loss of amplified epidermal growth factor receptor (EGFR) genes from glioblastoma multiforme (GBM). There is good reason to think that elimination of amplified EGFR genes from GBMs will negatively impact tumor growth. Hydroxyurea has previously been shown to induce the loss of amplified genes from extrachromosomal double minutes (dmin) but not from chromosomal homogeneously staining regions.

METHODS

Pulsed-field gel electrophoresis and Southern blot hybridization were used to demonstrate EGFR genes amplified as dmin. Giemsa-stained metaphase spreads were prepared in an attempt to visualize dmin. A GBM cell line containing amplified EGFR genes was treated continuously in vitro with 0 to 150 mumol/L hydroxyurea, and slot blot analysis was used to show the loss of amplified EGFR genes.

RESULTS

Amplified EGFR genes were found on dmin in 4 of 11 (36%) fresh human GBM biopsy specimens. None of the GBMs contained EGFR genes amplified as homogeneously staining regions. Amplified dmin were not microscopically visible when stained with Giemsa because of their small size. Slot blot analysis showed that these low doses of hydroxyurea accelerated the loss of amplified EGFR genes in a dose- and time-dependent fashion. Pulsed-field gel electrophoresis and Southern blot analysis confirmed that EGFR gene loss was accompanied by amplified dmin loss in a dose-dependent fashion.

CONCLUSION

These studies suggest the potential use of low-dose hydroxyurea in the treatment of GBMs.

Rejoining of DNA double-strand breaks in X-irradiated CHO cells studied by constant- and graded-field gel electrophoresis

Induction and repair of double-strand breaks (dsb) were measured in exponentially growing CHO-10A cells using the constant- and graded-field gel electrophoresis. Dsb repair was studied after an X-ray dose of 60 Gy. The repair curve obtained was biphasic with the respective half-times of tau 1 = 3.8 +/- 0.9 and tau 2 = 118 +/- 30 min. The number of non-reparable dsb was measured for X-ray doses up to 180 Gy and was found to be only a small fraction (14%) of all non-rejoinable breaks determined previously using the alkaline unwinding technique. The ratio of non-reparable dsb to the number of lethal events calculated from survival curves is 0.14:1. This result indicates that for CHO cells nonreparable dsb represent only a small fraction of lethal damage. This is in line with the cytogenetic observation that cell killing mainly results from mis-rejoined events (i.e. exchange aberrations, translocations, interstitial deletions). The kinetics of dsb rejoining were found to be independent of the size of the fragments involved (between 1 and 10 Mbp). In addition, the rejoining kinetics of DNA fragments < or = 1 Mbp did not show the formation of new DNA fragments with time after irradiation indicating the absence of programmed cell death in irradiated CHO cells.

A comparison of methods for calculating DNA double-strand break induction frequency in mammalian cells by pulsed-field gel electrophoresis

Pulsed-field electrophoresis (PFGE) has become one of the most widely used methods for the evaluation of radiation-induced DNA double-strand breaks (dsb). In most studies a simple quantification of DNA migration from the well in the gel has been used as the correlate with dsb formation. Here we have compared such a method, as calibrated with 125I-labelled UdR, with two methods which involved the analysis of the distribution of sizes of DNA fragments migrating in the gel. We conclude that the three methods produce similar absolute values for dsb induction frequency. It is not clear which is the single method of choice but the comparison of the analyses increases the information which can be derived from PFGE experiments.

DNA double-strand break measurement in mammalian cells by pulsed-field gel electrophoresis: an approach using restriction enzymes and gene probing

DNA samples prepared from human SP3 cells, which had been exposed to various doses of X-ray, were treated with NotI restriction endonuclease before being run in a contour-clamped homogeneous electrophoresis system. The restriction enzyme cuts the DNA at defined positions delivering DNA sizes which can be resolved by pulsed-field gel electrophoresis (PFGE). In order to investigate only one of the DNA fragments, a human lactoferrin cDNA, pHL-41, was hybridized to the DNA separated by PFGE. As a result, only the DNA fragment which contains the hybridized gene was detected resulting in a one-band pattern. The decrease of this band was found to be exponential with increasing radiation dose. From the slope, a double-strand break induction rate of (6.3 +/- 0.7) x 10(-3)/Mbp/Gy was deduced for 80 kV X-rays.

Hyperthermia inhibits the repair of DNA double-strand breaks induced by ionizing radiation as determined by pulsed-field gel electrophoresis

Hyperthermia is known to synergistically interact with X-rays to kill cells. We have used pulsed-field gel electrophoresis to investigate the effects of hyperthermia on cell survival and on repair of radiation-induced DNA double-strand breaks (dsbs). Combining hyperthermia (43 degrees C, 45 min) with radiation (7.5 Gy) resulted in a complete inhibition of dsb repair and a surviving fraction of 0.9%. Cells treated with hyperthermia alone resulted in a 55% cell survival with no increase in dsb levels over background. Cells treated with 7.5 Gy alone demonstrated 11% survival and exponential dsb repair. Dsb repair was equally inhibited by hyperthermia whether administered immediately before or after the radiation. We compared the rejoining of dsbs resulting from 7.5 Gy at 37 and 43 degrees C to determine whether dsbs were being repaired during hyperthermia. While repair occurred at 37 degrees C, no dsbs were repaired at 43 degrees C. Our results indicate that hyperthermia completely inhibits dsb repair.

Repair of DNA double-strand breaks induced in Saccharomyces cerevisiae using different gamma-ray dose-rates: a pulsed-field gel electrophoresis analysis

We investigated the effects of gamma-ray exposures at high dose-rate (HDR, 23.2 Gy/min) and low dose-rate (LDR, 0.47 Gy/min) on survival and the induction of DNA double-strand breaks (dsb) in a diploid wild-type (D7) and the repair-deficient mutant strain rad52/rad52 of Saccharomyces cerevisiae. Analysis by pulsed-field gel electrophoresis (PFGE) using a contour homogeneous electric field apparatus revealed that, at HDR, in the range 0-400 Gy, dsb are induced as a linear function of gamma-ray dose. Liquid holding recovery in non-nutrient medium (LHR) for 48 h of wild-type cells treated at HDR, significantly increased survival and reduced the yield of dsb. Such changes did not occur in rad52/rad52 cells defective in the repair of dsb. Thus, in gamma-irradiated wild-type cells, an efficient repair of dsb is taking place during LHR. Treatments of wild-type cells at LDR resulted in higher survival and an approximately two-fold lower yield of dsb than at HDR. Such a dose-rate effect was absent in rad52/rad52 cells suggesting that, in wild-type cells during LDR exposures, significant amounts of dsb can be repaired. This repair could be very much accentuated by 48-h LHR of wild-type cells treated at LDR. The relationship observed between gamma-ray survival and dsb repair clearly indicates that increases in survival of wild-type cells, during LDR as compared with HDR exposures and after LHR, are strongly related to the repair of dsb.

Asymmetric fusion between protoplasts of tomato (Lycopersicon esculentum Mill.) and gamma-irradiated protoplasts of potato (Solanum tuberosum L.): the effects of gamma irradiation

This paper describes the aggregation of nuclei in heterokaryons of tomato and unirradiated or irradiated potato protoplasts and the effects of gamma irradiation of potato and tomato protoplasts on single- and double-stranded DNA fragmentation, DNA repair and DNA synthesis as revealed by alkaline and pulsed field gel electrophoresis and an immunocytochemical technique. The prospects for obtaining highly asymmetric somatic hybrids of tomato and gamma-irradiated potato are discussed.

Computer simulation of pulsed field gel runs allows the quantitation of radiation-induced double-strand breaks in yeast

A procedure for the quantification of double-strand breaks in yeast is presented that utilizes pulsed field gel electrophoresis (PFGE) and a comparison of the observed DNA mass distribution in the gel lanes with calculated distributions. Calculation of profiles is performed as follows. If double-strand breaks are produced by sparsely ionizing radiation, one can assume that they are distributed randomly in the genome, and the resulting DNA mass distribution in molecular length can be predicted by means of a random breakage model. The input data for the computation of molecular length profiles are the breakage frequency per unit length, alpha, as adjustable parameter, and the molecular lengths of the intact chromosomes. The obtained DNA mass distributions in molecular length must then be transformed into distributions of DNA mass in migration distance. This requires a calibration of molecular length vs. migration distance that is specific for the gel lane in question. The computed profiles are then folded with a Lorentz distribution with adjusted spread parameter gamma to account for band broadening. The DNA profiles are calculated for different breakage frequencies alpha and for different values of gamma, and the parameters resulting in the best fit of the calculated to the observed profile are determined.

Combination of static-field gel electrophoresis and densitometric scanning for the determination of radiation-induced DNA double-strand breaks in CHO cells

An experimental setup using static-field gel electrophoresis (SFGE) was developed to determine radiation-induced DNA double-strand breaks (DSBs) in CHO-K1 cells after exposure to X-rays or heavy charged particles. The fraction of DNA eluted into the gel matrix depends on the quantity of DSBs introduced. In agreement with a recent report, SFGE and pulsed-field electrophoresis were found to be equally sensitive in DSB detection. With radiolabeled DNA from cell cultures, the absolute amount of DNA migrating out of agarose plugs into the gel was quantified by determining the radioactivity in the gel lane. Alternatively, relative measurements of the amount of DNA released into the gel were achieved with a standardized protocol for both SFGE and a subsequent densitometric scanning of photographic negatives from gels stained with ethidium bromide. After calibration with the radioactive method, the fractions of DNA retained could be calculated directly from the data obtained with the densitometric assay to set up classical dose-effect curves. This procedure was validated for its application with heavy ions using an 500 MeV/u lead beam.

The use of biphasic linear ramped pulsed field gel electrophoresis to quantify DNA damage based on fragment size distribution

PURPOSE

The development of biphasic linear pulse ramping gel electrophoresis has permitted resolution of DNA fragments from 200 Kbp to 6 Mbp in a single gel. We used this technique to measure radiation-induced DNA damage based on fragment size.

METHODS AND MATERIALS

Human colon cancer cells (HT29 and LS174T) and Chinese hamster ovary cells were embedded in agarose, deproteinized, irradiated with 5-80 Gy, and assessed for DNA double strand breakage using pulsed field gel electrophoresis. The frequency of DNA double strand breakage determined using a previously published method was compared to the breakage frequency calculated using the fragment size distribution.

RESULTS

Both methods produced similar estimates for breakage frequency of approximately 5 x 10(-9) breaks Gy-1 bp-1.

CONCLUSIONS

These findings suggest that biphasic linear pulse ramping gel electrophoresis can yield a quantitative estimate of DNA fragment distribution resulting from irradiation. The ability to quantify the distribution of DNA fragment sizes produced by irradiation should yield important information concerning the mechanisms of both DNA double strand break induction and repair.

Field alternation gel electrophoresis--status quo

Since the description of the original technique of field alternation gel electrophoresis (FAGE) about ten years ago there have been significant developments in the area. Between 1983 and early 1987 dramatic improvements in the technique and apparatus resulted in a 500- to 600-fold increase in the functional separation capacity of conventional agarose gel electrophoresis. Details of the improvements in technique and equipment was the subject of an earlier review [H. J. S. Dawkins, J. Chromatogr., 492 (1989) 615]. This review concentrates on the application of FAGE technology. The FAGE technique is no longer restricted to simply separating large DNA fragments. This method is presently being used for electrophoretic karyotyping, long-range genomic mapping, cloning of large DNA fragments into new vectors, the study of pathogenic chromosomal alterations and the structural analysis of chromosomes. The applications of FAGE in molecular biology and genetics is constantly expanding, with the full potential of this technique still to be realised.

Molecular biology of double-minute chromosomes

Double-minute chromosomes play a critical role in tumor cell genetics where they are frequently associated with the overexpression of oncogene products. They have been observed for many years in light microscopic examinations of metaphase chromosomes from tumor cells, but their origin remains unknown and is the subject of considerable speculation. However, molecular details of their structure and organization can now be described in conjunction with the microscopic examinations, to allow an evaluation of the various models that have been developed to explain the genesis of double-minutes. The evidence now favors simple models that invoke chromosome breakage and circularization of very large acentric chromosome fragments, permitting unequal segregation of the genes on the fragment during cell division. If there is selection for overexpression of one of the genes on the fragment, daughter cells with more fragments will grow faster than daughter cells with fewer fragments, and over time the population of cells will come to contain many double-minutes per cell.

Determination of the radiation sensitivity of the stromal cells in the murine long-term bone marrow culture by measuring the induction and rejoining of interphase chromosome breaks

PURPOSE

To determine the radiosensitivity of bone marrow stromal cells, the rate of interphase chromosome breakage and rejoining of stromal cells in the murine long term bone marrow culture and of human skin fibroblasts were compared.

METHODS AND MATERIALS

The cells were irradiated with doses up to 6 Gy and repair times up to 6 hr were investigated. After induction of premature chromosome condensation by fusing the cells with mitotic HeLa cells, the number of interphase chromosome fragments was counted.

RESULTS

The number of radiation induced breaks was found to be not significantly different for both cell types with 6.16 +/- 0.26 breaks per Gray for the fibroblasts and 5.96 +/- 0.20 breaks per Gray for the stromal cells. A significant difference was observed in the repair rate. The fibroblasts rejoined 39.6% of the breaks induced initially during the first hour after irradiation and 5.6 +/- 1.84 breaks remained unrejoined after 6 hr, while the stromal cells were able to rejoin 63.2% in 1 hr and had 2.05 +/- 0.07 breaks unrejoined after 6 hr.

CONCLUSION

If the well substantiated assumption is made, that the capacity to repair DNA double strand breaks or interphase chromosome breaks is correlated with the cellular radiosensitivity, this finding indicate, that murine bone marrow stromal cells are more radioresistant than human skin fibroblasts.

Reversibility of inhibition of DNA double strand break repair by 2-deoxy-D-glucose in Ehrlich ascites tumour cells

The glycolytic inhibitor 2-deoxy-D-glucose (2-DG), a potent therapeutic adjuvant in cancer radiotherapy, was tested for the reversibility of its inhibitory action on X-ray-induced DNA double strand break (dsb) repair. Cells were exposed to 40 Gy of X-rays and allowed to repair with or without 2-DG in suspension at 37 degrees C. DNA dsb rejoining was measured by pulsed field gel electrophoresis. The fraction of 14C-thymidine activity released from the plug (FAR) during electrophoresis was used as a measure for the number of dsb present in the DNA. After certain time intervals 2-DG was withdrawn from the cells and the extent of reversal of inhibition of dsb rejoining was measured. Biphasic repair of dsb was generally observed, with a fast component extending up to about 60 min after irradiation and a much slower progression of repair thereafter. Different mathematical models are considered for a quantitative description of these two components. The experimental data strongly indicate that only one type of dsb is primarily induced by irradiation which can be repaired fast with a time constant of about 0.05 min-1 (t1/2 approximately 13 min). In competition with this repair, other DNA dsb arise which are repaired slowly with a time constant of about 0.009 min-1 (t1/2 approximately 77 min). The time constant for the transformation of fast reparable dsb into slowly repaired dsb is about 0.026 min-1. Treatment with 2-DG inhibits the fast repair and, as a consequence, more DNA dsb are transformed into the type being repaired slowly. In competition with this slow repair, DNA dsb are fixed. Treatment with 2-DG also reduces slow repair processes and as a consequence the number of lesions being fixed is increased. Cell survival and ATP content of the cells showed a reversibility to the same extent as dsb repair, indicating the close relationship of these processes in living cells.

Application of pulsed field gel electrophoresis to determine gamma-ray-induced double-strand breaks in yeast chromosomal molecules

The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to gamma-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb. The two assays gave similar results for the frequency of dsb ((1.07 +/- 0.06) x 10(-9) Gy-1 bp-1 and (0.93 +/- 0.09) x 10(-9) Gy-1 bp-1, respectively). The dsb frequency was found to be linearly dependent on dose.

Application of programmable, autonomously controlled electrode (PACE) technology to the development of an improved pulsed field gel electrophoresis assay for DNA double-strand breaks in mammalian cells

PACE (programmable, autonomously controlled electrodes) pulsed field gel electrophoresis technology was used to develop a DNA double-strand break assay that simultaneously combined (1) resolution across a broad range of DNA sizes, (2) high sensitivity (in terms of detecting dsb at low doses) and (3) speed. A 48 h PACE/dsb assay resolves DNA fragments ranging in size from 0.2 to 6 Mb, and detects damage induced by as little as 2 Gy of gamma-radiation. A different set of electrophoretic conditions resolves DNA between 1.5 and 6 megabases in 23 h, with a detection limit of about 5 Gy. A third electrophoretic protocol, while not resolving DNA fragments greater than 50 kb in length, detects DNA dsb in CHO cells induced by 15 Gy or more of gamma-rays after only a 1 h run. In particular, the 48 h PACE/dsb assay should prove useful in studies aimed at understanding the mechanisms whereby a variety of biological, chemical and physical agents induce DNA dsb in eukaryotes.

Molecular structure and evolution of double-minute chromosomes in methotrexate-resistant cultured mouse cells

To determine whether microscopically visible double-minute chromosomes (DMs) are derived from submicroscopic precursors, we monitored the amplification of the dihydrofolate reductase (DHFR) gene in 10 independent isolates of methotrexate (MTX)-resistant mouse cells. At every other doubling in MTX concentration, the cells were examined both microscopically, to detect the presence of microscopically visible DMs, and by pulsed-field gel electrophoresis and hybridization to a DHFR-specific probe, to detect submicroscopic DMs. One of the cloned MTX-resistant isolates was examined in detail and was shown to originally contain amplified DHFR genes on circular DMs measuring 1 and 3 Mb in size; additionally, metaphase chromosome preparations from this cloned isolate were examined and were shown to contain microscopically visible DMs too large to enter a pulsed-field gel. During stepwise selection for increasing levels of MTX, the smaller DMs (not microscopically visible) were shown to be preferentially amplified, whereas the larger (microscopically visible) ones decreased in relative numbers. Rare-cutting NotI digestion patterns of total genomic DNA that includes the DMs containing the DHFR gene suggest that the DMs increase in copy number without any further significant rearrangements. We saw no evidence from any of the 10 isolates to suggest that microscopically visible DMs are formed from smaller submicroscopic precursors.

Molecular structure and evolution of double-minute chromosomes in methotrexate-resistant cultured mouse cells

To determine whether microscopically visible double-minute chromosomes (DMs) are derived from submicroscopic precursors, we monitored the amplification of the dihydrofolate reductase (DHFR) gene in 10 independent isolates of methotrexate (MTX)-resistant mouse cells. At every other doubling in MTX concentration, the cells were examined both microscopically, to detect the presence of microscopically visible DMs, and by pulsed-field gel electrophoresis and hybridization to a DHFR-specific probe, to detect submicroscopic DMs. One of the cloned MTX-resistant isolates was examined in detail and was shown to originally contain amplified DHFR genes on circular DMs measuring 1 and 3 Mb in size; additionally, metaphase chromosome preparations from this cloned isolate were examined and were shown to contain microscopically visible DMs too large to enter a pulsed-field gel. During stepwise selection for increasing levels of MTX, the smaller DMs (not microscopically visible) were shown to be preferentially amplified, whereas the larger (microscopically visible) ones decreased in relative numbers. Rare-cutting NotI digestion patterns of total genomic DNA that includes the DMs containing the DHFR gene suggest that the DMs increase in copy number without any further significant rearrangements. We saw no evidence from any of the 10 isolates to suggest that microscopically visible DMs are formed from smaller submicroscopic precursors.

Double-minute chromosomes as megabase cloning vehicles

Radiation-reduced chromosomes provide valuable reagents for cloning and mapping genes, but they require multiple rounds of x-ray deletion mutagenesis to excise unwanted chromosomal DNA while maintaining physical attachment of the desired DNA to functional host centromere and telomere sequences. This requirement for chromosomal rearrangements can result in undesirable x-ray induced chromosome chimeras where multiple non-contiguous chromosomal fragments are fused. We have developed a cloning system for maintaining large donor subchromosomal fragments of mammalian DNA in the megabase size range as acentric chromosome fragments (double-minutes) in cultured mouse cells. This strategy relies on randomly inserted selectable markers for donor fragment maintenance. As a test case, we have cloned random segments of Chinese hamster ovary (CHO) chromosomal DNA in mouse EMT-6 cells. This was done by cotransfecting plasmids pZIPNeo and pSV2dhfr into DHFR-CHO cells followed by isolation of a Neo + DHFR + CHO donor colony and radiation-fusion-hybridization (RFH) to EMT-6 cells. We then selected for initial resistance to G418 and then to increasing levels of methotrexate (MTX). Southern analysis of pulsed-field gel electrophoresis of rare-cutting restriction endonuclease digestions of DNA from five RFH isolates indicated that all five contain at least 600 kb of unrearranged CHO DNA. In situ hybridization with the plasmids pZIPNeo and pSV2dhfr to metaphase chromosomes of MTX-resistant hybrid EMT-6 lines indicated that these markers reside on double-minute chromosomes.

DNA damage by drugs and radiation: what is important and how is it measured?

DNA is the most important target for drug and radiation induced cell killing. The mode of cell killing by cytotoxic drugs and radiation has been derived by correlating the type and quantity of DNA damage induced with lethality. Cytotoxic drugs can be classified by their main mode of action, while ionising radiation causes a range of lesions with the DNA double-strand break (dsb) being the most significant. Strand-breaks are measured from the reduction in the size of DNA molecules following treatment. Molecule size can be derived from the rate that DNA fragments sediment when centrifuged, elute through filters or migrate under electrophoresis. The effect of strand-breaks on DNA loop supercoiling allow a sensitive assay of DNA damage. Specific assays for base damage and drug adducts include changes in chromatographic mobility or binding by specific antibodies. By comparing the levels of damage in the genome overall with damage in specific gene targets, regions susceptible to damage induction, and varying in repair efficiency, have been revealed.

Molecular assays of radiation-induced DNA damage

There is a need for assays of DNA damage in many areas of laboratory research applied to radiation therapy, in order to understand the molecular processes involved in cell killing by ionising radiation and to predict in vivo response. Assays exist which measure many types of DNA damage following ionising radiation. From studies of the dose-response relationships for different types of damage, the double-strand break (dsb) has been shown to be the most significant lesion. Assays for DNA dsb have been of low sensitivity, such that supralethal doses of radiation had to be used in order to study dsb induction or repair. New assays, such as pulsed-field gel electrophoresis, are sensitive to dsb in a dose range relevant to cell survival. In addition, these assays can assess the distribution of dsb in different parts of the genome and determine heterogeneity of damage induction and repair. Assays which measure the effects of strand breaks on DNA complexed with nuclear matrix can reveal features of chromatin organisation and their influence on cellular radiosensitivity.