Methods for analysis of DNA fragment distributions on pulsed field gel electrophoretic gels

DNA of a circular minichromosome linearized by restriction enzymes or other reagents is resistant to further cleavage: an influence of chromatin topology on the accessibility of DNA

The accessibility of DNA in chromatin is an essential factor in regulating its activities. We studied the accessibility of the DNA in a ∼170 kb circular minichromosome to DNA-cleaving reagents using pulsed-field gel electrophoresis and fibre-fluorescence in situ hybridization on combed DNA molecules. Only one of several potential sites in the minichromosome DNA was accessible to restriction enzymes in permeabilized cells, and in growing cells only a single site at an essentially random position was cut by poisoned topoisomerase II, neocarzinostatin and γ-radiation, which have multiple potential cleavage sites; further sites were then inaccessible in the linearized minichromosomes. Sequential exposure to combinations of these reagents also resulted in cleavage at only a single site. Minichromosome DNA containing single-strand breaks created by a nicking endonuclease to relax any unconstrained superhelicity was also cut at only a single position by a restriction enzyme. Further sites became accessible after ≥95% of histones H2A, H2B and H1, and most non-histone proteins were extracted. These observations suggest that a global rearrangement of the three-dimensional packing and interactions of nucleosomes occurs when a circular minichromosome is linearized and results in its DNA becoming inaccessible to probes.

Analysis of ionizing radiation-induced DNA damage and repair in three-dimensional human skin model system

Knowledge of cellular responses in tissue microenvironment is crucial for the accurate prediction of human health risks following chronic or acute exposure to ionizing radiation (IR). With this objective, we investigated the radio responses for the first time in three-dimensional (3D) artificial human skin tissue microenvironment after gamma-rays radiation. IR-induced DNA damage/repair response was assessed by immunological analysis of well-known DNA double strand break (DSB) repair proteins, i.e. 53BP1 and phosphorylated ataxia telangiectasia mutated(ser1981) (ATM(ser1981)). Efficient 53BP1 and phosphorylated ATM foci formation was observed in human EpiDerm tissue constructs after low and high doses of gamma-rays. Interestingly, EpiDerm tissue constructs displayed less 53BP1 and ATM foci number at all radiation doses (0.1, 1, 2.5 and 5 Gy) than that observed for 2D human fibroblasts. DSB repair efficiency judged by the disappearance of 53BP1 foci declined with increasing doses of gamma-rays and tissue constructs irradiated with 2.5 and 5 Gy of gamma-rays displayed 53BP1 foci persisting up to 72 h of analysis. Pretreatment of EpiDerm tissue constructs with LY294002, [an inhibitor of phosphatidylinositol-3 kinase and PI-3 kinase like kinases (PIKK)] completely abolished IR-induced 53BP1 foci formation and increased the apoptotic death. This observation indicates the importance of PIKK signalling pathway for efficient radiation responses in intact tissue constructs. In summary, we have successfully demonstrated the feasibility of monitoring the DNA damage response in human skin tissue microenvironment. In this system, 53BP1 can be used as a useful marker for monitoring the DSB repair efficiency.

Use of the PFGE assay for studies of DNA breakage induced by toxic chemicals

The relevance of the pulsed field gel electrophoresis (PFGE) assay for the estimation of the DNA damaging effects of chemicals was studied. Four chemicals were randomly chosen from the list of 50 Multicentre Evaluation of In Vitro Cytotoxicity (MEIC) reference chemicals with known human acute systemic toxicity: acetylsalicylic acid, paracetamol, ethylene glycol and sodium chloride. Human fibroblasts (VH-10) were used as a model system. For the estimation of cytotoxic effect, cell monolayers were treated with chemicals for 24 hours. Cloning efficiency (colony-forming ability) at different concentrations of the test chemicals was estimated, and the 50% inhibitory concentration (IC50) was determined. The IC50 values obtained demonstrated a correlation with human lethal blood concentrations. The induction of DNA double-strand breaks, measured by PFGE as the fraction of activity released, was detected after treatment with paracetamol. However, the other three chemicals tested mainly induced DNA degradation.

X-ray-induced DNA double-strand breaks in mouse l1210 cells: a new computational method for analyzing neutral filter elution data

The aim of this article is to present a method for studying the shape of the dose and repair responses for X-ray-induced double-strand breaks (DSBs) as measured by neutral filter elution (NFE). The approach is closely related to a method we developed for the use of specific molecular size markers and used for determination of the absolute number of randomly distributed radiation-induced DSBs by pulsed-field gel electrophoresis (PFGE). Mouse leukemia L1210 cells were X-irradiated with 0-50 Gy. Samples were then evaluated both with PFGE and with NFE. Assuming that with both migration (PFGE) and elution (NFE), a heterogeneous population of double-stranded DNA fragments will start with the smallest fragments and proceed with increasingly larger fragments, it is possible to match the migration behavior of fractions of fragments smaller than a certain size to the fraction eluted at a specific time. This assumption does not exclude the possibility of DNA being sheared in the NFE filter. The yield, as determined by the size markers in PFGE, was used to find the corresponding elution times in the NFE experiment. These experimentally used elution times could then reversely be interpreted as size markers which finally were used to calculate DSBs/Mbp as a function of X-ray dose. The resulting lines were almost straight. The data were also plotted as relative elution and showed that, as expected, the dose response then appears with a more pronounced sigmoid shape.

The fraction of DNA released on pulsed-field gel electrophoresis gels may differ significantly between genomes at low levels of double-strand breaks

A common way to use pulsed-field gel electrophoresis (PFGE) for measuring the induction and repair of DNA double-strand breaks (DSBs) in mammalian cells is by using the fraction of total DNA released, FR, from the plug. We have analyzed the general relationship between initial chromosome sizes and FR. It is shown that, because of the difference in initial chromosomal size, the discrepancy in FR values between human and rodent cells may become significant at doses of radiation producing approximately 5 DSBs/100 Mbp or less.

DNA double-strand break repair, DNA-PK, and DNA ligases in two human squamous carcinoma cell lines with different radiosensitivity

PURPOSE

Variation in sensitivity to radiotherapy among tumors has been related to the capacity of cells to repair radiation-induced DNA double-strand breaks (DSBs). DNA-dependent protein kinase (DNA-PK) and DNA ligases may affect DNA dsb rejoining. This study was performed to compare rate of rejoining of radiation-induced DSBs, DNA-PK, and DNA ligase activities in two human squamous carcinoma cell lines with different sensitivity to ionizing radiation.

METHODS AND MATERIALS

Cell survival of two human squamous carcinoma cell lines, UM-SCC-1 and UM-SCC-14A, was determined by an in vitro clonogenic assay. DSB rejoining was studied using pulsed field gel electrophoresis (PFGE). DNA-PK activity was determined using BIOTRAK DNA-PK enzyme assay system (Amersham). DNA ligase activity in crude cell extracts was measured using [5'-33P] Poly (dA) x (oligo (dT) as a substrate. Proteolytic degradation of proteins was analyzed by means of Western blotting.

RESULTS

Applying the commonly used linear-quadratic equation to describe cell survival, S = e-alphaD-betaD2, the two cell lines roughly have the same alpha value (approximately 0.40 Gy(-1)) whereas the beta value was considerably higher in UM-SCC-14A (0.067 Gy(-2)+/-0.007 Gy(-2) [SEM]) as compared to UM-SCC-1 (0.013 Gy(-2)+/-0.004 Gy(-2) [SEM]). Furthermore, UM-SCC-1 was more proficient in rejoining of X-ray-induced DSBs as compared to UM-SCC-14A as quantified by PFGE. The constitutive level of DNA-PK activity was 1.6 times higher in UM-SCC-1 as compared to UM-SCC-14A ( < 0.05). The constitutive level of DNA ligase activity was similar in the two cell lines.

CONCLUSIONS

The results suggest that the proficiency in rejoining of DSBs is associated with DNA-PK activity but not with total DNA ligase activity.

Discrimination between genotoxicity and cytotoxicity in the induction of DNA double-strand breaks in cells treated with etoposide, melphalan, cisplatin, potassium cyanide, Triton X-100, and gamma-irradiation

The dose-response relationships for DNA fragmentation (assessed by pulsed-field gel electrophoresis, PFGE) and for viability (evaluated by measuring the reduction of MTT dye which can be accomplished by viable cells only) were investigated in order to discriminate between genotoxicity and cytotoxicity in the pathogenesis of DNA double-strand breaks (DSB). Cultured human lung epithelial cells (A549) were treated with the DNA-intrastrand crosslinker cisplatin, the DNA-interstrand crosslinker melphalan and the topoisomerase II inhibitor etoposide. The cytotoxic mode of DSB induction was investigated by using the mitochondrial respiratory chain toxin potassium cyanide (KCN) and the detergent Triton X-100. gamma-Irradiation induced a linear dose response for DSB which were efficiently repaired and did not cause reduction in cell survival over a period of 72 h. With etoposide and melphalan a significant increase in DSB was seen 8 h after treatment initiation with concentrations that did not affect cell survival, implicating genotoxicity as the causal event. In contrast, induction of DSB by KCN and Triton X-100, and also by cisplatin, was seen only after cell viability was reduced to less than about 60%, indicating that DSB were the consequence of extragenomic damage. This mechanistic distinction of the two classes was supported by DNA fragment length analysis. In line with a genotoxic mechanism and absence of additional cytotoxic effects, the DNA fragments generated by gamma-irradiation as well as by etoposide and melphalan displayed a distribution between 1 and 4 Mbp with a peak around 2 Mbp. In contrast, DNA fragments induced by Triton X-100 and KCN peaked below 0.5 Mbp, implicating activation of DNA-degrading enzymes. This type of investigation is suggested for the study of chemicals for potential DNA interstrand crosslinking, an important promutagenic type of DNA damage. To avoid false positive results in genetic toxicity testing it is suggested that all assays include a dose-response relationship for both genotoxicity and viability.

Propylene oxide and epichlorohydrin induce DNA strand breaks in human diploid fibroblasts

The induction of DNA strand breaks in human diploid fibroblasts (VH-10) was demonstrated after in vitro exposure with two carcinogenic epoxides, propylene oxide (PO) and epichlorohydrin (ECH). Alkaline DNA unwinding (ADU), pulsed field gel electropharosis (PFGE), and the comet assay were used to measure DNA single. (SSBs) and double-strand breaks (DSBs). A dose-dependent increase of DNA strand breaks, measured by ADU, was observed in the dose range 2.5-20 mMh of PO and 0.25-2 mMh of ECH. The dose-response of ECH was about five times higher compared with that of PO (211 vs. 41 SSBs. 100 Mbp-1.mMh-1). The induction rates of DSBs, measured by PFGE, were found to be 18 times higher for ECH compared to PO (4.8 and 0.27 DSBs.100 Mbp-1.mMh-1 for ECH and PO, respectively). Using these two methods, the SSBs/ DSBs ratio was estimated to be 148 for PO and 44 for ECH. The data obtained by the comet assay also demonstrated a dose-dependent ability of PO and ECH to induce DNA damage. It was found that ECH was about six times more effective as an inducer of DNA strand breaks compared to PO (200 and 32x100 Mbp-1.mMh-1 for ECH and PO, respectively). The SSBs/DSBs ratios calculated using comet assay and PFGE data were 125 for ECH and 41 for PO. In addition, ECH is about 10 times more toxic than PO with respect to survival. These properties of ECH can at least in part be explained by its higher chemical reactivity connected with a higher rate of DNA alkylation.