Estimates of the rate of ligation during excision repair of ultraviolet-damaged DNA in mammalian cells

Functional evaluation of DNA repair in human biopsies and their relation to other cellular biomarkers

Thousands of DNA lesions are estimated to occur in each cell every day and almost all are recognized and repaired. DNA repair is an essential system that prevents accumulation of mutations which can lead to serious cellular malfunctions. Phenotypic evaluation of DNA repair activity of individuals is a relatively new approach. Methods to assess base and nucleotide excision repair pathways (BER and NER) in peripheral blood cells based on modified comet assay protocols have been widely applied in human epidemiological studies. These provided some interesting observations of individual DNA repair activity being suppressed among cancer patients. However, extension of these results to cancer target tissues requires a different approach. Here we describe the evaluation of BER and NER activities in extracts from deep-frozen colon biopsies using an upgraded version of the in vitro comet-based DNA repair assay in which 12 reactions on one microscope slide can be performed. The aim of this report is to provide a detailed, easy-to-follow protocol together with results of optimization experiments. Additionally, results obtained by functional assays were analyzed in the context of other cellular biomarkers, namely single nucleotide polymorphisms and gene expressions. We have shown that measuring DNA repair activity is not easily replaceable by genomic or transcriptomic approaches, but should be applied with the latter techniques in a complementary manner. The ability to measure DNA repair directly in cancer target tissues might finally answer questions about the tissue-specificity of DNA repair processes and their real involvement in the process of carcinogenesis.

Cobalt(II) inhibits the incision and the polymerization step of nucleotide excision repair in human fibroblasts

Compounds of cobalt are carcinogenic to experimental animals, but the mutagenicity in mammalian cells in culture is rather weak. In contrast, cobalt(II) has been shown to inhibit the removal of DNA damage induced by UVC light, indicating an interference with cellular DNA repair processes. In the present study it was investigated which step of the nucleotide excision repair is affected by cobalt(II) and which mechanisms are involved. In this context, the effect of non-cytotoxic cobalt(II) concentrations on the induction as well as on the repair of UVC-induced DNA lesions has been examined in human fibroblasts by using the alkaline unwinding technique under various conditions. Cobalt(II) concentrations as low as 50 microM inhibit the incision as well as the polymerization step. In contrast, the ligation of repair patches is not disturbed by this metal. By combining the alkaline unwinding technique with the repair enzyme T4 endonuclease V, it is demonstrated that the incision at the site of cyclobutane pyrimidine dimers is affected at concentrations of 150 microM and higher. As one mode of action, the competition with essential magnesium(II) ions by cobalt(II) ions could be identified.

Induction and repair of DNA damage in UV-irradiated human lymphocytes. Spectral differences and repair kinetics

The alkaline elution assay has been employed to study the induction and repair kinetics of DNA damage in human lymphocytes after irradiation with biologically relevant doses of UVB (297 and 302 nm) or UVA (365 nm) radiation. At 365 nm, when the predominant lesions are single-strand breaks, the rate of lesion induction was 1.5 x 10(-3) per 10(8) Da per kJ m-2. The number of breaks decayed with a half-life of about 50 min after a dose of 20 kJ m-2. In the UVB region, cyclobutyl pyrimidine dimers and 6-4 photoproducts are formed, both of which are repairable via the nucleotide excision repair pathway. By using repair inhibitors, the rate of induction of such lesions at 297 and 302 nm was found to be 0.07 per 10(8) Da per J m-2. Lesions were removed with a half-life of about 100 min. Mathematical modelling of the excision repair process revealed a time-dependent polymerization-ligation rate: after an initial lag phase the polymerization-ligation rate increased, reaching 50% of its maximum rate at 80-100 min after the start of repair incubation. This course of development might be due to a damage-associated regulation of DNA precursors synthesis.

DNA repair and recovery of RNA synthesis in uremic patients

A high frequency of cancer appears among uremic patients. As depressed DNA repair ability is thought to be one of the causes for malignancy in cancer prone diseases, the present study was undertaken to examine DNA repair in uremic patients. Unscheduled DNA repair synthesis in peripheral lymphocytes was measured after both ultraviolet (UV) and gamma irradiations. In hemodialysis (HD) patients the repairs were normal, but in chronic renal failure (CRF) patients not yet on dialysis treatment, both UV- and gamma-induced DNA repair abilities were depressed to about 60% of the control. Recovery of RNA synthesis after UV irradiation followed the same pattern: it was reduced in CRF but normal in HD cells. When CRF lymphocytes were incubated in normal plasma, the UV-stimulated DNA repair improved to a nearly normal level, whereas incubation of normal cells in CRF plasma depressed their repair capacity to 70% of the initial level. These results suggest that a plasmatic substance such as the carcinogenic heterocyclic amines may be involved in the impairment of DNA repair in chronic renal failure.

The mode of action of 1-beta-D-arabinofuranosylcytosine in inhibiting DNA repair; new evidence using a sensitive assay for repair DNA synthesis and ligation in permeable cells

Mammalian cells permeabilised by treatment with saponin are capable of UV excision repair. We have developed an assay system which permits measurement of the later stages of repair, i.e. repair synthesis and ligation. Incomplete repair sites are accumulated in UV-irradiated cells by incubating them with DNA synthesis inhibitors hydroxyurea and aphidicolin. On removal of the inhibitors at the time of permeabilisation, these incomplete sites, detected as DNA breaks, are rapidly ligated in a reaction that requires deoxyribonucleoside triphosphates and is blocked by aphidicolin. Thus ligation is possible only after a significant amount of DNA synthesis. We have used the assay to clarify the mode of inhibition of DNA repair by 1-beta-D-arabinofuranosylcytosine (ara C), another DNA polymerase inhibitor. It is well known that incomplete repair sites accumulated in whole cells with ara C are ligated at a slow rate, if at all. The hypothesis that ara C blocks or reduces further polymerisation after its incorporation into repair patches is disproved by our demonstration that, in permeable cells, the accumulated DNA breaks are ligated very rapidly. The likely explanation of the action of ara C is that, once phosphorylated, it remains in the cell as ara CTP and continues to inhibit polymerisation through competition with dCTP; in permeable cells, it readily leaks out.

Scanning electron microscope analysis of structural changes and aberrations in human chromosomes associated with the inhibition and reversal of inhibition of ultraviolet light induced DNA repair

Metaphase chromosomes appear decondensed in preparations from mitotic cells that have been irradiated with ultraviolet light (UV) and incubated with inhibitors of DNA synthesis; under these conditions DNA repair is inhibited and both single and double strand DNA breaks accumulate. After reversal of the inhibition chromosomes are condensed, but are often damaged. In this paper we show by scanning electron microscopy (SEM) that decondensed HeLa chromosomes are composed of fibre clusters similar to those previously described for the large chromosomes of the Indian muntjac. This suggests that the clusters may be a universal higher order packing unit in mammalian metaphase chromosomes. We also examine by SEM the nature of the aberrations that appear after the reversal of periods of inhibited repair; these include gaps, breaks, deletions and telomeric packing abnormalities. SEM analysis allows an extension and reconsideration of conclusions about chromatid continuity based on the study of conventional light microscope (LM) preparations.