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1Department of Radiation Oncology, University of Alabama-Birmingham, 2Department of Radiation Oncology, The Ohio State University Medical School, 3Department of Cell Biology, and Pharmacology and Toxicology, Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, University of Alabama-Birmingham
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The comet assay is an efficient way of detecting single- and double-strand breaks, including alkali-labile sites and DNA-DNA/DNA-protein cross-links on the DNA in all cells including hippocampal neurons. The method takes advantage of the differential migration of DNA in an electric field due to differences in amount of DNA damage.
Keywords: Neuroscience, Issue 70, Genetics, Cellular Biology, Molecular Biology, Medicine, Cancer Biology, Anatomy, Physiology, DNA, DNA damage, double strand break, single strand break, repair, neurons, comet assay, cell culture
Nowsheen, S., Xia, F., Yang, E. S. Assaying DNA Damage in Hippocampal Neurons Using the Comet Assay. J. Vis. Exp. (70), e50049, doi:10.3791/50049 (2012).
A number of drugs target the DNA repair pathways and induce cell kill by creating DNA damage. Thus, processes to directly measure DNA damage have been extensively evaluated. Traditional methods are time consuming, expensive, resource intensive and require replicating cells. In contrast, the comet assay, a single cell gel electrophoresis assay, is a faster, non-invasive, inexpensive, direct and sensitive measure of DNA damage and repair. All forms of DNA damage as well as DNA repair can be visualized at the single cell level using this powerful technique.
The principle underlying the comet assay is that intact DNA is highly ordered whereas DNA damage disrupts this organization. The damaged DNA seeps into the agarose matrix and when subjected to an electric field, the negatively charged DNA migrates towards the cathode which is positively charged. The large undamaged DNA strands are not able to migrate far from the nucleus. DNA damage creates smaller DNA fragments which travel farther than the intact DNA. Comet Assay, an image analysis software, measures and compares the overall fluorescent intensity of the DNA in the nucleus with DNA that has migrated out of the nucleus. Fluorescent signal from the migrated DNA is proportional to DNA damage. Longer brighter DNA tail signifies increased DNA damage. Some of the parameters that are measured are tail moment which is a measure of both the amount of DNA and distribution of DNA in the tail, tail length and percentage of DNA in the tail. This assay allows to measure DNA repair as well since resolution of DNA damage signifies repair has taken place. The limit of sensitivity is approximately 50 strand breaks per diploid mammalian cell 1,2. Cells treated with any DNA damaging agents, such as etoposide, may be used as a positive control. Thus the comet assay is a quick and effective procedure to measure DNA damage.
1. Cell Culture
2. Comet Assay
1. Slide Preparation
2. Neutral Comet Assay
3. Alkaline Comet Assay
4. Fixing and Staining Cells
4. Image Acquisition and Analysis
5. Representative Results
An example of comet assay analysis on neuronal cells is shown in Figure 2 and Figure 3. In this case, irradiation of the neuronal cells induces DNA damage. As the cells are subjected to the electrical field, the DNA migrates at different rates due to differences in size which is subsequently analyzed using the Comet Assay software. The more the DNA damage, the farther the DNA migrates out of the nucleus. This decreases the fluorescent intensity in the nucleus which is subsequently picked up by the software and results in higher tail moment. Table 1 depicts a representative table from comet assay analysis and Figure 4 shows a representative graph comparing DNA damage in neuronal cells following radiation as measured by the comet assay.
Figure 1. Flow chart of the comet assay. Click here to view larger figure.
Figure 2. Representative images of neuronal cells (A) without and (B) with comet tail.
Figure 3. Comet assay analysis using Comet Assay software. (A) Representative screen shots of image acquired using Carl Zeiss fluorescent microscope and analyzed using Comet Assay software. (B) Clicking on the nucleus or the "comet head" (circled in green) generates a fluorescent map and graph (circled in yellow) and a (C) data table (circled in red). Click here to view larger figure.
Figure 4. Representative graph obtained by plotting the mean tail moment obtained by analyzing DNA damage in irradiated and non-irradiated neuronal cells using neutral comet assay. As expected, 3Gy radiation (x-ray) induces DNA damage as depicted by the higher mean tail moment in the irradiated neuronal cells. Shown is the mean tail moment (+/- Standard error), **P<0.01.
Table 1. Representative table obtained by comet assay analysis on irradiated and non-irradiated neuronal cells. Click here to view larger figure.
The comet assay has the unique capacity of analyzing individual cells. This is advantageous in identification of subpopulations of cells that demonstrate differential response to cytotoxic agents. A few practical limitations have to be taken into account. The number of cells that can be evaluated individually may vary depending on the individual. The sample size needs to be increased if there is variance in DNA damage within a population. Viable single-cell suspension is critical for this assay since predominant presence of necrotic or apoptotic cells will add to error. The lysis and electrophoresis steps gets rid of apoptotic cells, small DNA fragments (smaller than 50kb), and mitochondrial DNA. Thus, they are not detected by the comet assay 1,3-11.
As mentioned above, the comet assay is an efficient way of detecting single- and double-strand breaks, including alkali-labile sites and DNA-DNA/DNA-protein cross-links on the DNA. Here we have outlined two distinct protocols: the alkaline assay allows the detection of single strand breaks as well as double strand breaks, whereas the neutral comet assay allows only the detection of double strand breaks Enzyme-modified comet assay can been applied to detect oxidative DNA adducts. For example, treatment with Endo III (endonuclease) and hOGG1 (glycosylase) recognize oxidized pyrimidines including thymine glycol and uracil glycol 12,13 and 8-oxo-7,8-dihydroguanine (8-oxoGua) 14,15 respectively. Formamidopyrimidine DNA-glycosylase (FPG) can be used similarly. For this modified assay, treatment with the enzymes precedes the unwinding step. The addition of lesion-specific endonucleases increases the sensitivity of the comet assay as well 13.
Here we use tail moment as the descriptor of DNA damage. Tail moment is calculated using the following formula: percentage of DNA in the tail multiplied by the length of the comet tail 1,3-7. The length of the comet tail (tail length) is the distance from the center of the nucleus to the farthest point of migration of the DNA. Head length is the diameter of the nucleus. Head intensity and tail intensity are the mean pixel intensities in the head and tail of the comet, respectively. Total area is the overall surface area of the comet 1,3-7.
Though there are other methods of measuring DNA damage such as γ-H2AX foci staining and pulsed-field gel electrophoresis, these assays have their drawbacks as well 4,6,11,16,17. For instance, replication stress is often a confounder in the measurement of γ-H2AX levels 18. Since formation of γ-H2AX foci is dependent on recruitment of DNA repair proteins, failure to recruit DNA repair proteins and a condensed chromatin structure may lead to falsely low γ-H2AX foci levels as well. Similarly, pulsed-field gel electrophoresis is very time intensive and is only beneficial for separation of large DNA molecules 19,20. Thus, the comet assay is a relatively easy, efficient, and inexpensive, direct and sensitive measure of DNA damage and repair 10,11,21.
No conflicts of interest declared.
This work was supported by the IMPACT Award from the Department of Radiation Oncology, University of Alabama-Birmingham Comprehensive Cancer Center, the Fighting Children's Cancer Foundation, and the Gabrielle's Angel Foundation (to ESY.).
|1.5 ml tubes||Santa Cruz Biotechnology, Inc||Sc-200271|
|10X TBE (Tris base, boric acid, EDTA)||Fisher Scientific||BP13331|
|15 ml tube||Fisher Scientific||0553851|
|Aluminum foil||Fisher Scientific||01213101|
|Comet Assay software||Comet Assay IV Image Analysis System|
|Electrophoresis chamber||Thermo Scientific||09528101|
|Fluorescent microscope||Zeiss Axio Vision||Any fluorescent microscope with green filter will suffice|
|Low melting point agarose||Promega||V2111|
|Phosphate buffered saline, calcium free, magnesium free||HyClone||SH3025601|
|Sodium lauryl sarcosinate||Fisher Scientific||S529|
|Water bath||Fisher Scientific||154622Q|
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