We would like to thank the LHW Stiftung, in Triesen Liechtenstein, for financially supporting our research on oxidative stress.

Studies on comet assay performed in the University of Basel, Department of Ophthalmology were approved by the Local Ethical Committee of Basel
1. Preparation of Reagents
<ol>
	<li>Prepare Dulbecco&#39;s Phosphate Buffered Saline (PBS) (Ca++, Mg++ free) solution by adding PBS (1 L packet) and 990 ml of dH2O to the media. Adjust the pH to 7.4. Store at RT.</li>
	<li>Prepare lysing solution: To prepare 1,000 ml add 2.5 M NaCl (146.1 g), 100 mM EDTA (37.2 g) and 10 mM Trizma base (1.2 g) in dH2O.</li>
	<li>Prepare electrophoresis buffer (300 mM NaOH/1 mM EDTA) by adding 30 ml of 10 M NaOH and 7.5 ml of 0.2M EDTA, q.s. to 1,500 ml dH2O and mix well. The total volume depends on the gel box capacity. Prior to use, measure the pH of the buffer to ensure a pH of &#62;13.</li>
	<li>Prepare neutralization buffer containing 0.4 M Tris (48.5 gm added to ~800 ml dH2O, adjust pH to 7.5), concentrated (&#62;10 M HCl) in 1,000 ml with dH2O. Store the solution at RT.</li>
	<li>Prepare staining solution. To Ethidium Bromide (EtBr; 10x Stock, 20 &#181;g/ml) add 10 mg of EtBr in 50 ml dH2O and store at RT. For 1x Stock - mix 1 ml with 9 ml dH2O. CAUTIOUS! Handle EtBr with adequate precaution as it is a known carcinogen.</li>
</ol>
2. Isolation of Leukocytes
<ol>
	<li>Obtain human blood samples (20 ml) with anti-coagulant such as heparin using venous puncture.</li>
	<li>Separate the lymphocytes using a density gradient cell separator such as Histopaque.
	<ol>
		<li>Briefly, dilute blood in 1:1 ratio with PBS or RPMI (without FBS) and layer over 600 &#181;l cell separator liquid.</li>
		<li>Centrifuge 1,800 x g for 20 min at 4 &#176;C. Aspirate the &#8216;buffy&#8217; coat into 3-5 ml of PBS/ RPMI and centrifuged at 300 x g for 10 min to pellet the lymphocytes.</li>
		<li>Retrieve lymphocytes from just above boundary between PBS (RPMI) and cell separator liquid, using a pipettor. Remove the leukocyte bands from the interface between plasma and the cell separator liquid layers of each tube and collect into one 50 ml tube.</li>
	</ol>
	</li>
	<li>Bring the total volume to 50 ml with cold Dulbecco&#8217;s Modified Eagle Medium (DMEM). Wash the cell suspension three times with DMEM at 300 x g for 10 min.</li>
	<li>Count the total numbers of cells using a Haemocytometer. Suspend the cells in PBS and aliquote into microcentrifuge tubes at 107 cells/tube.</li>
	<li>Pipet 0.4 ml of cells into a 5 ml plastic disposable tube. Add 1.2 ml 1% low-gelling-temperature agarose at 40 &#176;C. Mix and rapidly and pipet 1.2 ml of cell suspension onto the agarose-covered surface of a pre-coated slide. Avoid producing bubbles.</li>
	<li>Allow the agarose to gel for about 2 min. Be consistent with the time and temperature used for gelling, and ensure that agarose is fully set before submerging in lysis solution. After fully set, submerge into lysing solution at ~4 &#186;C.</li>
</ol>
3. Lysis and Electrophoresis
NOTE: The procedure described is for electrophoresis under pH &#62;13 alkaline conditions.
<ol>
	<li>After at least 2 hr at ~4 &#186;C, gently remove slides from the lysing Solution. Place slides side by side on the horizontal gel box near one end, sliding them as close together as possible.</li>
	<li>Fill the buffer reservoirs with freshly made pH &#62;13 electrophoresis buffer until the liquid level completely covers the slides (avoid bubbles over the agarose).</li>
	<li>Let slides sit in the alkaline buffer for 20 min to allow for unwinding of the DNA and the expression of alkali-labile damage.</li>
	<li>Turn on power supply to 25 volts (~0.75 V/cm) and adjust the current to 300 milliamperes by raising or lowering the buffer level. Electrophorese the slides for 30 min.</li>
	<li>Turn off the power. Gently lift the slides from the buffer and place on a drain tray. Drop wise coat the slides with neutralization Buffer. Allow the slides to sit for at least 5 min. Drain slides and repeat two more times.</li>
	<li>Stain the slides with 80 &#181;l 1x Ethidium Bromide (EtBr) and leave for 5 min and then dip in chilled distilled water to remove excess stain. Then place a coverslip over the slide and store them immediately. Store slides for a month at RT in dry conditions. 
	NOTE: Other DNA stains (e.g., SYBR-green) may also be used. Caution! wear protective gloves as most dyes are mutagenic.</li>
</ol>
4. Quantification of DNA Breaks
<ol>
	<li>To visualize the DNA damage, observe the EtBr-stained DNA slide under a 40X objective fluorescent microscope.</li>
	<li>Assess DNA damage quantitatively in the cells by measuring the length of DNA migration and the percentage of migrated DNA (Figure 1A). Quantify DNA damage (Figure 1B) by the Tail- moment and Olive-moment. Definitions of Tail-Moment and Olive &#8211;Moment have previously been given8-10. 
	NOTE: In our experience it&#39;s enough to stick by one of the parameters. The cells are photographed by setting the automated tool that scans over the microscope slide and photographs cells. Quantification of DNA breaks can be done by image analysis software packages. There are several different software packages that are custom made to capture the image of the cells and quantify DNA damage. We recommend using the same software package throughout the experiment. The lab technician identifies the intact cell or comet to be scored on the computer and clicks with the mouse on it. The comet or intact cell is then automatically scored.</li>
</ol>

<ol>
	<li>Ostling, O., Johanson, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microelectrophoretic+study+of+radiation-induced+DNA+damages+in+individual+mammalian+cells.">Microelectrophoretic study of radiation-induced DNA damages in individual mammalian cells.</a> Biochem Biophys Res Commun. 123 (1), 291-298 (1984).</li><li>Phillips, J. L., Singh, N. P., Lai, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electromagnetic+fields+and+DNA+damage.">Electromagnetic fields and DNA damage.</a> Pathophysiology. 16 (2-3), 79-88 (2009).</li><li>Dhawan, A., Bajpayee, M., Parmar, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comet+assay:+a+reliable+tool+for+the+assessment+of+DNA+damage+in+different+models.">Comet assay: a reliable tool for the assessment of DNA damage in different models.</a> Cell Biol Toxicol. 25 (1), 5-32 (2009).</li><li>Aiub, C. A., Pinto, L. F., Felzenszwalb, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA-repair+genes+and+vitamin+E+in+the+prevention+of+N-nitrosodiethylamine+mutagenicity.">DNA-repair genes and vitamin E in the prevention of N-nitrosodiethylamine mutagenicity.</a> Cell Biol Toxicol. 25 (4), 393-402 (2009).</li><li>Bartsch, H., Nair, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chronic+inflammation+and+oxidative+stress+in+the+genesis+and+perpetuation+of+cancer:+role+of+lipid+peroxidation,+DNA+damage,+and+repair.">Chronic inflammation and oxidative stress in the genesis and perpetuation of cancer: role of lipid peroxidation, DNA damage, and repair.</a> Langenbecks Arch Surg. 391 (5), 499-510 (2006).</li><li>Martin, L. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+damage+and+repair:+relevance+to+mechanisms+of+neurodegeneration.">DNA damage and repair: relevance to mechanisms of neurodegeneration.</a> J Neuropathol Exp Neurol. 67 (5), 377-387 (2008).</li><li>Choy, C. K., Benzie, I. F., Cho, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UV-mediated+DNA+strand+breaks+in+corneal+epithelial+cells+assessed+using+the+comet+assay+procedure.">UV-mediated DNA strand breaks in corneal epithelial cells assessed using the comet assay procedure.</a> Photochem Photobiol. 81 (3), 493-497 (2005).</li><li>Mozaffarieh, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comet+assay+analysis+of+single-stranded+DNA+breaks+in+circulating+leukocytes+of+glaucoma+patients.">Comet assay analysis of single-stranded DNA breaks in circulating leukocytes of glaucoma patients.</a> Mol Vis. 14, 1584-1588 (2008).</li><li>Mozaffarieh, M., Konieczka, K., Hauenstein, D., Schoetzau, A., Flammer, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Half+a+pack+of+cigarettes+a+day+more+than+doubles+DNA+breaks+in+circulating+leukocytes.">Half a pack of cigarettes a day more than doubles DNA breaks in circulating leukocytes.</a> Tob Induc Dis. 8 (14), (2010).</li><li>Mozaffarieh, M., Schotzau, A., Josifova, T., Flammer, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+ranibizumab+versus+photodynamic+therapy+on+DNA+damage+in+patients+with+exudative+macular+degeneration.">The effect of ranibizumab versus photodynamic therapy on DNA damage in patients with exudative macular degeneration.</a> Mol Vis. 15, 1194-1199 (2009).</li><li>Pertynska-Marczewska, M., Merhi, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationship+of+Advanced+Glycation+End+Products+With+Cardiovascular+Disease+in+Menopausal+Women.">Relationship of Advanced Glycation End Products With Cardiovascular Disease in Menopausal Women.</a> Reprod Sci. , (2014).</li><li>Singh, N. P., McCoy, M. T., Tice, R. R., Schneider, E. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+technique+for+quantitation+of+low+levels+of+DNA+damage+in+individual+cells).">A simple technique for quantitation of low levels of DNA damage in individual cells).</a> Exp Cell Res. 175, 184-191 (1988).</li><li>Gaiv&#227;o, I., Sierra, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+comet+assay:+insights,+uses,+and+future+perspectives.">Drosophila comet assay: insights, uses, and future perspectives.</a> Front Genet. 5, 304 (2014).</li><li>Zhang, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+damage+in+lens+epithelial+cells+and+peripheral+lymphocytes+from+age-related+cataract+patients.">DNA damage in lens epithelial cells and peripheral lymphocytes from age-related cataract patients.</a> Ophthalmic Res. 51 (3), 124-128 (2014).</li><li>Huet, S. A., Vasseur, L., Camus, S., Chesn&#233;, C., Fessard, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Performance+of+comet+and+micronucleus+assays+in+metabolic+competent+HepaRG+cells+to+predict+in+vivo+genotoxicity.">Performance of comet and micronucleus assays in metabolic competent HepaRG cells to predict in vivo genotoxicity.</a> Toxicol Sci. 138 (2), 300-309 (2014).</li><li>Danson, S., Ranson, M., Denneny, O., Cummings, J., Ward, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Validation+of+the+comet-X+assay+as+a+pharmacodynamic+assay+for+measuring+DNA+cross-linking+produced+by+the+novel+anticancer+agent+RH1+during+a+phase+I+clinical+trial.">Validation of the comet-X assay as a pharmacodynamic assay for measuring DNA cross-linking produced by the novel anticancer agent RH1 during a phase I clinical trial.</a> Cancer chemotherapy and pharmacology. 60, 851-861 (2007).</li><li>Moller, P., Moller, L., Godschalk, R. W., Jones, G. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessment+and+reduction+of+comet+assay+variation+in+relation+to+DNA+damage:+studies+from+the+European+Comet+Assay+Validation+Group.">Assessment and reduction of comet assay variation in relation to DNA damage: studies from the European Comet Assay Validation Group.</a> Mutagenesis. 25, 109-111 (2010).</li><li>Chan, S. W., Chevalier, S., Aprikian, A., Chen, J. Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simultaneous+quantification+of+mitochondrial+DNA+damage+and+copy+number+in+circulating+blood:+a+sensitive+approach+to+systemic+oxidative+stress.">Simultaneous quantification of mitochondrial DNA damage and copy number in circulating blood: a sensitive approach to systemic oxidative stress.</a> BioMed Res Int. , 157-547 (2013).</li><li>Sanchez-Quesada, J. L., Perez, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modified+lipoproteins+as+biomarkers+of+cardiovascular+risk+in+diabetes+mellitus.">Modified lipoproteins as biomarkers of cardiovascular risk in diabetes mellitus.</a> Endocrinol Nutr. 60, 518-528 (2013).</li><li>Gandhi, G., Kaur, G., Nisar, U. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cross-sectional+case+control+study+on+genetic+damage+in+individuals+residing+in+the+vicinity+of+a+mobile+phone+base+station.">Cross-sectional case control study on genetic damage in individuals residing in the vicinity of a mobile phone base station.</a> Electromagn Biol Med. 9, 1-11 (2014).</li><li>Cabarkapa, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protective+effect+of+dry+olive+leaf+extract+in+adrenaline+induced+DNA+damage+evaluated+using+in+vitro+comet+assay+with+human+peripheral+leukocytes.">Protective effect of dry olive leaf extract in adrenaline induced DNA damage evaluated using in vitro comet assay with human peripheral leukocytes.</a> Toxicol In Vitro. 28 (3), 451-456 (2014).</li></ol>

Swedish scientists Ostling and Johanson were the first in their field to use comet assay to quantify DNA damage in cells1. The neutral conditions that the two scientists used, however, only allowed the detection of double-stranded DNA breaks. Singh et al. later adapted the assay for use under alkaline conditions, which produced a sensitive version that could assess double and single-stranded DNA breaks and detect alkali-labile sites12. Since its initial development, the assay has been modified at various steps to make it suitable for assessing types of DNA damage in different cell types13-15.
As with all techniques, paying rigorous attention to technical details is important to obtain accurate results16. Based on our experience, best results are obtained if every methodological step&#8212;from solution preparation to comet quantification&#8212;is performed by expert laboratory technicians. The use of fresh and correctly prepared media, adequate pipetting techniques, exact timing and (as previously mentioned in the results section) the use of freshly prepared leukocytes are essential in order for lysis and gel electrophoresis to obtain accurate results17.
All the individual steps in this assay are equally important for obtaining reliable results.16 In general best results are obtained if every single methodological step from solution preparation till comet quantification is performed by expert lab technicians.Important seem the use of fresh and correctly prepared media, adequate pipetting techniques, exact timing and as already referred to in the results section the use of freshly prepared leukocytes for lysis and gel-electrophoresis to obtain adequate results from the assay17.
As do other methodologies, the comet assay technique has its advantages and drawbacks. Being a sensitive method, the assay is vulnerable to factors (e.g., UV light) which could augment DNA breaks and thus affect results. Any factor that may enhance oxidative stress, except that which is being researched, should be avoided. Stressors can increase level of oxidative stress not only in leukocytes but also in all other blood mediums and lymphocytes. As mentioned earlier there are many different and more direct ways of measuring oxidative stress18,19. The comet assay is one of many methods which has certain advantages. These include its relative low cost, the small number of cells required (&#60;10,000 cells) and thus the small samples of blood required per patient, the relative short period of time required to quantify DNA damage in cells (approximately 3 days), its sensitivity and its wide-spread applicability to asses DNA damage in different cell-types. In the past we choose to work with leukocytes since we had experience with this cell-type and it was applicable for the particular study planned. Another advantage of the comet assay is that it can be used to detect different types and levels of DNA damage and thus can be applied in various other areas of studies besides oxidative stress such as DNA repair studies, supplementation trials or genotoxicity studies.
Oxidative stress is now recognized as playing a critical role in the pathogenesis of multiple diseases. The comet assay method, while one of many ways of measuring oxidative stress18,19, is relatively simple, versatile and inexpensive. When mastered, this method can be used in all areas of medicine in which oxidative stress plays role 8-10,20,21.

Comet assay was first developed by Swedish scientists Ostling and Johanson1. DNA is a negatively charged molecule. During electrophoresis, smaller, damaged DNA fragments travel faster toward a positively charged anode2. The smaller the DNA fragments, the faster their migration toward the anode to form a typical &#8220;comet&#8221; with a &#8220;head&#8221; composed of intact, undamaged DNA and a &#8220;tail&#8221; composed of damaged DNA fragments3. Damaged DNA can be repaired by different mechanisms in the body4, which keep the generation of DNA breaks fairly balanced5. If, however, the balance is in favour of DNA breaks , the breaks can accumulate and will ultimately contribute to the development of a disease.
Our DNA suffers approximately 0.000165% damage at a given time6. Single stranded DNA breaks refer to a defect on one of the two strands of the DNA double helix whereas double-stranded DNA breaks are caused when both strands of the DNA double helix are damaged. There are various factors which may enhance the amount of DNA breaks at a given time such as the age of the cell, cigarette smoke, various drugs or oxidative stress7-9. If all factors leading to enhanced DNA breaks are kept constant, then the quantification of DNA breaks by means of comet assay is a good indirect parameter of oxidative stress.
The method of comet assay is used increasingly today in medicine including ophthalmology. One reason for this is that oxidative stress is more and more recognized as a pathogenetic mechanism for various diseases8-11 and comet assay is one method with which oxidative stress can indirectly be quantified.

<table><tbody><tr><td>Dimethylsulfoxide (DMSO)</td><td>Qualigens</td><td>(CPW59)</td><td></td></tr><tr><td>Disodium EDTA</td><td>HiMedia</td><td>(RM1370)</td><td></td></tr><tr><td>Ethidium Bromide</td><td>Sigma</td><td>(E-8751)</td><td></td></tr><tr><td>Histopaque</td><td>Sigma</td><td>(1077-1)</td><td></td></tr><tr><td>Phosphate Buffered Saline (PBS) (Ca++, Mg++ free)</td><td>HiMedia</td><td>(TS1006)</td><td></td></tr><tr><td>Sodium Chloride (NaCl)</td><td>Ranbaxy Rankem</td><td>(S0160)</td><td></td></tr><tr><td>Sodium Hydroxide (NaOH)</td><td>BDH-Merck</td><td>(89021)</td><td></td></tr><tr><td>Triton X-100</td><td>HiMedia</td><td>(RM 845)</td><td></td></tr><tr><td>Trizma Base</td><td>Spectrochem</td><td></td><td></td></tr><tr><td colspan="4">Materials required for gel electrophoresis</td></tr><tr><td>Normal Melting Agarose (NMA)</td><td>HiMedia</td><td>(RM273)</td><td></td></tr><tr><td>Low Melting Point Agarose (LMPA)</td><td>Sigma</td><td>(A9414)</td><td></td></tr><tr><td>Methanol - Qualigens</td><td></td><td></td><td></td></tr><tr><td>Coverslips (No. 1, 24 x 60 mm)</td><td>Blue Star</td><td></td><td></td></tr><tr><td>Microcentrifuge Tubes</td><td>Tarsons</td><td>(500010)</td><td></td></tr><tr><td>Micropipettor and Tips</td><td>Tarsons</td><td></td><td></td></tr><tr><td>Microscope Slides, Conventional / Micro gel electrophoresis (MGE) slides</td><td></td><td></td><td></td></tr></tbody></table>

comet assay as an indirect measure of systemic oxidative stress

Higher eukaryotic organisms cannot live without oxygen; yet, paradoxically, oxygen can be harmful to them. The oxygen molecule is chemically relatively inert because it has two unpaired electrons located in different pi * anti-bonding orbitals. These two electrons have parallel spins, meaning they rotate in the same direction about their own axes. This is why the oxygen molecule is not very reactive. Activation of oxygen may occur by two different mechanisms; either through reduction via one electron at a time (monovalent reduction), or through the absorption of sufficient energy to reverse the spin of one of the unpaired electrons. This results in the production of reactive oxidative species (ROS). There are a number of ways in which the human body eliminates ROS in its physiological state. If ROS production exceeds the repair capacity, oxidative stress results and damages different molecules. There are many different methods by which oxidative stress can be measured. This manuscript focuses on one of the methods named cell gel electrophoresis, also known as &#8220;comet assay&#8221; which allows measurement of DNA breaks. If all factors known to cause DNA damage, other than oxidative stress are kept constant, the amount of DNA damage measured by comet assay is a good parameter of oxidative stress. The principle is simple and relies upon the fact that DNA molecules are negatively charged. An intact DNA molecule has such a large size that it does not migrate during electrophoresis. DNA breaks, however, if present result in smaller fragments which move in the electrical field towards the anode. Smaller fragments migrate faster. As the fragments have different sizes the final result of the electrophoresis is not a distinct line but rather a continuum with the shape of a comet. The system allows a quantification of the resulting &#8220;comet&#8221; and thus of the DNA breaks in the cell.

Although the method of comet assay renders reproducible results, it can be influenced by a variety of factors. One such factor is whether or not the leukocytes are cryopreserved prior to lysis and gel-electrophoresis or whether this step is performed on freshly prepared leukocytes. Figure 2 shows that in Group 2, where leukocytes were cryopreserved prior to lysis and gel electrophoresis ss- DNA breaks were significantly higher, than in Group 1 where lysis and gel -electrophoresis was done on freshly prepared cells.
The assay can also be used to indirectly assess systemic oxidative stress. Table 1 shows the descriptive statistics for Tail- moment and Olive- moment in smokers and healthy subjects. The data reveals that smoking half a pack of cigarettes daily more than doubles ssDNA breaks in the circulating leukocytes9.
<img alt="Figure 1A" src="/files/ftp_upload/52763/52763fig1A.jpg" />
<img alt="Figure 1B" src="/files/ftp_upload/52763/52763fig1B.jpg" /> 
Figure 1.&#160;(A) Depicts the microscope used during comet assay analysis. (B) &#916; depicts a typical &#8220;comet&#8221; with a bright head and tail (damaged smaller DNA fragments). <a href="https://www.jove.com/files/ftp_upload/52763/52763fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/52763/52763fig2.jpg" /> 
Figure 2. ssDNA breaks were significantly higher when leukocytes were cryopreserved (Group 2) than when freshly prepared leukocytes were used prior to lysis and gel-electrophoresis.
<img alt="Table 1" src="/files/ftp_upload/52763/52763table1.jpg" /> 
Table 1. Smokers had more than double the number of ssDNA breaks in comparison to age and sex matched healthy non-smokers.

Watch this Scientific Journal Video about Comet Assay as an Indirect Measure of Systemic Oxidative Stress at JoVE.com

Comet Assay as an Indirect Measure of Systemic Oxidative Stress

Comet assay measures DNA breaks, induced by different factors. If all factors (except oxidative stress) causing DNA damage are kept constant, the amount of DNA damage is a good indirect parameter of oxidative stress. The goal of this protocol is to use comet assay for indirect measurement of oxidative stress.

Higher eukaryotic organisms cannot live without oxygen; yet, paradoxically, oxygen can be harmful to them. The oxygen molecule is chemically relatively ...

comet-assay-as-an-indirect-measure-of-systemic-oxidative-stress

Research

JoVE Journal

Biology

29.2K Views.  University of Basel. Comet assay measures DNA breaks, induced by different factors. If all factors (except oxidative stress) causing DNA damage are kept constant, the amount of DNA damage is a good indirect parameter of oxidative stress. The goal of this protocol is to use comet assay for indirect measurement of oxidative stress.

Video: Comet Assay as an Indirect Measure of Systemic Oxidative Stress

Evaluating In Vitro DNA Damage Using Comet Assay

DNA damage is a common phenomenon for each cell during its lifespan, and is defined as an alteration of the chemical structure of genomic DNA. Cancer therapies, such as radio- and chemotherapy, introduce enormous amount of additional DNA damage, leading to cell cycle arrest and apoptosis to limit cancer progression. Quantitative assessment of DNA damage during experimental cancer therapy is a key step to justify the effectiveness of a genotoxic agent. In this study, we focus on a single cell electrophoresis assay, also known as the comet assay, which can quantify single and double-strand DNA breaks in vitro. The comet assay is a DNA damage quantification method that is efficient and easy to perform, and has low time/budget demands and high reproducibility. Here, we highlight the utility of the comet assay for a preclinical study by evaluating the genotoxic effect of olaparib/temozolomide combination therapy to U251 glioma cells.

Evaluating In Vitro DNA Damage Using Comet Assay

The comet assay is an efficient method to detect DNA damage including single and double-stranded DNA breaks. We describe alkaline and neutral comet assays to measure DNA damage in cancer cells to evaluate the therapeutic effect of chemotherapy.

DNA damage is a common phenomenon for each cell during its lifespan, and is defined as an alteration of the chemical structure of genomic DNA. Cancer ...

Cancer Research

CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular metabolites. Ironically, at high doses DNA damaging agents are also used to treat cancer. The ability to quantify DNA damage responses is thus critical in the public health, pharmaceutical and clinical domains. Here, we describe a novel platform that exploits microfabrication techniques to pattern cells in a fixed microarray. The &#8216;CometChip&#8217; is based upon the well-established single cell gel electrophoresis assay (a.k.a. the comet assay), which estimates the level of DNA damage by evaluating the extent of DNA migration through a matrix in an electrical field. The type of damage measured by this assay includes abasic sites, crosslinks, and strand breaks. Instead of being randomly dispersed in agarose in the traditional assay, cells are captured into an agarose microwell array by gravity. The platform also expands from the size of a standard microscope slide to a 96-well format, enabling parallel processing. Here we describe the protocols of using the chip to evaluate DNA damage caused by known genotoxic agents and the cellular repair response followed after exposure. Through the integration of biological and engineering principles, this method potentiates robust and sensitive measurements of DNA damage in human cells and provides the necessary throughput for genotoxicity testing, drug development, epidemiological studies and clinical assays.

We describe here a platform that allows comet assay detection of DNA damage with unprecedented throughput. The device patterns mammalian cells into a microarray and enables parallel processing of 96 samples. The approach facilitates analysis of base level DNA damage, exposure-induced DNA damage and DNA repair kinetics.

DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular ...

Bioengineering

A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities 

The optokinetic reflex (OKR) is a basic visual reflex exhibited by most vertebrates and plays an important role in stabilizing the eye relative to the visual scene. However, the OKR requires that an animal detect moving stripes and it is possible that fish that fail to exhibit an OKR may not be completely blind. One zebrafish mutant, the no optokinetic response c (nrc) has no OKR under any light conditions tested and was reported to be completely blind. Previously, we have shown that OFF-ganglion cell activity can be recorded in these mutants. To determine whether mutant fish with no OKR such as the nrc mutant can detect simple light increments and decrements we developed the visual motor behavioral assay (VMR). In this assay, single zebrafish larvae are placed in each well of a 96-well plate allowing the simultaneous monitoring of larvae using an automated video-tracking system. The locomotor responses of each larva to 30 minutes light ON and 30 minutes light OFF were recorded and quantified. WT fish have a brief spike of motor activity upon lights ON, known as the startle response, followed by return to lower-than baseline activity, called a freeze. WT fish also sharply increase their locomotor activity immediately following lights OFF and only gradually (over several minutes) return to baseline locomotor activity. The nrc mutants respond similarly to light OFF as WT fish, but exhibit a slight reduction in their average activity as compared to WT fish. Motor activity in response to light ON in nrc mutants is delayed and sluggish. There is a slow rise time of the nrc mutant response to light ON as compared to WT light ON response. The results indicate that nrc fish are not completely blind. Because teleosts can detect light through non-retinal tissues, we confirmed that the immediate behavioral responses to light-intensity changes require intact eyes by using the chokh (chk) mutants, which completely lack eyes from the earliest stages of development. In our VMR assay, the chk mutants exhibit no startle response to either light ON or OFF, showing that the lateral eyes mediate this behavior. The VMR assay described here complements the well-established OKR assay, which does not test the ability of zebrafish larvae to respond to changes in light intensities. Additionally, the automation of the VMR assay lends itself to high-throughput screening for defects in light-intensity driven visual responses.

A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities

We developed the Visual-Motor Response to quantitate the motor output of larval zebrafish in response to light increments and decrements. We also examined zebrafish vision mutants, including the no optokinetic response (nrc) mutants, which were thought to be completely blind when tested by another vision assay, the optokinetic reflex.

The optokinetic reflex (OKR) is a basic visual reflex exhibited by most vertebrates and plays an important role in stabilizing the eye relative to the ...

Use of Frozen Tissue in the Comet Assay for the Evaluation of DNA Damage

The comet assay is gaining popularity as a means to assess DNA damage in cultured cells and tissues, particularly following exposure to chemicals or other environmental stressors. Use of the comet assay in regulatory testing for genotoxic potential in rodents has been driven by adoption of an Organisation for Economic Co-operation and Development (OECD) test guideline in 2014. Comet assay slides are typically prepared from fresh tissue at the time of necropsy; however, freezing tissue samples can avoid logistical challenges associated with simultaneous preparation of slides from multiple organs per animal and from many animals per study. Freezing also enables shipping samples from the exposure facility to a different laboratory for analysis, and storage of frozen tissue facilitates deferring a decision to generate DNA damage data for a given organ. The alkaline comet assay is useful for detecting exposure-related DNA double- and single-strand breaks, alkali-labile lesions, and strand breaks associated with incomplete DNA excision repair. However, DNA damage can also result from mechanical shearing or improper sample processing procedures, confounding the results of the assay. Reproducibility in collection and processing of tissue samples during necropsies may be difficult to control due to fluctuating laboratory personnel with varying levels of experience in harvesting tissues for the comet assay. Enhancing consistency through refresher training or deployment of mobile units staffed with experienced laboratory personnel is costly and may not always be feasible. To optimize consistent generation of high quality samples for comet assay analysis, a method for homogenizing flash frozen cubes of tissue using a customized tissue mincing device was evaluated. Samples prepared for the comet assay by this method compared favorably in quality to fresh and frozen tissue samples prepared by mincing during necropsy. Moreover, low baseline DNA damage was measured in cells from frozen cubes of tissue following prolonged storage.

This protocol describes several procedures for preparing high quality frozen tissue samples at the time of necropsy for use in the comet assay to assess DNA damage: 1) minced tissue, 2) scraped epithelial cells from the gastrointestinal tract, and 3) cubed tissue samples, requiring homogenization using a tissue mincing device.

The comet assay is gaining popularity as a means to assess DNA damage in cultured cells and tissues, particularly following exposure to chemicals or other ...

Genetics

Assaying DNA Damage in Hippocampal Neurons Using the Comet Assay

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.

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.

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 ...

Neuroscience

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein

Oxidative stress is an unavoidable byproduct of aerobic life. Molecular oxygen is essential for terrestrial metabolism, but it also takes part in many damaging reactions within living organisms. The combination of aerobic metabolism and iron, which is another vital compound for life, is enough to produce radicals through Fenton chemistry and degrade cellular components. DNA degradation is arguably the most damaging process involving intracellular radicals, as DNA repair is far from trivial. The assay presented in this article offers a quantitative technique to measure and visualize the effect of molecules and enzymes on radical-mediated DNA damage.
The DNA protection assay is a simple, quick, and robust tool for the in vitro characterization of the protective properties of proteins or chemicals. It involves exposing DNA to a damaging oxidative reaction and adding varying concentrations of the compound of interest. The reduction or increase of DNA damage as a function of compound concentration is then visualized using gel electrophoresis. In this article we demonstrate the technique of the DNA protection assay by measuring the protective properties of the DNA-binding protein from starved cells (Dps). Dps is a mini-ferritin that is utilized by more than 300 bacterial species to powerfully combat environmental stressors. Here we present the Dps purification protocol and the optimized assay conditions for evaluating DNA protection by Dps.

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein

The DNA-binding protein from starved cells (Dps) plays a crucial role in combating bacterial stress. This article discusses the purification of E. coli Dps and the protocol for an in vitro assay demonstrating Dps-mediated protection of DNA from degradation by reactive oxygen species.

Oxidative stress is an unavoidable byproduct of  aerobic life.  Molecular oxygen is  essential for terrestrial metabolism, but it also takes part in many ...

In Vivo Alkaline Comet Assay and Enzyme-modified Alkaline Comet Assay for Measuring DNA Strand Breaks and Oxidative DNA Damage in Rat Liver

Unrepaired DNA damage can lead to genetic instability, which in turn may enhance cancer development. Therefore, identifying potential DNA damaging agents is important for protecting public health. The in vivo alkaline comet assay, which detects DNA damage as strand breaks, is especially relevant for assessing the genotoxic hazards of xenobiotics, as its responses reflect the in vivo absorption, tissue distribution, metabolism and excretion (ADME) of chemicals, as well as DNA repair process. Compared to other in vivo DNA damage assays, the assay is rapid, sensitive, visual and inexpensive, and, by converting oxidative DNA damage into strand breaks using specific repair enzymes, the assay can measure oxidative DNA damage in an efficient and relatively artifact-free manner. Measurement of DNA damage with the comet assay can be performed using both acute and subchronic toxicology study designs, and by integrating the comet assay with other toxicological assessments, the assay addresses animal welfare requirements by making maximum use of animal resources. Another major advantage of the assays is that they only require a small amount of cells, and the cells do not have to be derived from proliferating cell populations. The assays also can be performed with a variety of human samples obtained from clinically or occupationally exposed individuals.

In Vivo Alkaline Comet Assay and Enzyme-modified Alkaline Comet Assay for Measuring DNA Strand Breaks and Oxidative DNA Damage in Rat Liver

The alkaline comet assay measures DNA strand breaks in eukaryotic cells. By adding an Endonuclease III or human 8-oxoguanine-DNA-N-glycosylase digestion step, the assay can efficiently detect oxidative DNA damage. We describe methods for using these assays to detect DNA damage in rat liver.

Unrepaired DNA damage can lead to genetic instability, which in turn may enhance cancer development. Therefore, identifying potential DNA damaging agents ...

A High-Throughput Comet Assay Approach for Assessing Cellular DNA Damage

Cells are continually exposed to agents arising from the internal and external environments, which may damage DNA. This damage can cause aberrant cell function, and therefore DNA damage may play a critical role in the development of, conceivably, all major human diseases, e.g., cancer, neurodegenerative and cardiovascular disease, and aging. Single-cell gel electrophoresis (i.e., the comet assay) is one of the most common and sensitive methods to study the formation and repair of a wide range of types of DNA damage (e.g., single- and double-strand breaks, alkali-labile sites, DNA-DNA crosslinks, and, in combination with certain repair enzymes, oxidized purines, and pyrimidines), in both in vitro and in vivo systems. However, the low sample throughput of the conventional assay and laborious sample workup are limiting factors to its widest possible application. With the "scoring" of comets increasingly automated, the limitation is now the ability to process significant numbers of comet slides. Here, a high-throughput (HTP) variant of the comet assay (HTP comet assay) has been developed, which significantly increases the number of samples analyzed, decreases assay run time, the number of individual slide manipulations, reagent requirements, and risk of physical damage to the gels. Furthermore, the footprint of the electrophoresis tank is significantly decreased due to the vertical orientation of the slides and integral cooling. Also reported here is a novel approach to chilling comet assay slides, which conveniently and efficiently facilitates the solidification of the comet gels. Here, the application of these devices to representative comet assay methods has been described. These simple innovations greatly support the use of the comet assay and its application to areas of study such as exposure biology, ecotoxicology, biomonitoring, toxicity screening/testing, together with understanding pathogenesis.

The comet assay is a popular means of detecting DNA damage. This study describes an approach to running slides in representative variants of the comet assay. This approach significantly increased the number of samples while decreasing assay run-time, the number of slide manipulations, and the risk of damage to gels.

Cells are continually exposed to agents arising from the internal and external environments, which may damage DNA. This damage can cause aberrant cell ...

Thiobarbituric Acid-Reactive Substances Assay to Assess Oxidative Stress in Human Serum

Label the glass tubes for the samples to be analyzed, then, add 100 microliters of the prepared sample to each tube. Add 200 microliters of 8.1% SDS to each sample, and gently swirl the glass tube in a circular motion to mix.
Add 1.5 milliliters of 3.5 molar sodium acetate buffer to each sample. Then, add 1.5 milliliters of aqueous 0.8% thiobarbituric acid solution. Bring the final volume in each tube to 4 milliliters by adding 700 microliters of deionized water. Tightly cap the glass tubes, and incubate them in a heating block set to 95 degrees Celsius for 1 hour. Cover the tubes with aluminum foil to prevent condensation. Then, remove the tubes from the block and incubate them on ice for 30 minutes.
After the incubation, centrifuge the samples and standards at 1,500 x g for 10 minutes at 4 degrees Celsius. Transfer 150 microliters of supernatant from each tube to a well in a 96-well plate, removing any air bubbles with a pipette tip.
Measure the absorbance of the samples at 532 nanometers. Then, subtract the average absorbance reading of the blank samples from all other absorbance readings.
Create a standard curve and use it to calculate unknown sample concentrations.

JoVE Encyclopedia of Experiments

Biological Techniques

Assay Techniques

Biochemical assays

EoE Sub Articles

Comet Assay for DNA Damage Detection in Cells

To begin, prepare 0.6% low melting point agarose in PBS, and place it in a water bath at 37 degrees Celsius. Labeled the frosted end of the pre-coated slides with name, date, and treatment information using a permanent marker or pencil.
Place a chilling plate on a flat bench, and insert two frozen cooling packs into the sliding drawer below the metal surface. Then, place the slides on the chilling plate to pre-chill for 1 to 2 minutes. Centrifuge and remove the supernatant from the sample tubes, and place them immediately back on ice. Resuspend the cell pellet with 200 microliters of 0.6% low melting point agarose, and mix by pipetting.
Next, add 80 microliters of agarose-containing cells onto a chilled slide, and quickly place a coverslip on the gel. Allow the gel to set on the chilling plate for 1 to 2 minutes. In the meantime, prepare 500 milliliters of working solution of lysis buffer, and pour it into the lysis dish.
After the gels have set, remove the coverslips quickly by gently holding the slide between thumb and forefinger, and sliding the coverslip off the gel. Then, place the slides inside a slide carrier, with all the black dot marks on the slides facing in the same direction. Place the slide carrier inside the lysis dish. Close the lid of the lysis dish, and put it for incubation.
Carefully remove the slide carrier from the lysis dish without disturbing the gels. Gently, place the slide carrier in a washing dish pre-loaded with ice-cold double-distilled water. Ensure that the slides are completely submerged, and leave the setup for 30 minutes.
Place a frozen cooling pack under the electrophoresis tank to maintain optimal buffer temperature. Then, add ice-cold electrophoresis working solution to the tank, and transfer the slide carrier into it. Orient the slides, such that the cell containing gels point toward the cathode.
Incubate the slides in the electrophoresis tank for 20 minutes, to allow the DNA to unwind. Then, turn on the power supply to perform electrophoresis for 20 minutes at 1.19 volts per centimeter. After the electrophoresis is complete, turn off the power supply, and remove the slide carrier from the electrophoresis tank. Allow the slide carrier to drain on tissue paper for 30 seconds.
Next, place the slide carrier into a dish containing neutralization buffer, and leave it for 20 minutes. Following this, place it in a washing dish containing ice-cold double-distilled water, and leave it for 20 minutes. After washing, remove the slide carrier from the water, and allow the slides to dry in an incubator at 37 degrees Celsius for 1 hour.
To rehydrate the slides, transfer the slide carrier to a washing dish containing ice-cold double-distilled water and leave it for 30 minutes. Then, place the slide carrier into a staining dish containing 2.5 micrograms per milliliter propidium iodide solution.
Close the lid of the staining dish, and incubate it for 20 minutes in the dark at room temperature. After incubation, transfer the slide carrier to a separate dish, and wash it with ice-cold double-distilled water for 20 minutes.
Remove the slide carrier from the dish, and dry it completely in the dark, either in a 37 degrees Celsius incubator or at room temperature. After the slides dry completely, store them in a slide box in the dark until ready for image analysis.

Comet Assay as an Indirect Measure of Systemic Oxidative Stress

Summary

Explore More Videos

Chapters in this video

Evaluating In Vitro DNA Damage Using Comet Assay

CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities

Use of Frozen Tissue in the Comet Assay for the Evaluation of DNA Damage

Assaying DNA Damage in Hippocampal Neurons Using the Comet Assay

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein

In Vivo Alkaline Comet Assay and Enzyme-modified Alkaline Comet Assay for Measuring DNA Strand Breaks and Oxidative DNA Damage in Rat Liver

A High-Throughput Comet Assay Approach for Assessing Cellular DNA Damage

Thiobarbituric Acid-Reactive Substances Assay to Assess Oxidative Stress in Human Serum

Comet Assay for DNA Damage Detection in Cells