All work was funded by Artios Pharma Ltd. Figure 1 and Figure 3 were created with Biorender.com.

1. Preparation and quality control&#160;(QC) of reporter substrates
NOTE: The plasmids encoding the reporter substrates can be propagated in standard Escherichia coli strains (e.g., DH5&#945; and derivates) and recovered by plasmid isolation. Plasmid details (size and antibiotic resistance) are described in Table 1 and Figure 1.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/66969/66969fig01.jpg" /> 
Figure 1: Schematics of extrachromosomal NanoLuc-based DSBR reporter assays. Schematic representation of DSBR reporter substrates, including their location within each source plasmid, main sequence features, and final layout after pathway-specific repair. The resection-independent MMEJ substrate core is excised from the source plasmid by digestion with XhoI/HindIII, after which caps must be ligated to both ends to produce the substrate for MMEJ. The blunt NHEJ reporter substrate is generated by excision from the source plasmid with EcoRV. The resection-dependent MMEJ, non-blunt NHEJ, long template HR, and SSA reporter substrates are generated by linearization of the source plasmids using either I-SceI (which produces non-cohesive ends) or HindIII (which produces cohesive ends). The short template HR reporter substrate is generated by linearization of the source plasmid using I-SceI (which produces cohesive ends). Repair of each reporter substrate by the target DSBR pathway reconstitutes an intact nanoluciferase ORF encoding functional NanoLuc. This figure was adapted from Rajendra et al.7. Abbreviations: DSBR = double strand break repair; NanoLuc = Nanoluciferase; MMEJ = microhomology-mediated end joining; NHEJ = non-homologous end joining; HR = homologous recombination; SSA = single strand annealing; ORF = open reading frame. <a href="https://www.jove.com/files/ftp_upload/66969/66969fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol>
	<li>Preparation of resection-independent MMEJ reporter substrate (Figure 1 and Figure 2A-C)
	<ol>
		<li>Preparation of ssDNA/dsDNA caps (Figure 2A)
		<ol>
			<li>Resuspend the four oligonucleotides listed in Table 2 individually in annealing buffer (20 mM Tris pH 7.5, 50 mM NaCl in molecular biology grade water) to generate a stock solution at 100 &#181;M.</li>
			<li>Annealing of ss/dsDNA caps
			<ol>
				<li>Mix 50 &#181;L each of the long and short oligonucleotides (100 &#181;M stock solution) for the left cap from step 1.1.1.1 in a 0.2 mL tube.</li>
				<li>Repeat for right cap oligonucleotides.</li>
				<li>Using a thermocycler, incubate each oligonucleotide mix at 99 &#176;C for 5 min then ramp down to 10 &#176;C at 1 &#176;C/min. 
				NOTE: This will produce the annealed left and right caps.</li>
			</ol>
			</li>
			<li>(QC, optional) Verification of oligonucleotide annealing by electrophoresis
			<ol>
				<li>Electrophorese 100 ng of each product from step 1.1.1.2 alongside individual oligonucleotides from step 1.1.1.1 and a low molecular weight DNA ladder in a 20% acrylamide-Tris-Borate-EDTA (TBE) gel at 200 V for 80 min.</li>
				<li>Stain the gel with TBE running buffer containing an appropriate fluorescent DNA dye for visualization of both ssDNA and dsDNA for at least 10-15 min.</li>
				<li>Visualize fluorescence on a gel documentation system (Figure 2A). 
				NOTE: Steps 1.1.1.3.1 to 1.1.1.3.3 are used to verify that caps have correctly annealed. The apparent sizes for the left cap and right cap should be ~120 bp and ~175 bp, respectively.</li>
			</ol>
			</li>
		</ol>
		</li>
		<li>Purification of reporter substrate core (Figure 2B)
		<ol>
			<li>Mix 100 &#181;g of the reporter core plasmid with 4 &#181;L of HindIII and 4 &#181;L of XhoI (4 U/&#181;g plasmid for each enzyme) and 20 &#181;L of 10x buffer. Bring the total volume to 200 &#181;L with double-distilled water (ddH2O) and incubate at 37 &#176;C for 2 h to overnight to digest plasmid. 
			NOTE: For digestion of larger or smaller quantities, scale the reaction proportionally.</li>
			<li>Incubate digestion reaction at 80 &#176;C for 20 min to heat inactivate restriction enzymes.</li>
			<li>Add 40 &#181;L of alkaline phosphatase (2 U/&#181;g plasmid) and 27 &#181;L of 10x buffer to the reaction mix from step 1.1.2.2. Incubate at 37 &#176;C for 2 h to dephosphorylate the plasmid. 
			NOTE: Scale reaction up or down as needed.</li>
			<li>Add 60 &#181;L of 6x loading dye to the reaction from step 1.1.2.3. Electrophorese alongside a high molecular weight DNA ladder in a 1.5 % (w/v) agarose-Tris-Acetate-EDTA (TAE) gel containing a fluorescent dsDNA stain at 120 V for 2.5 h or until bands are sufficiently resolved.</li>
			<li>Visualize fluorescence on a gel documentation system (Figure 2B).</li>
			<li>Excise the reporter core fragment (~1.5 kb) from the gel using a clean scalpel, taking care not to contaminate with vector backbone (~2.5 kb).</li>
			<li>Extract the reporter core fragment using a gel extraction kit, following the manufacturer&#39;s instructions.</li>
			<li>Measure the DNA concentration and quality (A260/280) by spectrophotometry.</li>
		</ol>
		</li>
		<li>Ligation of reporter substrate core with ssDNA/dsDNA caps and purification of final reporter substrate (Figure 2C)
		<ol>
			<li>Mix 30 &#181;g of the reporter core fragment from step 1.1.2.7 with 3.85 &#181;L of each annealed left and right cap from step 1.1.2 (approx. 6:1 molar ratio of cap:core DNA), 30 &#181;L of 10x ligase buffer, and 1.5 &#181;L of T4 DNA ligase (20 U/&#181;g DNA). Bring the total volume of the reaction to 300 &#181;L with ddH2O and incubate overnight at 16 &#176;C to ligate caps to reporter core fragment. 
			NOTE: Scale reaction up or down as required.</li>
			<li>(QC, optional) Electrophorese 200 ng of the resulting product from step 1.1.3.1 alongside the reporter substrate core and a high molecular weight DNA ladder in a 0.7% (w/v) agarose-TAE gel containing a fluorescent dsDNA stain at 120 V for at least 1.5 h. Verify that the band corresponding to the ligated product migrates at a slightly slower rate than the non-ligated reporter substrate core (Figure 2C). 
			NOTE: This QC step is to verify that the ligation of caps to the reporter core fragment has taken place correctly.</li>
			<li>Purify the DNA from the digestion reaction in step 1.3.1. using the preferred method (e.g., a bead-based or column-based method), following the manufacturer&#39;s instructions. 
			NOTE: The purification step 1.1.3.3 substantially reduces the presence of unligated caps.</li>
		</ol>
		</li>
		<li>Measure DNA concentration and quality (A260/280) by spectrophotometry.</li>
	</ol>
	</li>
	<li>Preparation of blunt NHEJ reporter substrate (Figure 1 and Figure 2D,E)
	<ol>
		<li>Mix 100 &#181;g of the reporter core plasmid with 5 &#181;L of EcoRV (5 U/&#181;g plasmid) and 20 &#181;L of 10x buffer. Bring the total volume to 200 &#181;L with ddH2O and incubate at 37 &#176;C for 2 h to overnight to digest plasmid. 
		NOTE: For digestion of larger or smaller quantities, scale the reaction proportionally.</li>
		<li>Incubate the digestion reaction at 65 &#176;C for 20 min to heat inactivate restriction enzyme.</li>
		<li>Add 50 &#181;L of 6x loading dye to the reaction from step 1.2.2. Electrophorese alongside a high molecular weight DNA ladder in a 1.5% (w/v) agarose-TAE gel containing a fluorescent dsDNA stain at 120 V for 2 h or until bands are sufficiently resolved.</li>
		<li>Visualize fluorescence on a gel documentation system (Figure 2D).</li>
		<li>Excise the reporter substrate (~1.7 kb) from the gel using a clean scalpel, taking care not to contaminate with the vector backbone (~2.6 kb).</li>
		<li>Extract the reporter core fragment using a gel extraction kit, following the manufacturer&#39;s instructions (Figure 2E).</li>
		<li>Measure the DNA concentration and quality (A260/280) by spectrophotometry.</li>
	</ol>
	</li>
	<li>Preparation of I-SceI-based reporter substrates (Figure 1) 
	NOTE: These substrates include resection-dependent MMEJ (Figure 2F), non-blunt NHEJ (Figure 2G), long template HR (Figure 2H), short template HR (Figure 2I), and SSA (Figure 2J).
	<ol>
		<li>Mix 100 &#181;g of the reporter core plasmid with 50 &#181;L of I-SceI (5 U/&#181;g plasmid) and 60 &#181;L of 10x buffer. Bring the total volume to 600 &#181;L with ddH2O and incubate at 37 &#176;C for 2 h to overnight to digest plasmid. 
		NOTE: For digestion of larger or smaller quantities, scale the reaction proportionally. Non-blunt NHEJ, resection-dependent MMEJ, long template HR and SSA plasmids can also be digested with HindIII, which will generate complementary cohesive ends.</li>
		<li>Incubate the digestion reaction at 65 &#176;C for 20 min to heat inactivate I-SceI. Set the temperature to 80 &#176;C during this step if HindIII was used for digestion instead.</li>
		<li>Purify DNA from the inactivated digestion reaction in step 1.3.2 using the preferred method (e.g., a bead-based or column-based method), following the manufacturer&#39;s instructions.</li>
		<li>Measure the DNA concentration and purity A260/280) by spectrophotometry.</li>
	</ol>
	</li>
	<li>Quality control of reporter substrates
	<ol>
		<li>Electrophorese 200 ng of the reporter substrate alongside a high molecular weight DNA ladder in a 0.7% (w/v) agarose-TAE gel containing a fluorescent dsDNA stain at 120 V for 2 h or until bands are sufficiently resolved. Load the original uncut reporter plasmid alongside as a control.</li>
		<li>Verify that the defined bands of the correct size are observed for each reporter substrate (refer to Table 1 and Figure 2F-J).</li>
	</ol>
	</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/66969/66969fig02.jpg" /> 
Figure 2: Gel electrophoretic analyses of DSBR reporter substrate generation. (A-C) Representative images from gel electrophoretic analysis of intermediates and final construct required for the generation of the resection-independent MMEJ reporter substrate. The adjacent images in&#160;panels (A) and&#160;(C) are from the same gels; irrelevant lanes have been omitted. (D,E) Representative images from gel electrophoretic analysis for source plasmid, EcoRV-digested products, and gel-extracted final construct required for the generation of the blunt NHEJ reporter substrate. (F-J) Representative images from gel electrophoretic analysis of source plasmids and linearised DSBR constructs for the I-SceI-digested reporter substrates: resection-dependent MMEJ, non-blunt NHEJ, long template HR, short template HR, SSA. Abbreviations: DSBR = double strand break repair; MMEJ = microhomology-mediated end joining; NHEJ = non-homologous end joining; HR = homologous recombination; SSA = single strand annealing. <a href="https://www.jove.com/files/ftp_upload/66969/66969fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
2. Transient transfection of DSBR reporter substrates
NOTE: An overview of the experimental workflow of assays and some potential permutations are outlined in Figure 3. The protocol below describes an experiment using HEK-293 cells, where these are reverse-transfected with the reporter substrate. Numbers below can be scaled up or down according to the number of wells to be used per plate. The following steps are calculated for an assay performed in one 96-well plate; see Discussion for additional considerations.
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/66969/66969fig03.jpg" /> 
Figure 3: Experimental workflow for DSBR reporter assays. Cells of interest are transfected with the linearised DSBR substrate (coding for a NanoLuc ORF that needs to be repaired through a specific DNA repair event) and a Firefly plasmid (transfection control). Then, 6-24 h post transfection, the Firefly luminescence and NanoLuc luminescence can be read sequentially following the addition of Nano-Glo Dual-Luciferase reagents. Example permutations to the core steps (shown within light blue boxes) can be used to test how genetic modulation (knockout, knockdown, or overexpression) or pharmacological treatment affects DSBR pathway proficiency in cells. Abbreviations: DSBR = double strand break repair; NanoLuc = Nanoluciferase; WT = wild type; KO = knockout. <a href="https://www.jove.com/files/ftp_upload/66969/66969fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol>
	<li>(Optional) If assessing the impact of compounds on the reporter assay, dispense compounds dissolved in vehicle (e.g., dimethyl sulfoxide [DMSO]) into wells of a 96-well plate according to a predefined experimental layout. Normalize vehicle concentration across all wells. 
	NOTE: Technical replicates are recommended. Include control wells (e.g., vehicle-only).</li>
	<li>In a 1.5 mL tube, dilute Firefly control plasmid (control luciferase) and NanoLuc DSBR reporter substrate (reporter luciferase) generated in steps 1.1, 1.2 or 1.3, in 500 &#181;L of transfection buffer. Use 0.66 &#181;g of control luciferase plasmid per 1 &#215; 106 cells. See Table 3 for the quantities of NanoLuc DSBR reporter substrate to use. 
	NOTE: A positive control plasmid that constitutively expresses the reporter luciferase can be used to validate instrument setup and transfection conditions or to check for non-specific effects on the reporter luciferase itself. As a starting point, we recommend 0.1 &#181;g of reporter luciferase plasmid and 0.66 &#181;g of control luciferase plasmid per 1 &#215; 106 cells.</li>
	<li>Add lipid-based transfection reagent to the diluted DNA from step 2.2 at a manufacturer&#39;s recommended ratio (e.g., 1:2, &#181;g DNA:&#181;L reagent for the reagent described in the Table of Materials), mix well by vortexing briefly, and incubate for 10 min at room temperature.</li>
	<li>Harvest cells by trypsinization, resuspend them in fresh medium containing 10% fetal bovine serum (FBS), and count them.</li>
	<li>Transfer 3 &#215; 106 cells into a 15 mL tube and resuspend in 8.5 mL of medium.</li>
	<li>Add the DNA transfection mix from step 2.3 into the cell suspension and mix several times by inversion.</li>
	<li>Plate 80 &#181;L of cell suspension (approximately 2.7 &#215; 104 cells) per well. 
	NOTE: The suspension containing cells and DNA transfection mix can be dispensed onto the plate either by pipetting manually or using an automated liquid handler for higher-throughput experiments.</li>
	<li>Incubate at 37 &#176;C/5% CO2 for 24 h.</li>
</ol>
3. Detection of luminescence
<ol>
	<li>Preparation of reagents
	<ol>
		<li>Follow the manufacturer&#39;s instructions for the preparation and addition of reporter (NanoLuc) and control (Firefly) luciferase reagents, which provide the substrates for both luciferases (Furimazine and 5&#180;-Fluoroluciferin, respectively):</li>
		<li>Prepare control luciferase reagent. Reconstitute according to the manufacturer&#39;s instructions and mix by inversion until the luciferase substrate is thoroughly dissolved.</li>
		<li>Prepare fresh reporter luciferase reagent according to the manufacturer&#39;s instructions. Calculate the amount of reagent needed to add 80 &#181;L/well and add substrate into an appropriate volume of assay buffer at a 1:100 ratio (luciferase substrate:buffer). For one 96-well plate, dilute 88 &#181;L of luciferase substrate into 8,800 &#181;L of buffer and mix by inversion. 
		NOTE: These quantities include an approximate 10% excess. Once reconstituted, the control luciferase reagent can be stored according to the manufacturer&#39;s instructions for future use. The reporter luciferase reagent must be prepared fresh for each use.</li>
	</ol>
	</li>
	<li>Serial detection of luminescence from control and reporter luciferases (96-well plate)
	<ol>
		<li>Allow the plate and luciferase reagents to reach room temperature.</li>
		<li>Add 80 &#181;L of control luciferase reagent per well.</li>
		<li>Shake the plate for 3 min on an orbital shaker at 450 rpm.</li>
		<li>Measure the control luciferase luminescence signal with a luminescence plate reader. 
		NOTE: Read emission at 580 nm (80 nm bandpass filter) or the total luminescence per well. This luminescence is used as a measure of transfection efficiency and cell density and can also inform about cellular toxicity caused by the test treatments.</li>
		<li>Add 80 &#181;L of reporter luciferase reagent per well. 
		NOTE: This reagent will inhibit the control luciferase; it also contains the substrate for the reporter luciferase.</li>
		<li>Shake the plate for 3 min on an orbital shaker at 450 rpm.</li>
		<li>Leave the plate to rest for 7 min at room temperature.</li>
		<li>Measure the reporter luciferase luminescence signal with a luminescence plate reader. 
		NOTE: Read emission at 470 nm (80 nm bandpass filter) or, alternatively, total luminescence per well. This luminescence gives information on the amount of reporter substrate that has been repaired by the DSBR pathway of interest.</li>
		<li>Export luminescence readings for downstream analysis.</li>
	</ol>
	</li>
</ol>
4. Data analysis
<ol>
	<li>Divide the reporter luciferase (NanoLuc) luminescence signal by the control luciferase (Firefly) luminescence signal originating from the same well to calculate the assay signal. Apply that calculation to all the wells as shown in equation (1). 
	<img alt="Equation 1" src="/files/ftp_upload/66969/66969eq01.jpg" style="margin: auto;" />&#160; &#160; &#160;(1)</li>
	<li>Calculate the average of the assay signals for the control wells (e.g., vehicle-only).</li>
	<li>Normalize the assay signals for test wells to the control well average using equation (2) to calculate Repair (%) per well. 
	<img alt="Equation 2" src="/files/ftp_upload/66969/66969eq02.jpg" style="margin: auto;" /> (2)</li>
	<li>(Optional, curve fitting) If testing multiple compound doses, plot the calculated Repair (%) against the compound concentration and fit a dose-response curve using a non-linear regression model. Use this curve for subsequent EC50 interpolation.</li>
</ol>

Quantifying DNA Double Strand Break Repair with Nanoluciferase Reporter Assays

<ol>
	<li>Jackson, S. P., Bartek, 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+DNA-damage+response+in+human+biology+and+disease.">The DNA-damage response in human biology and disease.</a> Nature. 461 (7267), 1071-1078 (2009).</li><li>Scully, R., Panday, A., Elango, R., Willis, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+double-strand+break+repair-pathway+choice+in+somatic+mammalian+cells.">DNA double-strand break repair-pathway choice in somatic mammalian cells.</a> Nat Rev Mol Cell Biol. 20 (11), 698-714 (2019).</li><li>Ramsden, D. A., Carvajal-Garcia, J., Gupta, G. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism,+cellular+functions+and+cancer+roles+of+polymerase-theta-mediated+DNA+end+joining.">Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining.</a> Nat Rev Mol Cell Biol. 23 (2), 125-140 (2022).</li><li>Ceccaldi, R., 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=Homologous-recombination-deficient+tumours+are+dependent+on+Pol&#952;-mediated+repair.">Homologous-recombination-deficient tumours are dependent on Pol&#952;-mediated repair.</a> Nature. 518 (7538), 258-262 (2015).</li><li>van de Kooij, B., van Attikum, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genomic+reporter+constructs+to+monitor+pathway-specific+repair+of+DNA+double-strand+breaks.">Genomic reporter constructs to monitor pathway-specific repair of DNA double-strand breaks.</a> Front Genet. 12, 809832 (2021).</li><li>Gunn, A., Stark, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=I-SceI-based+assays+to+examine+distinct+repair+outcomes+of+mammalian+chromosomal+double+strand+breaks.">I-SceI-based assays to examine distinct repair outcomes of mammalian chromosomal double strand breaks.</a> Methods Mol Biol. 920 (9), 379-391 (2012).</li><li>Rajendra, E., 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=titratable+and+high-throughput+reporter+assays+to+measure+DNA+double+strand+break+repair+activity+in+cells.">titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells.</a> Nucleic Acids Res. 52 (4), 1736-1752 (2024).</li><li>Hall, M. P., 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=Engineered+luciferase+reporter+from+a+deep+sea+shrimp+utilizing+a+novel+imidazopyrazinone+substrate.">Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate.</a> ACS Chem. Biol. 7 (11), 1848-1857 (2012).</li><li>Wyatt, D. W., 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=Essential+roles+for+polymerase+&#952;-mediated+end+joining+in+the+repair+of+chromosome+breaks.">Essential roles for polymerase &#952;-mediated end joining in the repair of chromosome breaks.</a> Mol Cell. 63 (4), 662-673 (2016).</li><li>Wood, R. D., Doubli&#233;, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome+protection+by+DNA+polymerase+&#952;.">Genome protection by DNA polymerase &#952;.</a> Annu Rev Genet. 56, 207-228 (2022).</li><li>Belan, O., 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=POLQ+seals+post-replicative+ssDNA+gaps+to+maintain+genome+stability+in+BRCA-deficient+cancer+cells.">POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells.</a> Mol Cell. 82 (24), 4664-4680 (2022).</li><li>Zatreanu, D., 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=Pol&#952;+inhibitors+elicit+BRCA-gene+synthetic+lethality+and+target+PARP+inhibitor+resistance.">Pol&#952; inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance.</a> Nat Commun. 12 (1), 3636 (2021).</li><li>Stockley, M. L., 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=Discovery,+characterization,+and+structure-based+optimization+of+small-molecule+in+vitro+and+in+vivo+probes+for+human+DNA+polymerase+theta.">Discovery, characterization, and structure-based optimization of small-molecule in vitro and in vivo probes for human DNA polymerase theta.</a> J Med Chem. 65 (20), 13879-13891 (2022).</li><li>Scott, D. E., 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=A+small-molecule+inhibitor+of+the+BRCA2-RAD51+interaction+modulates+RAD51+assembly+and+potentiates+DNA+damage-induced+cell+death.">A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death.</a> Cell Chem Biol. 28 (6), 835-847 (2021).</li><li>Schep, R., 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=Impact+of+chromatin+context+on+Cas9-induced+DNA+double-strand+break+repair+pathway+balance.">Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.</a> Mol Cell. 81 (10), 2216-2230 (2021).</li></ol>

D.G., E.R., B.M., A.G., S.J.B., G.C.M.S, and H.M.R.R. are all employees and shareholders of Artios Pharma Ltd. G.C.M.S. is a shareholder of AstraZeneca PLC. S.J.B. is a Founder Scientist and shareholder of Artios Pharma Ltd. A patent has been filed on some of the reporters outlined in this study (WO 2021/001647). Promega is the source of the NanoLuc&#174; technology and the modified NanoLuc&#174; polynucleotides. Artios Pharma was authorized by Promega to generate the modified NanoLuc&#174; polynucleotides.

Here, we have described protocols for the generation and implementation of a suite of extrachromosomal luminescence-based reporters for measuring the cellular proficiency of the four major DSBR pathways (HR, NHEJ, MMEJ, and SSA)7. Reporter substrates can be introduced into cells by transient transfection and used to assess DSBR activity using a sensitive and robust plate-based readout of NanoLuc luminescence, which is reconstituted upon engagement with cognate cellular DSBR pathways.
Several stages of reporter substrate generation, transfection of the substrates into cells, and data interpretation are critical to the successful execution of these assays. Although standard molecular biology techniques are used to generate the reporter substrates, visualizing the process by gel electrophoresis ensures the highest quality and purity of the substrates prior to transfection. As these assays are reliant on transient transfection, common considerations for these methods apply. These include optimizing seeding density, transfection conditions (including reagents and DNA quantities), and assessing suitability in forward and reverse transfection formats. These reporter assays have been successfully performed with a range of electroporation and lipofection protocols, and options should be fully explored prior to performing these assays. Care should also be taken to inspect the component NanoLuc and Firefly signals rather than just the composite repair signal derived by normalizing the NanoLuc signal (reporter substrate) to the Firefly signal (control). Artifacts can arise from the ratio being driven by changes in the Firefly signal. For example, assessing inhibition in dose-response mode using a highly specific compound should suppress the NanoLuc signal in a titratable manner without perturbing the Firefly signal, which should remain stable (Figure 4G,H). However, in cases where Firefly signals are perturbed, useful impacts on repair can still be determined by identifying a dose window where the Firefly signal is unaffected (Figure 5).
Compared with the most frequently used DSBR reporter assays, these extrachromosomal luminescence-based reporter assays have some distinct advantages. As DSBR pathways are highly conserved, even if cellular machinery varies between cell models, the assays can still report on DSBR proficiency and pathway choice. This opens up the assessment of DSBR to any model of interest to the user, as long as optimal transient transfection conditions are established in advance.
The use of Nanoluciferase as the reporter gene also offers advantages over fluorescent options, which have been used traditionally in DSBR reporter assays. NanoLuc is fast-maturing and luminescence is detected with high sensitivity using a plate reader8. Coupled to the speed of substrate repair (as the reporter substrates are transfected into cells with ready-to-repair DSB ends), this format of DSBR reporter assay is ideal for the rapid turnaround and quantitative robustness required for screening small molecules as part of an industrial drug discovery cascade. Indeed, we have recently described the implementation of the resection-independent MMEJ reporter assay in the discovery cascade used for the identification of small molecule inhibitors of the Pol&#952; polymerase domain13.
There is also flexibility in the implementation of the reporter assays to address specific questions about genetic and pharmacological perturbations of DSBR (Figure 3). For example, prior to transfection of the reporter substrates, cells can be transfected with siRNA against a gene of interest for 48-72 h. Alternatively, the effects of gene overexpression on DSBR pathways can be tested by performing plasmid transfection 24-48 h prior to the transfection of reporter substrates. For pharmacological studies, the present protocol already describes how the use of small molecules can be incorporated into the standard workflow, but alternative formats may include alterations in compound treatment regimes, such as pre-incubations or washouts.
The scalability of transient transfection could also support large-scale screening approaches in which batch transfection of reporter substrates is performed prior to screening. Furthermore, the duration of the assay from transfection to readout can also be varied. Although standard durations may be 16-24 h, some assays may be read out in as little as 6 h7. Concerns over toxicity from small molecules or siRNA that can compromise cell viability should also be considered in determining the assay duration.
In summary, the assays outlined in this study and fully described in a recent publication7 provide a rapid and robust assessment of cellular DSBR proficiency. They are highly sensitive and titratable, making them amenable to both genetic and pharmacological studies. Crucially, as the reporter substrates can be introduced into cells by transient transfection, they have the potential to be utilized in any transfectable cell model of interest, rather than being restricted to specific cell lines by stable integration as is the case with chromosomal DSBR reporters. However, a distinct limitation of these reporter extrachromosomal assays is that the lack of integration into the genome may not fully recapitulate the physiological, chromatinized context of DNA repair and its associated regulatory cues and orchestration15. To this end, extrachromosomal reporter assays are complementary to existing methods of DSBR assessment and expand the toolkit of resources suitable for both basic research and drug discovery.

DNA double strand breaks (DSBs) represent a particularly toxic class of DNA damage1 due to which cells have evolved multiple DSB repair (DSBR) pathways to repair these lesions. The four major DSBR mechanisms are homologous recombination (HR), non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and single strand annealing (SSA)2,3. DSBR pathways contribute to the maintenance of healthy tissue development and physiology and protect against diseases such as cancer. Furthermore, these repair mechanisms hold therapeutic potential for the development of small molecule modulators in precision oncology. For example, targeting DNA Polymerase &#952; (Pol&#952;), a pivotal enzyme in the MMEJ repair pathway, has attracted interest due to its synthetic lethality with HR deficiency in cancer4.
Understanding DSBR therefore has broad clinical implications and functional cellular assays capable of measuring the activity of all the major DSBR pathways are needed5. Assays must be suitable for both genetic and pharmacological interrogation and deployable across cell models of interest. To support small molecule drug discovery efforts, assays must be highly sensitive, titratable, have a fast turnaround, and be scalable to high-throughput formats suitable for compound screening.
In general, DSBR has been previously measured using fluorescence-based reporter assay systems stably integrated into the cell genome6. However, while physiological recapitulation of chromosomal DSBR is a distinct advantage, such assays are restricted to a host model in which the reporter is integrated, utilize labor-intensive sample preparation and analysis by flow cytometry, and have limited throughput, turnaround time, robustness, and sensitivity, all essential features necessary for drug discovery efforts.
Here we describe a suite of DSBR reporter assays that allow assessment of the four major DSBR pathways. The suite of reporter assay substrates is outlined in Figure 1 and further described in a recent publication7. They are extrachromosomal, allowing their introduction into cells by simple transient transfection, and the incorporation of a nanoluciferase reporter gene8, which must be reconstituted by engagement with specific DSBR mechanisms, engenders sensitivity, robustness, and scalability. The following DSBR reporter substrate variants are included in the protocol (Figure 1):
Resection-independent MMEJ: This linear substrate is composed of a core double-stranded DNA (dsDNA) region with single-stranded DNA (ssDNA) overhangs, which mimic resected DNA ends9. Four nucleotide microhomologies at the termini of the ssDNA regions encode the start codon for the reporter gene. Repair of this substrate through MMEJ restores the reporter gene open reading frame (ORF).
Resection-dependent MMEJ: The N-terminal reporter gene exon is interrupted by a segment containing a stop codon, which is flanked by 8 base-pair (bp) microhomologies. Nucleolytic end resection is required prior to MMEJ-mediated repair to restore the intact reporter gene.
Blunt NHEJ: The reporter gene is split into N- and C-terminal sections, of which the latter is placed upstream of the promoter. The DSB is produced using EcoRV and it requires direct ligation (without end processing) by NHEJ for both reporter gene portions to be re-joined and the reporter ORF to be restored.
Non-blunt NHEJ: The DSB is located within an intron and will have cohesive or non-cohesive ends depending on the choice of restriction enzyme. The repair of this substrate by NHEJ requires ligation to be preceded by end processing.
Long template HR: The N-terminal exon of the reporter gene is interrupted by a DNA segment containing restriction sites, which replace 22 bp of the original reporter gene sequence. To restore this sequence, repair by HR uses the 2.5 kilobase (kb) homology template placed downstream of the C-terminal exon.
Short template HR: The restriction site needed to generate the DSB replaces part of the native reporter gene sequence and introduces an in-frame stop codon. Like the long template version, this HR substrate requires the downstream homology template (360 bp) for accurate repair and restoration of the reporter ORF.
SSA: This substrate contains a premature stop codon located within the N-terminal exon of the reporter gene. The removal of this stop codon and reinstatement of the intact reporter gene sequence requires repair by SSA, which involves bi-directional long-range resection prior to alignment of the homologies.
For generation of the DSB, some of the reporter substrates can be digested with I-SceI (Figure 1). This will generate a linear substrate with non-cohesive ends in the resection-dependent MMEJ, non-blunt NHEJ, long template HR and SSA reporters, which have tandem I-SceI sites in inverted orientations. In the short template HR reporter substrate, digestion of the single I-SceI site will generate cohesive ends.&#160;The non-blunt NHEJ, resection-dependent MMEJ, long template HR and SSA plasmids can also be digested with HindIII, which will produce complementary cohesive ends.
We provide protocols for the generation of the reporter assay substrates and describe how the assays can be performed, providing details on how they can be used to quantify DSBR, including titratable responses to small molecules, assessing cellular potency, on-target activity, and pathway selectivity.

<table><tbody><tr><td>10x TBE buffer</td><td>Thermo Fisher</td><td>AM9863</td><td></td></tr><tr><td>20% TBE-acrylamide gel</td><td>Invitrogen</td><td>EC6315BOX</td><td></td></tr><tr><td>50x TAE buffer</td><td>Fisher Scientific</td><td>BP13321</td><td></td></tr><tr><td>6x Gel Loading Dye, Purple</td><td>NEB</td><td>B7024S</td><td></td></tr><tr><td>96-well white plate (with transparent bottom and lid)</td><td>Porvair</td><td>204012</td><td></td></tr><tr><td>Agarose</td><td>Cleaver Scientific</td><td>CSL-AG500</td><td></td></tr><tr><td>AMPure XP beads</td><td>Beckman Coulter</td><td>A63881</td><td>For bead-based purification of DNA</td></tr><tr><td>Antarctic phosphatase and 10X buffer</td><td>NEB</td><td>M0289L</td><td></td></tr><tr><td>CLARIOstar</td><td>BMG Labtech</td><td>430-101</td><td>Plate reader</td></tr><tr><td>Countess II Automated Cell Counter</td><td>Thermo Fisher</td><td>AMQAX1000</td><td>Cell counter</td></tr><tr><td>Custom oligonucleotides</td><td>Sigma-Aldrich</td><td>Custom order</td><td>For resection-independent MMEJ substrate. See Table 2.</td></tr><tr><td>D300e</td><td>Tecan</td><td>30100152</td><td>DMSO-based compound dispenser</td></tr><tr><td>D300e D4+ cassette</td><td>Tecan</td><td>30097371</td><td>High volume cassette for D300e compound dispenser</td></tr><tr><td>D300e T8+ cassette</td><td>Tecan</td><td>30097370</td><td>Low volume cassette for D300e compound dispenser</td></tr><tr><td>Dimethyl sulfoxide, cell culture grade</td><td>Sigma-Aldrich</td><td>D2650-100ML</td><td>Vehicle for compounds, used in Figure 4 and Figure 5</td></tr><tr><td>DSBR reporter source plasmids</td><td>Artios</td><td></td><td>Available to the academic community upon request&amp;nbsp;</td></tr><tr><td>EcoRV-HF and 10x CutSmart buffer</td><td>NEB</td><td>R3195M</td><td></td></tr><tr><td>Ethanol absolute</td><td>VWR</td><td>20821.365</td><td></td></tr><tr><td>Foetal Bovine Serum</td><td>PAN-Biotech</td><td>P30-3031&amp;nbsp;</td><td></td></tr><tr><td>GeneRuler Ultra Low Range DNA Ladder</td><td>Thermo Fisher</td><td>SM1211</td><td>Low molecular weight DNA ladder</td></tr><tr><td>HEK-293 cells</td><td>ATCC</td><td>CRL-1573</td><td>Example cell line used in protocol</td></tr><tr><td>HindIII-HF and 10x CutSmart buffer</td><td>NEB</td><td>R3104M</td><td></td></tr><tr><td>HyClone Molecular Biology grade water</td><td>Fisher Scientific</td><td>10275262</td><td></td></tr><tr><td>I-SceI and 10x Tango Buffer</td><td>Invitrogen</td><td>ER1771</td><td></td></tr><tr><td>Isopropanol</td><td>VWR</td><td>20842.33</td><td></td></tr><tr><td>JetPRIME reagent and buffer</td><td>PolyPlus</td><td>114-15</td><td>Lipid-based transfection reagent</td></tr><tr><td>MegaStar 1.6</td><td>VWR</td><td>521-1749</td><td>Centrifuge for 15 or 50 mL tubes</td></tr><tr><td>MEM Eagle</td><td>PAN-Biotech</td><td>P04-08056</td><td>Culture medium for HEK-293 cells</td></tr><tr><td>Microplate shaker</td><td>Fisherbrand</td><td>15504070</td><td>Microplate orbital shaker</td></tr><tr><td>MicroStar 17R</td><td>VWR</td><td>521-1647</td><td>Centrifuge for 1.5 or 2 mL tubes</td></tr><tr><td>MultiDrop</td><td>Thermo Fisher</td><td>5840300</td><td>Cell or water-based reagent dispenser</td></tr><tr><td>MultiDrop Standard Cassette</td><td>Thermo Fisher</td><td>24072670</td><td>Cassette for MultiDrop reagent dispenser</td></tr><tr><td>NanoDLR Stop &amp;amp; Glo Buffer and Substrate</td><td>Promega</td><td>N1630 or N1650</td><td>Reporter luciferase (NanoLuc) reagent to quench Firefly luminescence and detect NanoLuc luminescence. Part of the Nano-Glo Dual-Luciferase Reporter Assay System kit</td></tr><tr><td>ONE-Glo EX Luciferase Assay Buffer and Substrate</td><td>Promega</td><td>N1630 or N1650</td><td>Control luciferase (Firefly) assay reagent to detect Firefly. Part of the Nano-Glo Dual-Luciferase Reporter Assay System kit</td></tr><tr><td>PBS (without calcium or magnesium)</td><td>PAN-Biotech</td><td>P04-36500</td><td></td></tr><tr><td>pGL4 Firefly plasmid (or similar)</td><td>Promega</td><td>E1310 (or equivalent)</td><td>Firefly control plasmid</td></tr><tr><td>pNL1.1 NanoLuc plasmid (or similar)</td><td>Promega</td><td>N1091 (or equivalent)</td><td>NanoLuc control plasmid, for adjustment of equipment settings/optimisation experiments</td></tr><tr><td>QIAquick Gel Extraction Kit</td><td>Qiagen</td><td>28706</td><td></td></tr><tr><td>Quick-Load Purple 1 kb DNA Ladder</td><td>NEB</td><td>N0552S</td><td>High molecular weight DNA ladder</td></tr><tr><td>Sodium Acetate (3 M), pH 5.5</td><td>Thermo Fisher</td><td>AM9740</td><td>For pH adjustment during gel extraction with QIAquick Gel Extraction Kit</td></tr><tr><td>SYBR Gold (10,000x)</td><td>Invitrogen</td><td>S11494</td><td>For visualisation of ssDNA and dsDNA</td></tr><tr><td>SYBR Safe (10,000x)</td><td>Invitrogen</td><td>S33102</td><td>For visualisation of dsDNA only</td></tr><tr><td>T4 DNA Ligase and 10x Ligase buffer</td><td>NEB</td><td>M0202L</td><td></td></tr><tr><td>Trypan Blue stain 0.4%</td><td>Invitrogen</td><td>T10282</td><td>For measurement of viability during cell counting</td></tr><tr><td>Trypsin-EDTA solution; 0.25% Trypsin and 0.53 mM EDTA</td><td>Sigma-Aldrich</td><td>T4049-100ML</td><td></td></tr><tr><td>XhoI and 10x CutSmart buffer</td><td>NEB</td><td>R0146M</td><td></td></tr></tbody></table>

assessment of dna double strand break repair activity using high-throughput and quantitative luminescence-based reporter assays

The repair of DNA double strand breaks (DSBs) is crucial for the maintenance of genome stability and cell viability. DSB repair (DSBR) in cells is mediated through several mechanisms: homologous recombination (HR), non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and single strand annealing (SSA). Cellular assays are essential to measure the proficiency and modulation of these pathways in response to various stimuli.
Here, we present a suite of extrachromosomal reporter assays that each measure the reconstitution of a nanoluciferase reporter gene by one of the four major DSBR pathways in cells. Upon transient transfection into cells of interest, repair of pathway-specific reporter substrates can be measured in under 24 h by the detection of Nanoluciferase (NanoLuc) luminescence.
These robust assays are quantitative, sensitive, titratable, and amenable to a high-throughput screening format. These properties provide broad applications in DNA repair research and drug discovery, complementing the currently available toolkit of cellular DSBR assays.

Repair of each of the reporter assays can be detected and quantified using the same procedure. Correct repair of a substrate by its cognate repair pathway in cells will reconstitute an intact, functional ORF encoding NanoLuc. This luminescence signal can be detected using a plate reader.
The co-transfection with an intact plasmid encoding Firefly luciferase serves as a transfection control. This control serves two purposes. First, it provides a standard to normalize the NanoLuc signal to, as it should be unperturbed by modulation of DSBR by either genetic or pharmacological means. Second, it can provide an indication of off-target cellular perturbations that impact the luciferase signal, such as cell cycle modulation, effects on transcription/translation, or general toxicity.
The ratio of NanoLuc to Firefly serves as a surrogate readout of repair. Luminescence values can be exported and analyzed by normalizing the two luciferase signals from within the same well. In the case of genetic perturbation studies (e.g., comparing wild-type and KO or non-targeting and target siRNA), repair is usually normalized to the parental sample (wild-type cells or cells treated with non-targeting control siRNA). In the case of pharmacological modulation, values from a compound-treated sample are normalized to the value produced by vehicle treatment.
Full validation of the described reporter suite has been recently published7. Data exemplifying the characterization of genetic and pharmacological modulation of DSBR are shown in Figure 4 (adapted from 7). Pol&#952; is the key mediator of MMEJ and loss or inhibition of this enzyme is predicted to specifically ablate cellular MMEJ3,10. Using a cell line in which POLQ, the gene encoding Pol&#952;, has been knocked out11, the resection-independent MMEJ reporter assay demonstrates that MMEJ is indeed almost fully suppressed. Evaluation of the component NanoLuc and Firefly luminescence signals shows that the observed repair defect is driven by a reduction in the NanoLuc signal (encoded by the reporter substrate) while the Firefly signal (control) is unperturbed (Figure 4A-C). In contrast, the assessment of NHEJ proficiency using the blunt end NHEJ reporter demonstrates that POLQ knockout does not inhibit the repair of the reporter substrate (Figure 4D-F). Together, these genetic data support the specific role of Pol&#952; in MMEJ-mediated repair. These observations are fully recapitulated pharmacologically with ART55812,13, a recently reported highly potent and specific inhibitor of the polymerase domain of Pol&#952; (Figure 4G), where titratable inhibition of MMEJ is observed, which derives from a specific decrease in the NanoLuc and not the Firefly signal (Figure 4H). Furthermore, and in agreement with genetic data, there is no effect on NHEJ (Figure 4I,J). Together these data highlight how these reporters can be used to characterize the genetic modulation of DSBR pathways and show cellular potency and target/pathway specificity of small molecules.
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/66969/66969fig04.jpg" /> 
Figure 4: Effects of genetic knockout and pharmacological inhibition of Pol&#952; on MMEJ and NHEJ reporter signals. eHAP1 WT and POLQ(-) cells were transfected with a Firefly control plasmid and with (A-C) the resection-independent MMEJ reporter or (D-F) blunt end NHEJ reporter. Percentage of MMEJ or NHEJ repair is the ratio of NanoLuc luminescence over Firefly luminescence, normalized to the DMSO-treated control, 24 h post transfection. Data represent mean &#177; SEM of three biological replicates, each averaging 8 technical replicates. HEK-293 cells were transfected with a Firefly control plasmid and (G,H) the resection-independent MMEJ reporter or the (I,J) blunt end NHEJ reporter and treated with the Pol&#952; polymerase inhibitor ART558. Percentage of repair is the ratio of NanoLuc luminescence over Firefly luminescence, normalized to the DMSO-treated control, 24 h post transfection. Percentage inhibition of the individual luminescence signals in (G) and (I) was calculated relative to DMSO-treated control and shown respectively in (H) and (J). Data represent mean &#177; SEM of 2 biological replicates, each averaging 4 technical replicates. This figure was adapted from Rajendra et al.7. Abbreviations: NanoLuc = Nanoluciferase; MMEJ = microhomology-mediated end joining; NHEJ = non-homologous end joining; WT = wild type. <a href="https://www.jove.com/files/ftp_upload/66969/66969fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/66969/66969fig05.jpg" /> 
Figure 5: Inhibition of HR reporter signal by the RAD51 inhibitor CAM833. (A) HEK-293 cells were transfected with the long template HR reporter substrate, a Firefly luciferase control plasmid, and treated with the RAD51 inhibitor CAM83314. NanoLuc and Firefly luminescence was read 16 h after transfection. Percentage of HR repair is the ratio of NanoLuc luminescence over Firefly luminescence, normalized to the DMSO-treated control. Dashed lines highlight percentage HR inhibition and CAM833 concentration at the curve EC50. Data represent mean &#177; SEM of 2 biological replicates, each averaging 4 technical replicates. (B) Percentage inhibition of the individual luminescence signals in (A) was calculated relative to the DMSO-treated control. Dashed lines highlight percentage NanoLuc and Firefly inhibition at 3.33 &#181;M CAM833 (EC50). The decrease in Firefly signal at CAM833 concentrations &#8805; 10 &#181;M is indicative of compound toxicity at high doses; however, NanoLuc signal reduction is observed at concentrations where Firefly signal is unaffected, suggesting that CAM833 induces on-target HR inhibition. This figure was adapted from Rajendra et al.7. Abbreviations: NanoLuc = Nanoluciferase; HR = homologous recombination. <a href="https://www.jove.com/files/ftp_upload/66969/66969fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td colspan="2">Reporter substrate</td>
			<td>Source plasmid 
			(size in kb, resistance)</td>
			<td colspan="3">DSB generation</td>
			<td>Expected size of final reporter substrate (kb)</td>
		</tr>
		<tr>
			<td colspan="2">Resection-independent MMEJ</td>
			<td>4.0, Kan</td>
			<td colspan="3">Resected 3&#39; tails through ligation of caps</td>
			<td>1.6</td>
		</tr>
		<tr>
			<td colspan="2">Resection-dependent MMEJ</td>
			<td>6.5, Kan</td>
			<td colspan="3">I-SceI (non-cohesive), HindIII (cohesive)</td>
			<td>6.5</td>
		</tr>
		<tr>
			<td colspan="2">Blunt NHEJ</td>
			<td>4.3, Kan</td>
			<td colspan="3">Blunt ends upon excision from plasmid by EcoRV</td>
			<td>1.7</td>
		</tr>
		<tr>
			<td colspan="2">Non-blunt NHEJ</td>
			<td>6.7, Kan</td>
			<td colspan="3">I-SceI (non-cohesive), HindIII (cohesive)</td>
			<td>6.5</td>
		</tr>
		<tr>
			<td colspan="2">Long template HR</td>
			<td>9.2, Kan</td>
			<td colspan="3">I-SceI (non-cohesive), HindIII (cohesive)</td>
			<td>9.2</td>
		</tr>
		<tr>
			<td colspan="2">Short template HR</td>
			<td>9.3, Amp</td>
			<td colspan="3">I-SceI (cohesive)</td>
			<td>9.3</td>
		</tr>
		<tr>
			<td colspan="2">SSA</td>
			<td>9.5, Kan</td>
			<td colspan="3">I-SceI (non-cohesive), HindIII (cohesive)</td>
			<td>9.5</td>
		</tr>
	</tbody>
</table>
Table 1: Reporter substrate plasmids. Abbreviations: DSB = double strand break; MMEJ = microhomology-mediated end joining; NHEJ = non-homologous end joining; HR = homologous recombination; SSA = single strand annealing; Kan = kanamycin; Amp = ampicillin.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td colspan="3">Sequence (5&#8217;-3&#8217;)</td>
			<td>Supplier</td>
			<td>Purification</td>
			<td>Function</td>
		</tr>
		<tr>
			<td colspan="3">5&#8217;[Phos]TCGAGGACTTGGTCCAGGTT 
			GTAGCCGGCTGTCTGTCGCCAGTCC 
			CCAACGAAATCTTCGAGTGTGAAGACCAT</td>
			<td>Sigma</td>
			<td>PAGE</td>
			<td>Left cap, long oligonucleotide</td>
		</tr>
		<tr>
			<td colspan="3">5&#8217;[Phos]GCCGGCTACAACCTGGACCAAGTCC</td>
			<td>Sigma</td>
			<td>PAGE</td>
			<td>Left cap, short oligonucleotide</td>
		</tr>
		<tr>
			<td colspan="3">5&#8217;[Phos]AGCTTTATTGCGGTAGTTTATCA 
			CAGTTAAATTGCTAACGCAGTCAGTGG 
			GCCTCGGCGGCCAAGCTAGGCAATCC 
			GGTACTGTTGGTAAAGCCACCATGG</td>
			<td>Sigma</td>
			<td>PAGE</td>
			<td>Right cap, long oligonucleotide</td>
		</tr>
		<tr>
			<td colspan="3">5&#8217;[Phos]CGAGGCCCACTGACTGCGTTA 
			GCAATTTAACTGTGATAAACTACCGCAATAA</td>
			<td>Sigma</td>
			<td>PAGE</td>
			<td>Right cap, short oligonucleotide</td>
		</tr>
	</tbody>
</table>
Table 2: Oligonucleotides for caps for generation of resection-independent MMEJ reporter substrate. Abbreviations: ssDNA = single-stranded DNA; dsDNA = double-stranded DNA; MMEJ = microhomology-mediated end joining; PAGE = polyacrylamide gel electrophoresis. Microhomologies are underlined.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Reporter assay</td>
			<td>NanoLuc reporter substrate DNA (&#181;g DNA/1x106 cells)</td>
			<td>Firefly control luciferase plasmid (&#181;g DNA/1x106 cells)</td>
		</tr>
		<tr>
			<td>Resection-independent MMEJ</td>
			<td>0.5</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>Resection-dependent MMEJ</td>
			<td>1</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>Blunt NHEJ</td>
			<td>0.5</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>Non-blunt NHEJ</td>
			<td>0.5</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>Long template HR</td>
			<td>1</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>Short template HR</td>
			<td>2</td>
			<td>0.66</td>
		</tr>
		<tr>
			<td>SSA</td>
			<td>1</td>
			<td>0.66</td>
		</tr>
	</tbody>
</table>
Table 3: DNA quantities for transient transfection of NanoLuc reporter substrates and Firefly control luciferase plasmid (HEK-293, 96-well plate format). Abbreviations: MMEJ = microhomology-mediated end joining; NHEJ = non-homologous end joining; HR = homologous recombination; SSA = single strand annealing.

Author Spotlight: Developing Novel Anticancer Therapeutics Targeting the DNA Damage Response

We present protocols for the assessment of double strand break repair pathway proficiency in cells using a suite of luminescence-based extrachromosomal reporter substrates.

Assessment of DNA Double Strand Break Repair Activity Using High-throughput and Quantitative Luminescence-Based Reporter Assays

The repair of DNA double strand breaks (DSBs) is crucial for the maintenance of genome stability and cell viability. DSB repair (DSBR) in cells is ...

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1.0K Views.  Artios Pharma Ltd, Cambridge. We present protocols for the assessment of double strand break repair pathway proficiency in cells using a suite of luminescence-based extrachromosomal reporter substrates.

Video: Author Spotlight: Developing Novel Anticancer Therapeutics Targeting the DNA Damage Response

A Syngeneic Mouse Model of Metastatic Renal Cell Carcinoma for Quantitative and Longitudinal Assessment of Preclinical Therapies

Renal cell carcinoma (RCC) affects &#62; 60,000 people in the United States annually, and ~ 30% of RCC patients have multiple metastases at the time of diagnosis. Metastatic RCC (mRCC) is incurable, with a median survival time of only 18 months. Immune-based interventions (e.g., interferon (IFN) and interleukin (IL)-2) induce durable responses in a fraction of mRCC patients, and multikinase inhibitors (e.g., sunitinib or sorafenib) or anti-VEGF receptor monoclonal antibodies (mAb) are largely palliative, as complete remissions are rare. Such shortcomings in current therapies for mRCC patients provide the rationale for the development of novel treatment protocols. A key component in the preclinical testing of new therapies for mRCC is a suitable animal model. Beneficial features that recapitulate the human condition include a primary renal tumor, renal tumor metastases, and an intact immune system to investigate any therapy-driven immune effector responses and the formation of tumor-induced immunosuppressive factors. This report describes an orthotopic mRCC mouse model that has all of these features. We describe an intrarenal implantation technique using the mouse renal adenocarcinoma cell line Renca, followed by the assessment of tumor growth in the kidney (primary site) and lungs (metastatic site).

Implementation of an orthotopic model of renal cell carcinoma in immunocompetent mice affords the investigator a clinically-relevant system defined by the presence of a primary renal tumor and lung metastases in the same animal. This system can be used to preclinically test a variety of treatments in vivo.

Renal cell carcinoma (RCC) affects &#62; 60,000 people in the United States annually, and ~ 30% of RCC patients have multiple metastases at the time of ...

Application of Laser Micro-irradiation for Examination of Single and Double Strand Break Repair in Mammalian Cells

Highly coordinated DNA repair pathways exist to detect, excise and replace damaged DNA bases, and coordinate repair of DNA strand breaks. While molecular biology techniques have clarified structure, enzymatic functions, and kinetics of repair proteins, there is still a need to understand how repair is coordinated within the nucleus. Laser micro-irradiation offers a powerful tool for inducing DNA damage and monitoring the recruitment of repair proteins. Induction of DNA damage by laser micro-irradiation can occur with a range of wavelengths, and users can reliably induce single strand breaks, base lesions and double strand breaks with a range of doses. Here, laser micro-irradiation is used to examine repair of single and double strand breaks induced by two common confocal laser wavelengths, 355 nm and 405 nm. Further, proper characterization of the applied laser dose for inducing specific damage mixtures is described, so users can reproducibly perform laser micro-irradiation data acquisition and analysis.

Confocal fluorescence microscopy and laser micro-irradiation offer tools for inducing DNA damage and monitoring the response of DNA repair proteins in selected sub-nuclear areas. This technique has significantly advanced our knowledge of damage detection, signaling, and recruitment. This manuscript demonstrates these technologies to examine single and double strand break repair.

Highly coordinated DNA repair pathways exist to detect, excise and replace damaged DNA bases, and coordinate repair of DNA strand breaks. While molecular ...

A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells

The purpose of this method is to provide a flexible, rapid, and quantitative technique to examine the kinetics of DNA-protein crosslink (DPC) repair in mammalian cell lines. Rather than globally assaying removal of xenobiotic-induced or spontaneous chromosomal DPC removal, this assay examines the repair of a homogeneous, chemically defined lesion specifically introduced at one site within a plasmid DNA substrate. Importantly, this approach avoids the use of radioactive materials and is not dependent on expensive or highly-specialized technology. Instead, it relies on standard recombinant DNA procedures and widely available real-time, quantitative polymerase chain reaction (qPCR) instrumentation. Given the inherent flexibility of the strategy utilized, the size of the crosslinked protein, as well as the nature of the chemical linkage and the precise DNA sequence context of the attachment site can be varied to address the respective contributions of these parameters to the overall efficiency of DPC repair. Using this method, plasmids containing a site-specific DPC were transfected into cells and low molecular weight DNA recovered at various times post-transfection. Recovered DNA is then subjected to strand-specific primer extension (SSPE) using a primer complementary to the damaged strand of the plasmid. Since the DPC lesion blocks Taq DNA polymerase, the ratio of repaired to un-repaired DNA can be quantitatively assessed using qPCR. Cycle threshold (CT) values are used to calculate percent repair at various time points in the respective cell lines. This SSPE-qPCR method can also be used to quantitatively assess the repair kinetics of any DNA adduct that blocks Taq polymerase.

The goal of this protocol is to quantify the repair of defined DNA-protein crosslinks on plasmid DNA. Lesioned plasmids are transfected into recipient mammalian cell lines and low-molecular weight harvested at multiple time points post-transfection. DNA repair kinetics are quantified using strand-specific primer extension followed by qPCR.

The purpose of this method is to provide a flexible, rapid, and quantitative technique to examine the kinetics of DNA-protein crosslink (DPC) repair in ...

Genetics

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

The repair of double-stranded breaks (DSBs) in DNA is a highly coordinated process, necessitating the formation and resolution of multi-protein repair complexes. This process is regulated by a myriad of proteins that promote the association and disassociation of proteins to these lesions. Thanks in large part to the ability to perform functional screens of a vast library of proteins, there is a greater appreciation of the genes necessary for the double-strand DNA break repair. Often knockout or chemical inhibitor screens identify proteins involved in repair processes by using increased toxicity as a marker for a protein that is required for DSB repair. Although useful for identifying novel cellular proteins involved in maintaining genome fidelity, functional analysis requires the determination of whether the protein of interest promotes localization, formation, or resolution of repair complexes. 
The accumulation of repair proteins can be readily detected as distinct nuclear foci by immunofluorescence microscopy. Thus, association and disassociation of these proteins at sites of DNA damage can be accessed by observing these nuclear foci at representative intervals after the induction of double-strand DNA breaks. This approach can also identify mis-localized repair factor proteins, if repair defects do not simultaneously occur with incomplete delays in repair. In this scenario, long-lasting double-strand DNA breaks can be engineered by expressing a rare cutting endonuclease (e.g., I-SceI) in cells where the recognition site for the said enzyme has been integrated into the cellular genome. The resulting lesion is particularly hard to resolve as faithful repair will reintroduce the enzyme's recognition site, prompting another round of cleavage. As a result, differences in the kinetics of repair are eliminated. If repair complexes are not formed, localization has been impeded. This protocol describes the methodology necessary to identify changes in repair kinetics as well as repair protein localization.

Repair of double-strand DNA breaks is a dynamic process, requiring not only formation of repair complexes at the breaks, but also their resolution after the lesion is addressed. Here, we use immunofluorescence microscopy for transient and long-lasting double-stranded breaks as a tool to dissect this genome maintenance mechanism.

The repair of double-stranded breaks (DSBs) in DNA is a highly coordinated process, necessitating the formation and resolution of multi-protein repair ...

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Double strand breaks (DSBs) in DNA are the most cytotoxic type of DNA damage. Because a myriad of insults can result in these lesions (e.g., replication stress, ionizing radiation, unrepaired UV damage), DSBs occur in most cells each day. In addition to cell death, unrepaired DSBs reduce genome integrity and the resulting mutations can drive tumorigenesis. These risks and the prevalence of DSBs motivate investigations into the mechanisms by which cells repair these lesions. Next generation sequencing can be paired with the induction of DSBs by ionizing radiation to provide a powerful tool to precisely define the mutations associated with DSB repair defects. However, this approach requires computationally challenging and cost prohibitive whole genome sequencing to detect the repair of the randomly occurring DSBs associated with ionizing radiation. Rare cutting endonucleases, such as I-Sce1, provide the ability to generate a single DSB, but their recognition sites must be inserted into the genome of interest. As a result, the site of repair is inherently artificial. Recent advances allow guide RNA (sgRNA) to direct a Cas9 endonuclease to any genome locus of interest. This could be applied to the study of DSB repair making next generation sequencing more cost effective by allowing it to be focused on the DNA flanking the Cas9-induced DSB. The goal of the manuscript is to demonstrate the feasibility of this approach by presenting a protocol that can define mutations that stem from the repair of a DSB upstream of the CD4 gene. The protocol can be adapted to determine changes in the mutagenic potential of DSB associated with exogenous factors, such as repair inhibitors, viral protein expression, mutations, and environmental exposures with relatively limited computation requirements. Once an organism's genome has been sequenced, this method can be theoretically employed at any genomic locus and in any cell culture model of that organism that can be transfected. Similar adaptations of the approach could allow comparisons of repair fidelity between different loci in the same genetic background.

Presented here is sgRNA/CAS9 endonuclease and next-generation sequencing protocol that can be used to identify the mutations associated with double strand break repair near the CD4 promoter.

Double strand breaks (DSBs) in DNA are the most cytotoxic type of DNA damage. Because a myriad of insults can result in these lesions (e.g., replication ...

Analysis of DNA Double-strand Break (DSB) Repair in Mammalian Cells

DNA double-strand breaks are the most dangerous DNA lesions that may lead to massive loss of genetic information and cell death. Cells repair DSBs using two major pathways: nonhomologous end joining (NHEJ) and homologous recombination (HR). Perturbations of NHEJ and HR are often associated with premature aging and tumorigenesis, hence it is important to have a quantitative way of measuring each DSB repair pathway. Our laboratory has developed fluorescent reporter constructs that allow sensitive and quantitative measurement of NHEJ and HR. The constructs are based on an engineered GFP gene containing recognition sites for a rare-cutting I-SceI endonuclease for induction of DSBs. The starting constructs are GFP negative as the GFP gene is inactivated by an additional exon, or by mutations. Successful repair of the I-SceI-induced breaks by NHEJ or HR restores the functional GFP gene. The number of GFP positive cells counted by flow cytometry provides quantitative measure of NHEJ or HR efficiency.

Analysis of DNA Double-strand Break DSB Repair in Mammalian Cells

This article describes GFP-based fluorescence in vivo assays that separately quantify homologous recombination and nonhomologous end joining in mammalian cells.

DNA double-strand breaks are the most dangerous DNA lesions that may lead to massive loss of genetic information and cell death.  Cells repair DSBs using ...

Biology

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base excision repair (BER) molecular beacons. The substrate (beacon) is comprised of a deoxyoligonucleotide containing a single base lesion with a 6-Carboxyfluorescein (6-FAM) moiety conjugated to the 5'end and a Dabcyl moiety conjugated to the 3' end of the oligonucleotide. The BER molecular beacon is 43 bases in length and the sequence is designed to promote the formation of a stem-loop structure with 13 nucleotides in the loop and 15 base pairs in the stem1,2. When folded in this configuration the 6-FAM moiety is quenched by Dabcyl in a non-fluorescent manner via F&ouml;rster Resonance Energy Transfer (FRET)3,4. The lesion is positioned such that following base lesion removal and strand scission the remaining 5 base oligonucleotide containing the 6-FAM moiety is released from the stem. Release and detachment from the quencher (Dabcyl) results in an increase of fluorescence that is proportionate to the level of DNA repair. By collecting multiple reads of the fluorescence values, real-time assessment of BER activity is possible. The use of standard quantitative real-time PCR instruments allows the simultaneous analysis of numerous samples. The design of these BER molecular beacons, with a single base lesion, is amenable to kinetic analyses, BER quantification and inhibitor validation and is adaptable for quantification of DNA Repair activity in tissue and tumor cell lysates or with purified proteins. The analysis of BER activity in tumor lysates or tissue aspirates using these molecular beacons may be applicable to functional biomarker measurements. Further, the analysis of BER activity with purified proteins using this quantitative assay provides a rapid, high-throughput method for the discovery and validation of BER inhibitors.

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates. The assay yields rates of DNA Repair activity amenable to kinetic analysis and is adaptable for quantification of DNA Repair activity in tissue and tumor lysates or with purified proteins.

We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base ...

Live-Cell Imaging of Transcriptional Activity at DNA Double-Strand Breaks

DNA double-strand breaks (DSB) are the most severe type of DNA damage. Despite the catastrophic consequences on genome integrity, it remains so far elusive how DSBs affect transcription. A reason for this was the lack of suitable tools to simultaneously monitor transcription and the induction of a genic DSB with sufficient temporal and spatial resolution. This work describes a set of new reporters that directly visualize transcription in live cells immediately after the induction of a DSB in the DNA template. Bacteriophage RNA stem-loops are employed to monitor the transcription with single-molecule sensitivity. For targetting the DSB to a specific gene region, the reporter genes are engineered to contain a single recognition sequence of the homing endonuclease I-SceI, otherwise absent from the human genome. A single copy of each reporter gene was integrated into the genome of human cell lines. This experimental system allows the detection of single RNA molecules generated by the canonical gene transcription or by DNA break-induced transcription initiation. These reporters provide an unprecedented opportunity for interpreting the reciprocal interactions between transcription and DNA damage and to disclose hitherto unappreciated aspects of DNA break-induced transcription.

This protocol presents a new reporter gene system and the experimental setup to detect transcription at DNA double-strand breaks with single-molecule sensitivity.

DNA double-strand breaks (DSB) are the most severe type of DNA damage. Despite the catastrophic consequences on genome integrity, it remains so far ...

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 ...

FACS Analysis of GFP and mCherry Reporter Cells to Evaluate NHEJ & HR Efficiency

Analysis of Nonhomologous End Joining and Homologous Recombination Efficiency in HEK-293T Cells Using GFP-Based Reporter Systems

DNA double-strand breaks (DSBs) represent the most perilous DNA lesions, capable of inducing substantial genetic information loss and cellular demise. In response, cells employ two primary mechanisms for DSB repair: nonhomologous end joining (NHEJ) and homologous recombination (HR). Quantifying the efficiency of NHEJ and HR separately is crucial for exploring the relevant mechanisms and factors associated with each. The NHEJ assay and HR assay are established methods used to measure the efficiency of their respective repair pathways. These methods rely on meticulously designed plasmids containing a disrupted green fluorescent protein (GFP) gene with recognition sites for endonuclease I-SceI, which induces DSBs. Here, we describe the extrachromosomal NHEJ assay and HR assay, which involve co-transfecting HEK-293T cells with EJ5-GFP/DR-GFP plasmids, an I-SceI expressing plasmid, and an mCherry expressing plasmid. Quantitative results of NHEJ and HR efficiency are obtained by calculating the ratio of GFP-positive cells to mCherry-positive cells, as counted by flow cytometry. In contrast to chromosomally integrated assays, these extrachromosomal assays are more suitable for conducting comparative investigations involving multiple established stable cell lines.

Author Spotlight: Decoding DNA Repair by Extrachromosomal NHEJ Assay and HR Assays

This protocol describes an extrachromosomal nonhomologous end joining (NHEJ) assay and homologous recombination (HR) assay to quantify the efficiency of NHEJ and HR in HEK-293T cells.

DNA double-strand breaks (DSBs) represent the most perilous DNA lesions, capable of inducing substantial genetic information loss and cellular demise. In ...