This research was supported, in part, by the Intramural Research Program of the NIH, National Institute on Aging, United States (Z01-AG000746&#8211;08). J.H. is supported by the National Natural Science Foundations of China (21708007 and 31871365).

1. Cell preparation
<ol>
	<li>Day 1
	<ol>
		<li>Pre-treat 35 mm glass-bottomed culture dishes with a cell adhesive solution.</li>
		<li>Plate cells in the pre-treated dishes one day before treatment. Cell should be actively dividing and 50&#8211;70% confluent on the day of the experiment. 
		NOTE: HeLa cells were used in this experiment with Dulbecco Modified Eagle Medium DMEM, supplemented with 10% fetal bovine serum, 1x penicillin /streptomycin. There is no restriction for adherent cell lines. However, non-adherent cells must be centrifuged onto slides and fixed prior to the analysis by PLA.</li>
	</ol>
	</li>
	<li>Day 2
	<ol>
		<li>Prepare a stock solution of Digoxigenin Trimethyl psoralen (Dig-TMP) by resuspending a frozen aliquot of previously synthesized Dig-TMP in 1:1 EtOH:H2O. Determine the concentration by measuring OD at 250 nm of a 100x dilution (in H2O) of the dissolved Dig-TMP. The extinction coefficient of Dig-TMP is 25,000. Verify the concentration by measuring OD at 250 nm before each use and calculate stock concentration: Abs x 100 x 106/25,000 = Concentration (in &#181;M). Generally, the stock solution is around 3 mM. The solution can be stored in &#8211;20 &#176;C for about a month. 
		NOTE: Dig-TMP must be chemically synthesized in advance, following the procedure described here. Reflux 4&#39;-chloromethyl-4,5&#39;,8-trimethylpsoralen with 4,7,10-trioxa-1,13-tridecanedi-amine in toluene under nitrogen for 12 h. Remove the solvent and recover the 4&#39;-[N-(13-amino-4,7,10-trioxatrideca)] aminomethyl-4,5&#39;,8-trimethylpsoralen product by silica gel chromatography. Conjugate the product to digoxigenin NHS ester in dimethyl formamide and triethylamine at 50 &#176;C for 18 h. Remove the solvent and purify the residue by preparative thin layer silica gel chromatography. Elute the product band chloroform: methanol: 28% ammonium hydroxide (8:1:0.1) mixture. Evaporate the solvents and dissolve the pellet in 50% EtOH:H2O.</li>
		<li>Add Dig-TMP stock in 50% EtOH:H2O to the cell culture medium to a final concentration of 5 &#181;M. Bring the medium to 37 &#176;C. Aspirate the medium from the plates, add the pre-warmed Dig-TMP containing media, and place plates in an incubator (37 &#176;C, 5% CO2) for 30 min to allow the Dig-TMP to equilibrate.</li>
		<li>While the cells are incubating, pre-warm the UV box (see Table of Materials) to 37 &#176;C.</li>
		<li>Place the plates in the pre-warmed UV box and expose the cells to a dose of 3 J/cm2 of UVA light for 5 min for this experiment. Plates were placed on top of a thermo-block maintained at 37 &#176;C, during irradiation. Calculate the time using the formula: 
		<img alt="Equation 1" src="/files/ftp_upload/61689/61689equ01.jpg" /></li>
		<li>Aspirate the medium using a pipette, add fresh pre-warmed medium and place plates back in the incubator at 37 &#176;C, 5% CO2 for 1 h.</li>
		<li>Remove media and wash dishes once gently with phosphate buffered saline (PBS).</li>
		<li>Remove PBS and add 0.1% formaldehyde (FA) in PBS for 5 min at room temperature (RT). This prevents cell detachment during CSK-R (cytoskeleton extraction buffer containing RNase, described in 1.2.9.) pretreatment required to extract the cytoplasmic elements and reduce PLA background.</li>
		<li>Aspirate off FA and wash dishes with PBS once.</li>
		<li>Add CSK-R buffer and incubate for 5 min at RT to remove cytoplasm [CSK-R buffer: 10 mM PIPES, pH 7.0, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.5%Triton X-100, 300 &#181;g/mL RNase A]. Aspirate the buffer, add fresh CSK-R, and incubate for 5 min at RT. 
		NOTE: A stock of CSK buffer can be stored at 4 &#176;C, and Triton X and RNaseA added right before use.</li>
		<li>Wash with PBS thrice.</li>
		<li>Fix cells with 4% formaldehyde in PBS for 10 min at RT.</li>
		<li>Wash cells with PBS. Perform this step three times.</li>
		<li>Add cold 100% methanol and incubate for 20 min at -20 &#176;C.</li>
		<li>Wash cells with PBS thrice. At this point cells can be stored in PBS in a humid chamber at 4 &#176;C for up to a week.</li>
		<li>Incubate cells in 80 &#181;L of 5 mM TritonX-100 for 10 min at 4 &#176;C.</li>
		<li>Incubate cells with 100 &#181;L of 5 mM EDTA in PBS supplemented with 1 &#181;L of 100 mg/mL RNase A for 30 min at 37 &#176;C.</li>
		<li>Wash cells with PBS thrice.</li>
		<li>Store cells in blocking buffer (5% BSA and 10% goat serum in PBS) in a humid chamber overnight at 4 &#176;C.</li>
	</ol>
	</li>
</ol>
2. Proximity ligation assay
NOTE: Perform proximity ligation assay on Day 3.
<ol>
	<li>Antibody staining
	<ol>
		<li>Prepare 40 &#956;L of the primary antibody solution per plate: Add the appropriate volume of primary antibodies to achieve desired dilution (mouse anti Digoxigenin and rabbit antibody against a replisome component such as MCM5, CDC45, PSF1 or pMCM2, dilutions specified in Table of Materials) into blocking buffer (to reach a final volume of 24 &#956;L). Mix by tapping and let it stand for 20 min at RT. Prepare a master mix for multiple samples and mix by tapping before applying to the wells.</li>
		<li>Add 40 &#956;L of primary antibody solution to the center of the well and incubate in a humid chamber for 1 h at 37 &#176;C. During staining, allow the PLA probes and blocking buffer to warm to the room temperature.</li>
		<li>Wash cells with PBS-T [PBS-T: 0.05% Tween-20 in 1X PBS] at RT. Perform this step three times.</li>
		<li>While washing, prepare 40 &#956;L of PLA probe solution per dish (PLA probes consist of a secondary antibody recognizing either rabbit or mouse IgG, covalently linked to a PLUS or MINUS oligonucleotide): 8 &#956;L of PLA probe anti mouse-PLUS + 8 &#956;L of PLA probe anti rabbit-MINUS antibody + 24 &#956;L of blocking buffer. Mix and let it stand for 20 min at RT. Prepare a master mix for multiple samples and mix well before applying to the wells. Place the solution in the middle of the well in the plate.</li>
		<li>Remove last wash, add 40 &#956;L of PLA probe solution to the center of the well, and incubate in a humid chamber for 1 h at 37 &#176;C.</li>
		<li>Wash in buffer A thrice, for 10 min each, on a tilting platform at RT. During washing, bring the ligation mix to RT.</li>
	</ol>
	</li>
	<li>Ligation and amplification
	<ol>
		<li>Prepare 40 &#956;L of Ligation mix per plate: 8 &#956;L (5x) of ligation stock + 31 &#956;L of distilled water + 1 &#956;L of ligase. Prepare master mix for multiple plates and mix well before applying to the wells.</li>
		<li>Add 40 &#956;L of ligation solution to each plate and incubate in a humid chamber for 30 min. at 37 &#176;C.</li>
		<li>Wash cells 3x with buffer A, each for 2 min, on a tilting platform at RT.</li>
		<li>Prepare 40 &#956;L of amplification solution per dish: 8 &#956;L (5x) of amplification stock + 31.5 &#956;L of distilled water + 0.5 &#956;L of DNA Polymerase. Prepare a master mix for multiple samples and mix well before applying to the wells.</li>
		<li>Add 40 &#956;L of amplification solution to each plate and incubate in a humid chamber at 37 &#176;C for 100 min.</li>
		<li>Aspirate off the amplification solution and wash with buffer B. Perform 6 washes each for 10 min, on a tilting platform at RT.</li>
		<li>Wash once with 0.01x buffer B for 1 min at RT.</li>
		<li>Aspirate buffer B and incubate plates with secondary antibodies, Alexa Fluor 488 anti-mouse IgG and Alexa Fluor 568 anti-rabbit IgG in blocking solution at appropriate dilutions in blocking buffer, in a humid chamber, for 30 min at 37 &#176;C or overnight at 4 &#176;C.</li>
		<li>Wash cells three times with PBS-T, for 10 min each on a tilting platform at RT.</li>
		<li>Aspirate PBS-T and mount in mounting medium with DAPI. The mounted plates can be imaged immediately or stored at 4 &#176;C in the dark for no more than 4 days before imaging.</li>
	</ol>
	</li>
</ol>
3. Imaging and quantification
<ol>
	<li>Perform imaging in an epifluorescent or confocal microscope (if 3D imaging is desirable, cover at least 3 &#181;m in 15 stacks). Perform experiments in triplicate&#160;and image enough number of fields to make at least 100 observations per sample or condition. Image all fields and samples, including controls, using the same exposure settings.</li>
	<li>Quantify with an appropriate image analysis software (see Table of Materials for open source and commercial software capable of performing this analysis in single or multiple plane-images).
	<ol>
		<li>Segment cell nuclei based on the DAPI staining. Perform detection of nuclear PLA dots. Assign PLA dots to their corresponding nucleus. Export PLA dots per nucleus results as a csv file (see Supplementary File 1 and Supplementary File 2).</li>
	</ol>
	</li>
	<li>Statistical analysis (see Table of Materials for suggested open source and commercial software).
	<ol>
		<li>Verify if the samples follow a normal distribution with a Shapiro-Wilk test.</li>
		<li>Determine whether there is a significant difference between two samples using a Student-t test (if normal distribution assumption met) or a Wilcoxon-Rank Sum test (if normal distribution assumption is violated for a sample).</li>
	</ol>
	</li>
	<li>Data visualization: Generate dot plots combined with box plots to visualize data distribution, median (Q2), 25th (Q1) and 75th percentile for the different samples (See Table of Materials for suggested open source and commercial software).</li>
</ol>
4. 3D display of pMCM2: ICL interactions
<ol>
	<li>Image PLA plates on a spinning disk confocal microscope, using a Plan Fluor 60x/1.25 numerical aperture oil objective. Acquire 16 stacks covering 1.6 mm and generate the 3D reconstruction with the appropriate image analysis software (see Table of Materials).</li>
</ol>

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The authors have nothing to disclose.

Although the PLA is a very powerful technique, there are technical concerns that must be solved in order to obtain clear and reproducible results. The antibodies must be of high affinity and specificity. Furthermore, it is important to reduce the non-specific background signals as much as possible. We have found that membranes and cellular debris contribute to the background, and we have removed them as much as possible. The washes with detergent containing buffers prior to fixing, and the wash with methanol after fixing...

An erratum was issued for: <a href="https://www.jove.com/t/6517">Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion</a>.
The Authors section was updated from:
Jing Zhang*1 
Jing Huang*2 
Ryan C. James3 
Julia Gichimu1 
Manikandan Paramasivam4 
Durga Pokharel5 
Himabindu Gali6 
Marina A. Bellani1 
Michael M Seidman1 
1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health 
2Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University 
3Department of Molecular Biology and Genetics, Cornell University 
4Department of Cellular and Molecular Medicine, University of Copenhagen 
5Horizon Discovery 
6Boston University School of Medicine 
* These authors contributed equally
to:
Jing Zhang*1 
Jing Huang*2 
Ishani Majumdar1 
Ryan C. James3 
Julia Gichimu1 
Manikandan Paramasivam4 
Durga Pokharel5 
Himabindu Gali6 
Marina A. Bellani1 
Michael M Seidman1 
1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health 
2Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University 
3Department of Molecular Biology and Genetics, Cornell University 
4Department of Cellular and Molecular Medicine, University of Copenhagen 
5Horizon Discovery 
6Boston University School of Medicine 
* These authors contributed equally

An erratum was issued for: <a href="https://www.jove.com/t/6517">Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion</a>. The Authors section was updated.

Erratum: Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion

The cellular response to double strand breaks is well documented owing to a succession of increasingly powerful methods for directing breaks to specific genomic sites1,2,3. The certainty of location enables unambiguous characterization of proteins and other factors that accumulate at the site and participate in the DNA Damage Response (DDR) thereby driving the Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR) pathways that repair breaks. Of course, many breaks are introduced by agents such as radiation and chemical species that do not attack specific sequences4. However, for these there are procedures available that can convert the ends to structures amenable for tagging and localization5,6. Breaks are also introduced by biological processes, such as immunoglobulin rearrangement, and recent technology permits their localization, as well7. The relationship between responding factors and those sites can then be determined.
Breaks also appear as an indirect consequence of adducts formed by compounds that are not inherent breakers but disrupt DNA transactions such as transcription and replication. They may be formed as a feature of the cellular response to these obstructions, perhaps during repair or because they provoke a structure that is vulnerable to nuclease attack. Typically, the physical relationship between the adduct, the break, and the association with responding factors is inferential. For example, ICLs are formed by chemotherapeutics such as cisplatin and Mitomycin C8 and as a reaction product of abasic sites9. ICLs are well known as potent blocks to replication forks10, thereby stalling forks which can be cleaved by nucleases11. The covalent linkage between strands is often relieved by pathways that have obligate breaks as intermediates12,13, necessitating homologous recombination to rebuild the replication fork14. In most experiments the investigator follows the response of factors of interest to the breaks which are formed downstream of the collision of a replication fork with an ICL. However, because there has been no technology for the localization of a provocative lesion, the proximity of the replisome, and its component parts, to the ICL can only be assumed.
We have developed a strategy to enable the analysis of protein associations with non-sequence specific covalent adducts, illustrated here by ICLs. In our system these are introduced by psoralen, a photoactive natural product used for thousands of years as a therapeutic for skin disorders15. Our approach is based on two important features of psoralens. The first is their high frequency of crosslink formation, which can exceed 90% of adducts, in contrast to the less than 10% formed by popular compounds such as cisplatin or Mitomycin C8,16. The second is the accessibility of the compound to conjugation without loss of crosslinking capacity. We have covalently linked trimethyl psoralen to Digoxigenin (Dig), a long established immunotag. This enables detection of the psoralen adducts in genomic DNA by immunostaining of the Dig tag, and visualization by conventional immunofluorescence17.
This reagent was applied, in our previous work, to the analysis of replication fork encounters with ICLs using a DNA fiber-based assay16. In that work we found that replication could continue past an intact ICL. This was dependent on the ATR kinase, which is activated by replication stress. The replication restart was unexpected given the structure of the CMG replicative helicase. This consists of the MCM hetero-hexamer (M) that forms an offset gapped ring around the template strand for leading strand synthesis which is locked by the proteins of the GINS complex (G, consisting of PSF1, 2, 3, and SLD5) and CDC45 (C)18. The proposal that replication could restart on the side of the ICL distal to the side of the replisome collision argued for a change in the structure of the replisome. To address the question of which components were in the replisome at the time of the encounter with an ICL we developed the approach described here. We exploited the Dig tag as a partner in Proximity Ligation Assays (PLA)19 to interrogate the close association of the ICL with proteins of the replisome20.

<table>
	<tbody>
		<tr>
			<td>Alexa Fluor 568, Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody</td>
			<td>Invitrogen</td>
			<td>A-10011</td>
			<td>1 in 1000</td>
		</tr>
		<tr>
			<td>35 mm plates with glass 1.5 coverslip</td>
			<td>MatTek</td>
			<td>P35-1.5-14-C</td>
			<td>Glass Bottom Microwell Dishes 35mm Petri Dish Microwell</td>
		</tr>
		<tr>
			<td>Alexa Fluor 488,Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody</td>
			<td>Invitrogen</td>
			<td>A-10001</td>
			<td>1 in 1000</td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>SeraCare</td>
			<td>1900-0012</td>
			<td>Blocking solution, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>CDC45 antibody (rabbit)</td>
			<td>Abcam</td>
			<td>ab126762</td>
			<td>1 in 200</td>
		</tr>
		<tr>
			<td>Cell adhesive</td>
			<td>Life Science</td>
			<td>354240</td>
			<td>for cell-TAK solution</td>
		</tr>
		<tr>
			<td>Confocal microscope</td>
			<td>Nikkon</td>
			<td>Nikon TE2000 spinning disk microscope</td>
			<td>equiped with Volocity software</td>
		</tr>
		<tr>
			<td>Digoxigenin (Dig) antibody (mouse)</td>
			<td>Abcam</td>
			<td>ab420</td>
			<td>1 in 200</td>
		</tr>
		<tr>
			<td>Dig-TMP</td>
			<td>synthesized in the Seidman Lab</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Duolink Amplification reagents (5&#215;)</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82010</td>
			<td>reagents need to be stored at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Duolink in situ detection reagents</td>
			<td>Sigma-Aldrich</td>
			<td>DUO92007</td>
			<td>reagents need to be stored at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Duolink in situ oligonucleotide PLA probe MINUS</td>
			<td>Sigma-Aldrich</td>
			<td>DUO92004</td>
			<td>anti-mouse MINUS, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Duolink in situ oligonucleotide PLA probe PLUS</td>
			<td>Sigma-Aldrich</td>
			<td>DUO92002</td>
			<td>anti-rabbit PLUS, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Duolink in situ wash buffer A</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82046</td>
			<td>Duolink Wash Buffers, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Duolink in situ wash buffer B</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82048</td>
			<td>Duolink Wash Buffers, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>epifluorescent microscope</td>
			<td>Zeiss</td>
			<td>Axiovert 200M microscope</td>
			<td>Equipped with the Axio Vision software packages (Zeiss, Germany)</td>
		</tr>
		<tr>
			<td>Formaldehyde 16%</td>
			<td>Fisher Scientific</td>
			<td>PI28906</td>
			<td>for fix solution</td>
		</tr>
		<tr>
			<td>Goat serum</td>
			<td>Thermo</td>
			<td>31873</td>
			<td>Blocking solution, reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Image analysis software</td>
			<td>open source</td>
			<td>Cell profiler</td>
			<td>works for analysis of single plane images</td>
		</tr>
		<tr>
			<td>Image analysis software-license required</td>
			<td>Bitplane</td>
			<td>Imaris</td>
			<td>Cell Biology module needed. Can quantify PLA dots/nuclei in image stacks (3D) and do 3D reconstructions</td>
		</tr>
		<tr>
			<td>Ligase (1 unit/&#956;l)</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82029</td>
			<td>reagents need to be stored at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Ligation reagent (5&#215;)</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82009</td>
			<td>reagents need to be stored at -20 &#176;C</td>
		</tr>
		<tr>
			<td>MCM2 antibody (rabbit)</td>
			<td>Abcam</td>
			<td>ab4461</td>
			<td>1 in 200</td>
		</tr>
		<tr>
			<td>MCM5 antibody (rabbit monoclonal)</td>
			<td>Abcam</td>
			<td>Ab75975</td>
			<td>1 in 1000</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Lab ALLEY</td>
			<td>A2076</td>
			<td>pre-cold at -20&#176;C before use</td>
		</tr>
		<tr>
			<td>phosphoMCM2S108 antibody (rabbit)</td>
			<td>Abcam</td>
			<td>ab109271</td>
			<td>1 in 200</td>
		</tr>
		<tr>
			<td>Polymerase (10 unit/&#956;l)</td>
			<td>Sigma-Aldrich</td>
			<td>DUO82030</td>
			<td>reagents need to be stored at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Prolong gold mounting media with DAPI</td>
			<td>ThermoFisher Scientific</td>
			<td>P36935</td>
			<td></td>
		</tr>
		<tr>
			<td>PSF1 antibody (rabbit)</td>
			<td>Abcam</td>
			<td>ab181112</td>
			<td>1 in 200</td>
		</tr>
		<tr>
			<td>RNAse A 100 mg/ml</td>
			<td>Qiagen</td>
			<td>19101</td>
			<td>reagents need to be stored at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Statistical analysis and data visualization software</td>
			<td>open source</td>
			<td>R studio</td>
			<td>ggplot2 package for generation of dot plot and box plots</td>
		</tr>
		<tr>
			<td>Statistical analysis and data visualization software-license required</td>
			<td>Systat Software</td>
			<td>Sigmaplot V13</td>
			<td></td>
		</tr>
		<tr>
			<td>TMP (trioxalen)</td>
			<td>Sigma-Aldrich</td>
			<td>T6137_1G</td>
			<td></td>
		</tr>
		<tr>
			<td>TritonX-100</td>
			<td>Sigma-Aldrich</td>
			<td>T8787_250ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Sigma-Aldrich</td>
			<td>P9416_100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>UV box</td>
			<td>Southern New England Ultraviolet</td>
			<td></td>
			<td>Discontinued. See Opsytec UV test chamber as a possible replacement</td>
		</tr>
		<tr>
			<td>UV test Chamber</td>
			<td>Opsytec</td>
			<td>UV TEST CHAMBER BS-04</td>
			<td></td>
		</tr>
		<tr>
			<td>VE-821</td>
			<td>Selleckchem</td>
			<td>S8007</td>
			<td>final concentrtion is 1&#181;M</td>
		</tr>
	</tbody>
</table>

visualization of replisome encounters with an antigen tagged blocking lesion

Considerable insight is present into the cellular response to double strand breaks (DSBs), induced by nucleases, radiation, and other DNA breakers. In part, this reflects the availability of methods for the identification of break sites, and characterization of factors recruited to DSBs at those sequences. However, DSBs also appear as intermediates during the processing of DNA adducts formed by compounds that do not directly cause breaks, and do not react at specific sequence sites. Consequently, for most of these agents, technologies that permit the analysis of binding interactions with response factors and repair proteins are unknown. For example, DNA interstrand crosslinks (ICLs) can provoke breaks following replication fork encounters. Although formed by drugs widely used as cancer chemotherapeutics, there has been no methodology for monitoring their interactions with replication proteins.
Here, we describe our strategy for following the cellular response to fork collisions with these challenging adducts. We linked a steroid antigen to psoralen, which forms photoactivation dependent ICLs in nuclei of living cells. The ICLs were visualized by immunofluorescence against the antigen tag. The tag can also be a partner in the Proximity Ligation Assay (PLA) which reports the close association of two antigens. The PLA was exploited to distinguish proteins that were closely associated with the tagged ICLs from those that were not. It was possible to define replisome proteins that were retained after encounters with ICLs and identify others that were lost. This approach is applicable to any structure or DNA adduct that can be detected immunologically.

PLA of Dig-TMP with replisome proteins 
The structure of the Dig-TMP is shown in Figure 1. The details of the synthesis, in which trimethyl psoralen was conjugated through a glycol linker to digoxigenin, have been discussed previously17,21. Incubation of cells with the compound followed by exposure to 365 nm light (UVA) photoactivates the compound and drives the crosslinking reaction. Slightly more than 90% of a...

Watch this Scientific Journal Video about Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion at JoVE.com

Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion

While replication fork collisions with DNA adducts can induce double strand breaks, less is known about the interaction between replisomes and blocking lesions. We have employed the proximity ligation assay to visualize these encounters and to characterize the consequences for replisome composition.

Considerable insight is present into the cellular response to double strand breaks (DSBs), induced by nucleases, radiation, and other DNA breakers. In ...

visualization-replisome-encounters-with-an-antigen-tagged-blocking

Research

JoVE Journal

Biology

1.3K Views.  National Institutes of Health. While replication fork collisions with DNA adducts can induce double strand breaks, less is known about the interaction between replisomes and blocking lesions. We have employed the proximity ligation assay to visualize these encounters and to characterize the consequences for replisome composition.

Video: Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion

Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard cuticle which makes it difficult to use protocols of classical histology. In addition, histological sectioning destroys the sample and can therefore not be used for unique material. Hence, a non-destructive method is desirable which allows to view inside small samples without the need of sectioning.
We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows us to reconstruct the internal organization in its natural state without the artefacts produced by histological sectioning. These date can be used for quantitative morphology, landmarks, or for the visualization of animated movies to understand the structure of hidden body parts and to follow complete organ systems or tissues through the samples.

We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows the reconstruction of internal structures in their natural state without the artefacts produced by histological sectioning.

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard ...

Homemade Site Directed Mutagenesis of Whole Plasmids

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. With this method the cloned target gene can be altered by substitution, deletion or insertion of a few bases directly into a plasmid. It works by simply amplifying the whole plasmid, in a non PCR-based thermocycling reaction. During the reaction mutagenic primers, carrying the desired mutation, are integrated into the newly synthesized plasmid. In this video tutorial we demonstrate an easy and cost effective way to introduce base substitutions into a plasmid. The protocol works with standard reagents and is independent from commercial kits, which often are very expensive. Applying this protocol can reduce the total cost of a reaction to an eighth of what it costs using some of the commercial kits. In this video we also comment on critical steps during the process and give detailed instructions on how to design the mutagenic primers.

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. Here we demonstrate an easy and cost effective way to introduce base substitutions into a plasmid using standard reagents.

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. With this method the cloned ...

High-throughput Purification of Affinity-tagged Recombinant Proteins

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.
In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates1-5.
Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex6-8. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase9-11. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase4. Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.
This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.

We describe a method for the affinity-tagged purification of recombinant proteins using liquid-handling robotics. This method is generally applicable to the small-scale purification of soluble His-tagged proteins in a high-throughput format.

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further ...

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging (ESI)

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in cell biology. Many phenomena cannot be explained by in vitro analysis in simplified systems and need additional structural information in situ, particularly in the range between 1 nm and 0.1 &#181;m, in order to be fully understood. Here, electron spectroscopic imaging, a transmission electron microscopy technique that allows simultaneous mapping of the distribution of proteins and nucleic acids, and an expression tag, miniSOG, are combined to study the structure and organization of DNA double-strand break repair foci.

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Electron spectroscopic imaging can image and distinguish nucleic acid from protein at nanometer resolution. It can be combined with the miniSOG system, which is able to specifically label tagged proteins in transmission electron microscopy samples. We illustrate the use of these technologies using double-strand break repair foci as an example.

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in ...

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

We present an approach for visualizing fluorescent protein DNA binding peptide (FP-DBP)-stained large DNA molecules tethered on the polyethylene glycol (PEG) and avidin-coated glass surface and stretched with microfluidic shear flows.

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating ...

Utilizing pHluorin-tagged Receptors to Monitor Subcellular Localization and Trafficking

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular organelles and those localized on the plasma membrane. Traditional fluorescence-based measurements lack the capability to distinguish membrane proteins residing in different organelles. Cutting edge methodologies transcend traditional methods by coupling pH-sensitive fluorophores with total internal reflection fluorescence microscopy (TIRFM). TIRF illumination excites the sample up to approximately 150 nm from the glass-sample interface, thus decreasing background, increasing the signal to noise ratio, and enhancing resolution. The excitation volume in TIRFM encompasses the plasma membrane and nearby organelles such as the peripheral ER. Superecliptic pHluorin (SEP) is a pH sensitive version of GFP. Genetically encoding SEP into the extracellular domain of a membrane protein of interest positions the fluorophore on the luminal side of the ER and in the extracellular region of the cell. SEP is fluorescent when the pH is greater than 6, but remains in an off state at lower pH values. Therefore, receptors tagged with SEP fluoresce when residing in the endoplasmic reticulum (ER) or upon insertion in the plasma membrane (PM) but not when confined to a trafficking vesicle or other organelles such as the Golgi. The extracellular pH can be adjusted to dictate the fluorescence of receptors on the plasma membrane. The difference in fluorescence between TIRF images at neutral and acidic extracellular pH for the same cell corresponds to a relative number of receptors on the plasma membrane. This allows a simultaneous measurement of intracellular and plasma membrane resident receptors. Single vesicle insertion events can also be measured when the extracellular pH is neutral, corresponding to a low pH trafficking vesicle fusing with the plasma membrane and transitioning into a fluorescent state. This versatile technique can be exploited to study localization, expression, and trafficking of membrane proteins.

Labeling the extracellular domain of a membrane protein with a pH sensitive fluorophore, superecliptic pHluorin (SEP), allows subcellular localization, expression, and trafficking to be determined. Imaging SEP-labeled proteins with total internal reflection fluorescence microscopy (TIRFM) enables the quantification of protein levels in the peripheral ER and plasma membrane.

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular ...

Visualization and Quantification of Mesenchymal Cell Adipogenic Differentiation Potential with a Lineage Specific Marker

Several dyes are currently available for use in detecting differentiation of mesenchymal cells into adipocytes. Dyes, such as Oil Red O, are cheap, easy to use and widely utilized by laboratories analyzing the adipogenic potential of mesenchymal cells. However, they are not specific to changes in gene transcription. We have developed a gene-specific differentiation assay to analyze when a mesenchymal cell has switched its fate to an adipogenic lineage. Immuno-labelling against fatty acid binding protein-4 (FABP4), a lineage-specific marker of adipogenic differentiation, enabled visualization and quantification of differentiated cells. The ability to quantify adipogenic differentiation potential of mesenchymal cells in a 96 well microplate format has promising implications for a number of applications. Hundreds of clinical trials involve the use of adult mesenchymal stromal cells and it is currently difficult to correlate therapeutic outcomes within and especially between such clinical trials. This simple high-throughput FABP4 assay provides a quantitative assay for assessing the differentiation potential of patient-derived cells and is a robust tool for comparing different isolation and expansion methods. This is particularly important given the increasing recognition of the heterogeneity of the cells being administered to patients in mesenchymal cell products. The assay also has potential utility in high throughput drug screening, particularly in obesity and pre-diabetes research.

Traditional methods of assessing adipogenic differentiation are cheap and easy to use, but are not specific to changes in gene expression. We have developed an assay to quantify mesenchymal cell differentiation into mature adipocytes using a lineage specific marker. This assay has diverse applications across basic research and clinical medicine.

Several dyes are currently available for use in detecting differentiation of mesenchymal cells into adipocytes. Dyes, such as Oil Red O, are cheap, easy ...

Noninvasive Monitoring of Lesion Size in a Heterologous Mouse Model of Endometriosis

Here, we describe a protocol for the implementation of a heterologous mouse model in which progression of endometriosis can be assessed in real time through noninvasive monitoring of fluorescence emitted by implanted ectopic human endometrial tissue. For this purpose, biopsies of human endometrium are obtained from donor women ongoing oocyte donation. Human endometrial fragments are cultured in the presence of adenoviruses engineered to express cDNA for the reporter fluorescent protein mCherry. Upon visualization, labeled tissues with an optimal rate of fluorescence after infection are subsequently chosen for the implantation in recipient mice. One week prior to the implantation surgery, recipient mice are oophorectomized, and estradiol pellets are placed subcutaneously to sustain the survival and growth of lesions. On the day of surgery mice are anesthetized, and peritoneal cavity accessed through a small (1.5 cm) incision by the linea-alba. Fluorescently labeled implants are tweezed, briefly soaked in glue and attached to the peritoneal layer. Incisions are sutured, and animals left to recover for a couple of days. Fluorescence emitted by endometriotic implants is usually non-invasively monitored every 3 days for 4 weeks with an in vivo imaging system. Variations in the size of endometriotic implants can be estimated in real time by quantification of the mCherry signal and normalization against the initial time-point showing maximal fluorescence intensity.
Traditional preclinical rodents of models of endometriosis do not allow non-invasive monitoring of lesion in real time but rather allow evaluation of the effects of drugs assayed at the end point. This protocol allows one to track lesions in real time and is more useful to explore the therapeutic potential of drugs in preclinical models of endometriosis. The main limitation of the model thus generated is that non-invasive monitoring is not possible over long periods of time due to the episomal expression of Ad-virus.

Here, we present a protocol for live-imaging of fluorescently labeled human endometrial fragments grafted in mice. The method allows studying the effects of drugs of choice on endometriotic lesion size through monitoring and quantification of fluorescence emitted by the fluorescent reporter on real time

Here, we describe a protocol for the implementation of a heterologous mouse model in which progression of endometriosis can be assessed in real time ...

Visualization of 3D White Adipose Tissue Structure Using Whole-mount Staining

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various techniques have been developed to study the morphology and biology of adipose tissue. However, conventional visualization methods are limited to studying the tissue in 2D sections, failing to capture the 3D architecture of the whole organ. Here we present whole-mount staining, an immunohistochemistry method that preserves intact adipose tissue morphology with minimal processing steps. Hence, the structures of adipocytes and other cellular components are maintained without distortion, achieving the most representative 3D visualization of the tissue. In addition, whole-mount staining can be combined with lineage tracing methods to determine cell fate decisions. However, this technique has some limitations to providing accurate information regarding deeper parts of adipose tissue. To overcome this limitation, whole-mount staining can be further combined with tissue clearing techniques to remove the opaqueness of tissue and allow for complete visualization of entire adipose tissue anatomy using light-sheet fluorescent microscopy. Therefore, a higher resolution and more accurate representation of adipose tissue structures can be captured with the combination of these techniques.

The focus of the present study is to demonstrate the whole-mount immunostaining and visualization technique as an ideal method for 3D imaging of adipose tissue architecture and cellular component.

Adipose tissue is an important metabolic organ with high plasticity and is responsive to environmental stimuli and nutrient status. As such, various ...

Application of Passive Head Motion to Generate Defined Accelerations at the Heads of Rodents

Exercise is widely recognized as effective for various diseases and physical disorders, including those related to brain dysfunction. However, molecular mechanisms behind the beneficial effects of exercise are poorly understood. Many physical workouts, particularly those classified as aerobic exercises such as jogging and walking, produce impulsive forces at the time of foot contact with the ground. Therefore, it was speculated that mechanical impact might be implicated in how exercise contributes to organismal homeostasis. For testing this hypothesis on the brain, a custom-designed ''passive head motion'' (hereafter referred to as PHM) system was developed that can generate vertical accelerations with controlled and defined magnitudes and modes and reproduce mechanical stimulation that might be applied to the heads of rodents during treadmill running at moderate velocities, a typical intervention to test the effects of exercise in animals. By using this system, it was demonstrated that PHM recapitulates the serotonin (5-hydroxytryptamine, hereafter referred to as 5-HT) receptor subtype 2A (5-HT2A) signaling in the prefrontal cortex (PFC) neurons of mice. This work provides detailed protocols for applying PHM and measuring its resultant mechanical accelerations at rodents' heads.

The present protocol describes a custom-designed ''passive head motion'' system, which reproduces mechanical accelerations at rodents' heads generated during their treadmill running at moderate velocities. It allows dissecting mechanical factors/elements from the beneficial effects of physical exercise.

Exercise is widely recognized as effective for various diseases and physical disorders, including those related to brain dysfunction. However, molecular ...