Helsinki University Library is thanked for the financial support in publishing.

spaNOTE: This protocol is based on an associated publication by Hilander et al.13 .
1. Preparation of buffers and solutions
NOTE: All the buffers and solutions used in the protocol are summarized in Table 1. The given volumes of the buffers are sufficient to prepare and run 10 samples. All the buffers can be stored at +4 &#176;C for up to one year.&#160;
<ol>
	<li>Prepare 20 mL of 3x gel buffer containing 1.5 M aminocaproic acid, 150 mM Bis-tris in distilled water (dH2O). Adjust pH to 7.0.</li>
	<li>Prepare 10 mL of 2 M aminocaproic acid in dH2O.</li>
	<li>Prepare 1 mL of the mitochondrial buffer by combining the following: 0.5 mL of 3x gel buffer, 0.5 mL of 2 M aminocaproic acid and 4 &#181;L of 500 mM EDTA.</li>
	<li>Prepare 1,000 mL of cathode buffer containing 15 mM of Bis-tris and 50 mM of tricine in dH2O. Adjust pH to 7.0.
	<ol>
		<li>Prepare 200 mL of blue cathode buffer by adding 0.04 g of Coomassie blue G-250 to 200 mL of cathode buffer.</li>
	</ol>
	</li>
	<li>Prepare 1,000 mL of anode buffer containing 50 mM Bis-tris in dH2O. Adjust pH to 7.0.</li>
	<li>Prepare 2.5 mL of sample buffer containing 750 mM aminocaproic acid and 5% Coomassie blue G-250 in dH2O.</li>
</ol>
2. Preparation of mitochondrial lysates
<ol>
	<li>Plate the cells the day before the collection. For HEK293 or 143B cells, use Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM) with 10% fetal bovine serum, 1% L-glutamine, 100 mg/mL penicillin and 100 mg/mL streptomycin. Grow the cells in a cell culture incubator at +37 &#176;C in a 5% CO2 humidified atmosphere. Ensure that there are at least 500,000 cells for each sample on the day of collection.</li>
	<li>Gently wash the cells once with ice-cold PBS. Avoid detaching the cells from the plate. Scrape the cells and pellet them at 800 x g for 10 min at +4 &#176;C.&#160;</li>
	<li>Wash the cell pellet twice with ice-cold PBS, and centrifuge as in step 2.2. Measure the protein concentration with the Bradford method using a commercial kit. Pellet the cells at 800 x g for 10 min at +4 &#176;C. 
	NOTE: After the cell collection, perform all steps at +4 &#176;C and do not vortex.&#160;</li>
	<li>Prepare 20 mL of PBS with protease inhibitor by adding 200 &#181;L of 100x protease inhibitor to 20 mL of PBS. Keep on ice. Resuspend the cells in PBS with protease inhibitor to a final protein concentration of 5 mg/mL.
	<ol>
		<li>To calculate the volume of PBS with protease inhibitor needed to resuspend the cells at 5 mg/mL, calculate the protein amount in each sample. For this calculation, use the protein concentration measured in step 2.3 and the volume of PBS used to resuspend the cells after washing in step 2.3.</li>
	</ol>
	</li>
	<li>Prepare 1 mL of 3.3 mM digitonin in PBS with protease inhibitor. Add 3.3 mM digitonin to a final concentration of 1.65 mM. Mix well and incubate on ice for 5 min.&#160;
	<ol>
		<li>To prepare 1 mL of 3.3 mM digitonin in PBS with protease inhibitor, dissolve 4 mg of digitonin in 1 mL of PBS at 100 &#176;C until no precipitate is visible and cool on ice immediately. Add 10 &#181;L of 100x protease inhibitor to 1 mL of digitonin solution. 
		NOTE: Use only a fresh solution of digitonin. 
		CAUTION: Digitonin is toxic! Use a face mask, gloves and a lab coat.</li>
	</ol>
	</li>
	<li>Add PBS with proteinase inhibitor (prepared in step 2.4) to the final volume of 1.5 mL. Centrifuge at 10,000 x g for 10 min at +4 &#176;C. Remove the supernatant. In this step, mitochondria are pelleted.&#160;</li>
	<li>Resuspend the mitochondrial pellet in mitochondrial buffer. The volume of mitochondrial buffer is half of the volume of PBS in step 2.4.</li>
	<li>Prepare fresh 10% lauryl maltoside in PBS containing protease inhibitor (prepared in step 2.4). 1 mL is sufficient for 10 samples. Add 10% lauryl maltoside to the final concentration of 1%. Incubate on ice for 15 min (this step can be longer up to a couple of hours).</li>
	<li>Centrifuge at 20,000 x g for 20 min at +4 &#176;C. Collect the supernatant into a new tube. Measure the protein concentration by the Bradford method using a kit. Add sample buffer, a volume that is half of the volume of lauryl maltoside used in step 2.8. Samples can be stored at -80 &#176;C for up to 6 months.</li>
</ol>
3. Preparation of gradient gel for BN-PAGE
<ol>
	<li>Pour the gradient gel for BN-PAGE at room temperature. Place the gradient maker on a stir plate and connect it with flexible tubing to the peristaltic pump. Attach an infusion set with the needle to the tubing. Place a magnetic stirrer into the proximal chamber of&#160;the gradient maker. Wash the tubing with dH2O at maximum pump speed for 10 min.</li>
	<li>Empty the tubing and the gradient maker. Use a pipet to remove any leftover dH2O in the channel between chambers of the gradient maker. Close the channel and tubing with the valve.</li>
	<li>Using casting frame and clamps assemble two glass plates in the holder, which has a hole on the bottom, and place it on the stand. Make sure that it is more or less on a straight surface with a water balance. Place the needle connected to the tubing between the glass plates.&#160;</li>
	<li>Prepare 6% and 15% gel solutions (Table 2). Keep on ice. Add ammonium persulphate (APS) and tetramethylenediamine&#160;(TEMED) (they start polymerization) last. Mix gently to avoid making air bubbles.</li>
	<li>Load the proximal end of the gradient-gel-mixer tubing chamber with 6% gel and the distal end with 15% gel. The total volume of the gel should be equal to the volume of the separating gel between the glass plates. Thus, use 2.6 mL of 6% gel and 2.1 mL of 15% gel to the gradient gel mixer for one 8.3 cm x 7.3 cm sized gel.</li>
	<li>Switch on the magnetic stirrer, and open the tubing and channel between chambers of the gradient maker. Immediately switch on the peristaltic pump to 5 mL/min. Fill the glass plates, and do not allow bubbles to enter the gel. Remove the needle when there is no gel in the tubing.</li>
	<li>Gently overlay the gel with dH2O. Keep the gel at room temperature for at least 1 h for polymerization.</li>
	<li>Immediately after pouring the gel, wash the tubing by filling the gradient chambers with dH2O and using the peristaltic pump at maximal speed. When preparing two and more gels, always clean the system in between.</li>
	<li>Prepare 1x gel buffer by mixing 3 mL of 3x gel buffer and add 6 mL of dH2O. Remove dH2O from the surface of the gel with filter paper gently. Wash the surface of the gel with 1x gel buffer. Remove 1x gel buffer with filter paper gently.
	<ol>
		<li>Avoid fibers from the filter paper on the gel. To ensure this, cut the paper to small pieces with scissors, but do not tear the paper.</li>
	</ol>
	</li>
	<li>Place the comb between the glass plates, but do not immerse it fully to be able to pour the stacking gel under the comb. Prepare the 4% stacking gel (Table 2). Add APS and TEMED last as they start polymerization easily. Mix gently avoiding air bubbles.</li>
	<li>Overlay the stacking gel, avoiding bubbles under the comb, and immerse the comb fully. Let the stacking gel polymerize for at least 30 min. Remove the comb and wash the wells with 1x gel buffer using a pipet.
	<ol>
		<li>After polymerization, the gel can be stored at +4 &#176;C for a couple of days. To store the gel, wrap the gel in paper soaked with dH2O and plastic film to prevent drying of the gel.</li>
	</ol>
	</li>
</ol>
4. Blue native gel electrophoresis
NOTE: To prevent degradation of OXPHOS complexes run electrophoresis at +4 &#176;C. Use pre-chilled buffers.&#160;
<ol>
	<li>Load the gel cassette with the blue cathode buffer until the bottom of the wells. Loading of the samples is easier when the cassette is not filled to the top. Wash the wells with the blue cathode buffer and then fill the wells with the blue cathode buffer using pipet.</li>
	<li>Load the samples (5-30 &#181;g of protein) into wells. Gently fill the gel cassette to the top with the blue cathode buffer and the tank with anode buffer.</li>
	<li>Run the gel for 15 min at a constant voltage of 40 V. Then increase the voltage to 80 V (or use a constant current of 6 mA), do not exceed 10 mA. Run the gel until the dye reaches 2/3 of the gel length.</li>
	<li>Replace the blue cathode buffer with cathode buffer and continue electrophoresis until the dye front has run out. In total, electrophoresis takes about 3 hours.</li>
	<li>Retrieve the glass plates and transfer the proteins to the polyvinylidene fluoride (PVDF) membrane by semi-dry blotting. Use a constant voltage of 25 V and a current limited to 1.0 A for 30 min.
	<ol>
		<li>Alternatively, use wet blotting to transfer the OXPHOS complexes to a PVDF membrane.&#160;</li>
	</ol>
	</li>
	<li>Continue with blocking of the membrane and antibody incubation according to the standard immunoblotting protocol. Use the primary antibodies against subunits of OXPHOS complexes sequentially.&#160; 
	NOTE: For example, use anti-NDUFA9 antibody (1:2000) for complex I, anti-SDHA antibody (1:2000) for complex II, anti-UQCRC2 antibody (1:1000) for complex III, anti-COX1 antibody (1:2000) for complex IV and anti-ATP5A antibody (1:2000) for complex V. The list of the antibodies is presented in the Table of Materials.</li>
</ol>

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Y., Blum, A., Liu, J., Finkel, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+mitochondria+in+aging.">The role of mitochondria in aging.</a> The Journal of Clinical Investigation. 128 (9), 3662-3670 (2018).</li><li>Nunnari, J., Suomalainen, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria:+in+sickness+and+in+health.">Mitochondria: in sickness and in health.</a> Cell. 148 (6), 1145-1159 (2012).</li><li>Cogliati, S., Lorenzi, I., Rigoni, G., Caicci, F., Soriano, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+Mitochondrial+Electron+Transport+Chain+Assembly.">Regulation of Mitochondrial Electron Transport Chain Assembly.</a> Journal of Molecular Biology. , (2018).</li><li>Fernandez-Vizarra, E., Tiranti, V., Zeviani, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+of+the+oxidative+phosphorylation+system+in+humans:+what+we+have+learned+by+studying+its+defects.">Assembly of the oxidative phosphorylation system in humans: what we have learned by studying its defects.</a> Biochimica et Biophysica Acta. 1793 (1), 200-211 (2009).</li><li>Signes, A., Fernandez-Vizarra, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+of+mammalian+oxidative+phosphorylation+complexes+I-V+and+supercomplexes.">Assembly of mammalian oxidative phosphorylation complexes I-V and supercomplexes.</a> Essays in Biochemistry. 62 (3), 255-270 (2018).</li><li>Schagger, H., von Jagow, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blue+native+electrophoresis+for+isolation+of+membrane+protein+complexes+in+enzymatically+active+form.">Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form.</a> Analytical Biochemistry. 199 (2), 223-231 (1991).</li><li>Wittig, I., Braun, H. P., Schagger, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blue+native+PAGE.">Blue native PAGE.</a> Nature Protocols. 1 (1), 418-428 (2006).</li><li>Gotz, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exome+sequencing+identifies+mitochondrial+alanyl-tRNA+synthetase+mutations+in+infantile+mitochondrial+cardiomyopathy.">Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy.</a> American Journal of Human Genetics. 88 (5), 635-642 (2011).</li><li>Wittig, I., Schagger, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advantages+and+limitations+of+clear-native+PAGE.">Advantages and limitations of clear-native PAGE.</a> Proteomics. 5 (17), 4338-4346 (2005).</li><li>Luo, X., Wu, J., Jin, Z., Yan, L. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-Gradient+Blue+Native+Polyacrylamide+Gel+Electrophoresis.">Non-Gradient Blue Native Polyacrylamide Gel Electrophoresis.</a> Current Protocols in Protein Science. 87, 19.29.1-19.29.12 (2017).</li><li>Jha, P., Wang, X., Auwerx, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+Mitochondrial+Respiratory+Chain+Supercomplexes+Using+Blue+Native+Polyacrylamide+Gel+Electrophoresis+(BN-PAGE).">Analysis of Mitochondrial Respiratory Chain Supercomplexes Using Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE).</a> Current Protocols in Mouse Biology. 6 (1), 1-14 (2016).</li><li>Preston, C. .. C., 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=Aging-induced+alterations+in+gene+transcripts+and+functional+activity+of+mitochondrial+oxidative+phosphorylation+complexes+in+the+heart.">Aging-induced alterations in gene transcripts and functional activity of mitochondrial oxidative phosphorylation complexes in the heart.</a> Mechanisms of Ageing and Development. 129 (6), 304-312 (2008).</li><li>Hilander, T., Konovalova, S., Terzioglu, M., Tyynismaa, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+Mitochondrial+Protein+Synthesis:+De+Novo+Translation,+Steady-State+Levels,+and+Assembled+OXPHOS+Complexes.">Analysis of Mitochondrial Protein Synthesis: De Novo Translation, Steady-State Levels, and Assembled OXPHOS Complexes.</a> Current Protocols In Toxicology. , e56 (2018).</li><li>Lobo-Jarne, T., Ugalde, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Respiratory+chain+supercomplexes:+Structures,+function+and+biogenesis.">Respiratory chain supercomplexes: Structures, function and biogenesis.</a> Seminars in Cell &amp; Developmental Biology. 76, 179-190 (2018).</li><li>Fiala, G., Schamel, W. W., Blumenthal, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blue+native+polyacrylamide+gel+electrophoresis+(BN-PAGE)+for+analysis+of+multiprotein+complexes+from+cellular+lysates.">Blue native polyacrylamide gel electrophoresis (BN-PAGE) for analysis of multiprotein complexes from cellular lysates.</a> Journal of Visualized Experiments. (48), (2011).</li><li>Itahana, K., Clegg, H. V., Zhang, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ARF+in+the+mitochondria:+the+last+frontier?.">ARF in the mitochondria: the last frontier?.</a> Cell Cycle (Georgetown, Tex). 7 (23), 3641-3646 (2008).</li><li>Wittig, I., Beckhaus, T., Wumaier, Z., Karas, M., Schagger, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+estimation+of+native+proteins+by+blue+native+electrophoresis:+principles+and+practical+hints.">Mass estimation of native proteins by blue native electrophoresis: principles and practical hints.</a> Molecular &amp; Cellular Proteomics. 9 (10), (2010).</li><li>Konovalova, S., 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=Redox+regulation+of+GRPEL2+nucleotide+exchange+factor+for+mitochondrial+HSP70+chaperone.">Redox regulation of GRPEL2 nucleotide exchange factor for mitochondrial HSP70 chaperone.</a> Redox Biology. 19, 37-45 (2018).</li><li>Konovalova, S., 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=Exposure+to+arginine+analog+canavanine+induces+aberrant+mitochondrial+translation+products,+mitoribosome+stalling,+and+instability+of+the+mitochondrial+proteome.">Exposure to arginine analog canavanine induces aberrant mitochondrial translation products, mitoribosome stalling, and instability of the mitochondrial proteome.</a> The International Journal of Biochemistry &amp; Cell Biology. 65, 268-274 (2015).</li><li>Ahmed, S. T., 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=Using+a+quantitative+quadruple+immunofluorescent+assay+to+diagnose+isolated+mitochondrial+Complex+I+deficiency.">Using a quantitative quadruple immunofluorescent assay to diagnose isolated mitochondrial Complex I deficiency.</a> Scientific Reports. 7 (1), (2017).</li></ol>

No conflicts of interest declared.

One of the most critical parts of the protocol is to preserve intact OXPHOS complexes during sample preparation, storage and gel electrophoresis. Thus, mitochondria should be isolated at +4 &#176;C and the samples should not undergo freeze-thaw cycles. OXPHOS complexes can only tolerate one freeze-thaw cycle during the whole procedure. Multiple freeze-thaw cycles destroy OXPHOS complexes (Figure 1B). Control and experimental samples that are to be compared should be prepared in parallel to avoid any differences in storage conditions, which might give misleading results. If it is not possible to perform all the steps of the protocol in parallel with all the samples, we recommend to freeze washed cell pellets at -80 &#176;C (step 1.4 in this protocol) and later carry out the rest of the protocol for all the samples together at least until gel electrophoresis. Special attention should be paid to the cleanliness of the electrophoresis apparatus (tank, cassette). If the same apparatus is used for SDS-PAGE, wash it very well before BN-PAGE. Any residual SDS can cause dissociation of the OXPHOS complexes during electrophoresis.
High-quality gradient gels are another critical part of the protocol. Precast gels for blue native PAGE are commercially available; however, it is not recommended to use them, since the buffers used for commercial gels might have a composition, which is different from the sample buffers. The gradient of the gel used here (6-15%) is optimal for separation of individual OXPHOS complexes. To detect higher-order supramolecular structures of OXPHOS, also known as respiratory chain supercomplexes14, some optimization is required11.
For the visualization of OXPHOS complexes use the specific antibodies sequentially, based on their properties. For example, use first the antibody that gives the weakest signal and the antibody with the strongest signal last. This is important since the stripping weakens the detection (Figure 1D). The composition of respiratory chain complexes can be investigated if after BN-PAGE the gel is subjected to the second dimension SDS-PAGE15.
The protocol described here suggests using antibodies against individual OXPHOS complexes sequentially. However, the commercially available OXPHOS antibody cocktail can be used to detect all five OXPHOS complexes simultaneously. Nevertheless, to be able to detect incompletely assembled OXPHOS complexes and define their identity, antibodies against individual OXPHOS complexes should be used sequentially. This step is time-consuming; however, it can be essential for testing new experimental conditions and models.&#160;
The concentration of digitonin used for mitochondrial isolation should be optimized for the specific cell type. As a detergent, digitonin permeabilizes cell membranes. The optimal concentration of digitonin efficiently permeabilizes the plasma membrane of the cells leaving the mitochondrial membranes intact. Too low&#160;concentration of digitonin causes high contamination of the mitochondrial extracts while too high&#160;concentration damages the mitochondrial membranes and reduces the total mitochondrial yield. The optimal digitonin/protein ratio (g/g) varies from 0.3 to 1. Western blot analysis of proteins extracted from pellets and supernatants can be used to test the optimal concentration of digitonin16.
This protocol does not include protein loading control on the immunoblot; therefore, the protein concentration of extracted complexes should be carefully measured at least in triplicates to ensure equal loading. In addition, the samples can be run in BN-PAGE in replicates. If the assembly of selective OXPHOS complexes is impaired, unaffected complexes can serve as loading controls.
The estimation of the molecular mass of the protein complexes in the BN-PAGE is challenging18. The current protocol does not include the molecular weight marker; therefore, to estimate the assembly of the OXPHOS complexes, the control samples containing unaffected complexes should always be included in the analysis. The control samples for BN-PAGE are usually untreated or wild type cells.&#160;
The method presented here is optimized for the detection of mitochondrial respiratory chain complexes; however, it can also be applied for the evaluation of oligomerization of mitochondrial proteins19. In addition, the assembly rate of OXPHOS complexes can be studied by first depleting mitochondrial-encoded subunit containing complexes by chloramphenicol and then following their recovery after removal of chloramphenicol10. Thus, BN-PAGE can be used to evaluate steady-state levels and assembly of OXPHOS for different applications including molecular diagnostics of human mitochondrial disorders9,11.

Mitochondria are multifunctional organelles playing an important role in energy production, regulation of cellular metabolism, signaling, apoptosis, aging, etc.1,2,3. The energy production in mitochondria relies on the oxidative phosphorylation function that couples respiration with ATP synthesis. In human cells, the mitochondrial oxidative phosphorylation system (OXPHOS) is composed of five complexes. Complexes I-IV create an electrochemical proton gradient in the mitochondrial intermembrane space that is used by complex V to produce ATP. Each OXPHOS complex is multimeric and, except complex II, composed of the subunits encoded by both nuclear and mitochondrial genes. Any defects in the core components of the OXPHOS complexes caused by mutations or environmental stress can perturb the assembly and functionality of the oxidative phosphorylation system. In addition, the proper assembly of functional OXPHOS complexes requires a large number of assembly factors4,5,6.&#160;
Blue native polyacrylamide gel electrophoresis (BN-PAGE) is a fundamental technique enabling analysis of intact protein complexes and can be used to study the assembly of OXPHOS complexes. First, mitochondria are isolated from the cells by digitonin, which is a mild detergent that permeabilizes the plasma membrane of the cells. Then, by using lauryl maltoside, OXPHOS complexes are released from the mitochondrial membranes. By using gradient gel electrophoresis, the OXPHOS complexes are separated according to their mass. Coomassie blue G-250 (not R-250) added to the sample buffer and the blue cathode buffer dissociates detergent-labile associations but preserves individual respiratory chain complexes intact8. During the electrophoresis, the blue cathode buffer containing dye is replaced by the cathode buffer without dye, which ensures efficient transfer of OXPHOS complexes to the PVDF membrane8. To visualize OXPHOS complexes, the PVDF membrane is sequentially incubated with antibodies corresponding to the selected subunits of the five OXPHOS complexes.
The method described here with some modifications can be applied to any cultured cells. In addition, this method can be used for analysis of OXPHOS complexes in mitochondria isolated from tissue samples9. BN-PAGE requires at least 5-10 &#181;g of mitochondria for each sample per run. Using the method described here, 500,000 cultured cells such as HEK293, SH-SY5Y or 143B cells can yield approximately 10 &#181;g of mitochondria. However, a sufficient amount of the cells for the BN analysis depends on the specific cell type.
The most common method to study mitochondrial OXPHOS proteins is SDS-PAGE and western blotting. However, SDS-PAGE allows studying only individual OXPHOS subunits and, in contrast to BN-PAGE, cannot be used to evaluate the assembly of entire OXPHOS complexes. Clear native-PAGE separates protein complexes in native conditions without the presence of negatively charged dye and has a significantly lower resolution compared to BN-PAGE. However, clear native-PAGE is milder than BN-PAGE so it can retain labile supramolecular assemblies of protein complexes such as OXPHOS supercomplexes that are dissociated under the BN-PAGE conditions10. In this protocol, the gradient gel is used to separate complexes; however, alternatively, non-gradient separation can be used if the relatively expensive gradient maker is not available11.&#160;
Important, the method described here allows analyzing the assembly of OXPHOS complexes, while the functionality of the complexes is not assessed. A high-resolution BN-PAGE followed by in-gel activity assay11 as well as spectrophotometric enzymatic activity assay of the mitochondrial complexes12 are efficient techniques for the functional analysis of the OXPHOS complexes. However, both of these methods do not assay the assembly of OXPHOS complexes.
Thus, BN-PAGE is the optimal method to investigate the assembly of individual OXPHOS complexes. For example, some mitochondrial disorders, such as Leber hereditary optic neuropathy (LHON), mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS), are associated with altered assembly of one or more components of the OXPHOS system5. By using the BN-PAGE method described here, the molecular mechanisms of mitochondrial diseases can be studied.&#160;

<table border="0" cellpadding="0" cellspacing="0" style="width:693px;" width="693">
	<tbody>
		<tr height="19">
			<td height="19" style="height:19px;width:316px;">100 mm cell plates</td>
			<td style="width:97px;">Thermo Fisher Scientific</td>
			<td style="width:111px;">130182</td>
			<td style="width:169px;"></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">40% Acrylamide/Bis 37.5:1</td>
			<td>Bio-Rad</td>
			<td>161-0148</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Aminocaproic acid</td>
			<td>Sigma</td>
			<td>A2504</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Ammonium persulfate</td>
			<td>Sigma</td>
			<td>A3678</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Anti-ATP5A</td>
			<td>Abcam</td>
			<td>14748</td>
			<td>Complex V subunit</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Anti-MTCOI</td>
			<td>Abcam</td>
			<td>14705</td>
			<td>Complex VI subunit</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Anti-NDUFA9</td>
			<td>Abcam</td>
			<td>14713</td>
			<td>Complex I subunit</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Anti-SDHA</td>
			<td>Abcam</td>
			<td>14715</td>
			<td>Complex II subunit</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Anti-UQCRC2</td>
			<td>Abcam</td>
			<td>14745</td>
			<td>Complex III subunit</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Bis-tris</td>
			<td>Sigma</td>
			<td>B7535</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Bradford protein assay kit</td>
			<td>BioRad</td>
			<td>5000006</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Cell scrapers</td>
			<td>Fisher</td>
			<td>11597692</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Coomassie blue G250 (Serva Blue G)</td>
			<td>Serva</td>
			<td>35050</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Digitonin</td>
			<td>Sigma</td>
			<td>D141</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">DMEM</td>
			<td>Lonza</td>
			<td>12-614F/12</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">EDTA</td>
			<td>Life Technologies</td>
			<td>15575-038</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">FBS</td>
			<td>Life Technologies</td>
			<td>10270106</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Fetal bovine serum</td>
			<td>Life Technologies</td>
			<td>10270106</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Glycerol</td>
			<td>(Sigma</td>
			<td>G5516</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Gradient maker</td>
			<td>Bio-Rad</td>
			<td>1654120</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Lauryl maltoside (n-Dodecyl &#946;-D-maltoside)</td>
			<td>Sigma</td>
			<td>D4641</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">L-glutamine</td>
			<td>Life Technologies</td>
			<td>25030024</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">L-glutamine</td>
			<td>Gibco</td>
			<td>25030</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">N,N,N&#8242;,N&#8242;-Tetramethylethylenediamine (TEMED)</td>
			<td>Sigma</td>
			<td>T9281</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">PBS</td>
			<td>Life Technologies</td>
			<td>BE17-516F</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Penicillin/Streptomycin</td>
			<td>Lonza</td>
			<td>17-602E</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Penicillin/streptomycin</td>
			<td>Gibco</td>
			<td>15140</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Power supply</td>
			<td>GE Healthcare&#160;</td>
			<td>EPS 301</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Protease inhibitors</td>
			<td>Thermo Scientific</td>
			<td>10137963</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Trans-blot turbo mini PVDF</td>
			<td>BioRad</td>
			<td>1704156</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Tricine</td>
			<td>Sigma</td>
			<td>T9784</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Trypsin-EDTA</td>
			<td>Gibco</td>
			<td>15400054</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Vertical electrophoresis apparatus</td>
			<td>BioRad</td>
			<td>1658004</td>
			<td></td>
		</tr>
	</tbody>
</table>

analysis of mitochondrial respiratory chain complexes in cultured human cells using blue native polyacrylamide gel electrophoresis and immunoblotting

Mitochondrial respiration is performed by oxidative phosphorylation (OXPHOS) complexes within mitochondria. Internal and environmental factors can perturb the assembly and stability of OXPHOS complexes. This protocol describes the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis (BN-PAGE) in application to cultured human cells. First, mitochondria are extracted from the cells using digitonin, then using lauryl maltoside, the intact OXPHOS complexes are isolated from the mitochondrial membranes. The OXPHOS complexes are then resolved by gradient gel electrophoresis in the presence of the negatively charged dye, Coomassie blue, which prevents protein aggregation and ensures electrophoretic mobility of protein complexes towards the cathode. Finally, the OXPHOS complexes are detected by standard immunoblotting. Thus, BN-PAGE is a convenient and inexpensive technique that can be used to evaluate the assembly of entire OXPHOS complexes, in contrast to the basic SDS-PAGE allowing the study of only individual OXPHOS complex subunits.

Using BN-PAGE, defects in the assembly of mitochondrial OXPHOS complexes can be investigated. Figure 1A shows the assembly of respiratory chain complexes in human neuroblastoma cells (SH-SY5Y) treated with chloramphenicol, which specifically inhibits translation of mtDNA-encoded OXPHOS subunits. Chloramphenicol depleted the OXPHOS complexes that contained mitochondrially-encoded subunits (complex I, III, IV; Figure 1A), while complex II, which is exclusively encoded by nuclear genes, was compensatorily upregulated. Complex V was not immunoblotted here.
Multiple freeze-thaw cycles destroy OXPHOS complexes. Figure 1B demonstrates the degradation of OXPHOS complexes by the freeze-thaw cycles. Mitochondrial respiratory complexes in sample 3 that have undergone multiple freeze-thaw cycles have a lower band intensity and are shifted in comparison to the same samples, which were frozen only once. An uncropped western blot image of Figure 1B is shown in Supplementary Figure 1.
The quality of the gel is important for sharp and clear bands. Figure 1C shows an immunoblot from a gel that did not polymerize well. Stripping of the membrane also can affect the detection of OXPHOS complexes. In Figure 1D, complex I was detected before or after stripping. The signal to noise ratio is much lower after stripping.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/59269/59269fig1.jpg" /> 
Figure 1. BN-PAGE immunoblots from successful and sub-optimal experiments.&#160;(A) Depletion of OXPHOS complexes by inhibitor of mitochondrial translation. Human neuroblastoma cells (SH-SY5Y) were treated with chloramphenicol (CAP) for 48 hours. CTRL, control cells without chloramphenicol treatment. The lower panel shows the quantification of the immunoblot. The value of the control is taken as 1 (shown as a dashed line). Data are presented as mean &#177; SD, n = 3, *P &#60; 0.0001 as compared to control using unpaired Student&#8217;s t-tests. (B) Disruption of OXPHOS complexes by multiple freeze-thaw cycles. Samples 1-3 were prepared from human osteosarcoma cells (143B) in the same conditions. Samples number 1 and 2 were frozen and melted only once, while the sample number 3 underwent four freeze-thaw cycles. (C) BN-PAGE immunoblots of OXPHOS complexes isolated from HEK293 cells. The smearing of the bands is caused by low quality of the gel. (D) Effect of stripping on the detection of OXPHOS complexes. Detection of Complex I in human neuroblastoma cells (SH-SY5Y) before and after stripping of the same membrane. OXPHOS complexes were detected using anti-NDUFA9 antibody (complex I), anti-SDHA antibody (complex II), anti-UQCRC2 antibody (complex III) and anti-COX1 antibody (complex IV). <a href="https://www.jove.com/files/ftp_upload/59269/59269fig1large.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>Buffer or solution</td>
			<td>Composition</td>
			<td>Recipe</td>
		</tr>
		<tr>
			<td rowspan="4">3 x gel buffer</td>
			<td>1.5 M aminocaproic acid</td>
			<td>3.94 g of aminocaproic acid</td>
		</tr>
		<tr>
			<td>150 mM Bis-tris</td>
			<td>0.63 g of Bis-tris</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>Add dH2O to 20 mL</td>
		</tr>
		<tr>
			<td>pH 7.0</td>
			<td>Adjust pH to 7.0</td>
		</tr>
		<tr>
			<td rowspan="4">Cathode buffer</td>
			<td>15 mM Bis-tris</td>
			<td>3.14 g of Bis-tris</td>
		</tr>
		<tr>
			<td>50 mM tricine</td>
			<td>8.96 g of tricine</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>Add dH2O to 1000 mL</td>
		</tr>
		<tr>
			<td>pH 7.0</td>
			<td>Adjust pH to 7.0</td>
		</tr>
		<tr>
			<td rowspan="5">Blue cathode buffer</td>
			<td>0.02% coomassie blue G</td>
			<td>0.04 g of Serva blue G</td>
		</tr>
		<tr>
			<td>15 mM Bis-tris</td>
			<td rowspan="4">200 mL of Cathode buffer</td>
		</tr>
		<tr>
			<td>50 mM tricine</td>
		</tr>
		<tr>
			<td>dH2O</td>
		</tr>
		<tr>
			<td>pH 7.0</td>
		</tr>
		<tr>
			<td rowspan="3">Anode buffer</td>
			<td>50 mM Bis-tris</td>
			<td>20.93 g</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>Add dH2O to 2000 mL</td>
		</tr>
		<tr>
			<td>pH 7.0</td>
			<td>Adjust pH to 7.0</td>
		</tr>
		<tr>
			<td rowspan="5">Mitochondrial buffer</td>
			<td>1.75 M aminocaproic acid</td>
			<td>0.5 mL of 3 x gel buffer</td>
		</tr>
		<tr>
			<td>75 mM Bis-tris</td>
			<td>0.5 mL of 2 M aminocaproic acid</td>
		</tr>
		<tr>
			<td>2 mM EDTA</td>
			<td>4 &#181;L of 500 mM EDTA</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>&#160;-</td>
		</tr>
		<tr>
			<td>pH 7.0</td>
			<td>&#160;-</td>
		</tr>
		<tr>
			<td rowspan="3">Sample buffer</td>
			<td>750 mM aminocaproic acid</td>
			<td>0.94 mL of 2 M aminocaproic acid</td>
		</tr>
		<tr>
			<td>5% comassie blue G</td>
			<td>0.125 g of Serva blue G</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>Add dH2O to 2.5 mL</td>
		</tr>
		<tr>
			<td rowspan="2">2M aminocaproic acid</td>
			<td>2 M aminocaproic acid</td>
			<td>2.62 g of aminocaproic acid</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>Add dH2O to 10 mL</td>
		</tr>
	</tbody>
</table>
Table 1. Buffers and solutions used for BN-PAGE.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Blue native gels</td>
			<td>Separating 6% gel</td>
			<td>Separating 15% gel</td>
			<td>Stacking 4% gel</td>
		</tr>
		<tr>
			<td>3 x gel buffer</td>
			<td>3.3 mL&#160;</td>
			<td>3.3 mL</td>
			<td>1.64 mL</td>
		</tr>
		<tr>
			<td>40% Acrylamide/Bis 37.5:1</td>
			<td>1.5 mL</td>
			<td>3.75 mL</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td>dH2O</td>
			<td>5.14 mL</td>
			<td>0.93 mL</td>
			<td>2.77 mL</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>0</td>
			<td>2 mL</td>
			<td>0</td>
		</tr>
		<tr>
			<td>10% Ammonium persulfate*</td>
			<td>60 &#181;L</td>
			<td>10 &#181;L&#160;</td>
			<td>60 &#181;L</td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>4 &#181;L</td>
			<td>2 &#181;L</td>
			<td>6 &#181;L</td>
		</tr>
		<tr>
			<td>Total volume</td>
			<td>10 mL</td>
			<td>10 mL</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td colspan="4">*Make always fresh 10% ammonium persulfate in dH2O</td>
		</tr>
	</tbody>
</table>
Table 2. Recipes of gel for BN-PAGE.
Supplementary Figure 1. Uncropped western blot image of Figure 1B. <a href="https://www.jove.com/files/ftp_upload/59269/Supplementary_figure_1.eps" target="_blank">Please click here to download this figure.</a>

Watch this Scientific Journal Video about Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting at JoVE.

Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting

This protocol demonstrates the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis. Here the method applied to cultured human cells is described.

Mitochondrial respiration is performed by oxidative phosphorylation (OXPHOS) complexes within mitochondria. Internal and environmental factors can perturb ...

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15.7K Views.  University of Helsinki. This protocol demonstrates the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis. Here the method applied to cultured human cells is described.

Video: Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting

Denaturing Gradient Gel Electrophoresis (DGGE)

Denaturing Gradient Gel Electrophoresis DGGE

Okay.Hi, my name is Celeste Peterson and I'm a fellow at Harvard University studying microbial bio film communities. So I am profiling the bacterial communities by looking at their 60 N sequence and how this sequence changes over time in space. And to do that, I'm using DDGE.This is not a normal acry of my well, it needs to be kept at 60 degrees when it's run and the buffer needs to be pumped continuously. So we're gonna warm up the buffer for about an hour until it's at 60 degrees, and then we can run the towel. Now I'm gonna wash this plate with dilute uc solution, peeling around for impurities, andone, light that up.Anything like that can cause regularities. It is important to wipe off all the water. So when I assemble the gel, I'll put that chip on the outside of the gel.So the gel will be in between these two pieces of glass and the chip will be on the outside and it won't affect the gel in between. So now I'm gonna assemble the gel in these clamps and then I squeeze them together and tighten by turning to the right. As with any gel, it's important to make sure that the bottom is flush.To prevent making, we now turn the gel around and put it in here to get sealed with the gasket. So it's important when you do this that the gel, that the plates are actually lined up with the gasket here. So these knobs on the side then go in and you press down to type the seal.So this is a 30 mil syringe. And this part and this part come with the bio red kit and it just on like this. And that's just to get rid of the excess water in the tubes.So put the tubing onto the gel to load the gel. First you put an adapter into the tubing and then a needle look with that small adapter and put it right in the center of the gel just so it's fairly below the bottom glass. Then this wire adapter goes into the long tubing and it's going to connect to equal syringes containing the high and the low density solution.So these are pre-prepared solutions. The blue one, I've added a dye here that just indicates that this is the most denaturing solution and this is the least fitting train solution, the low density one. And they have everything in them.And now I'm gonna to make, gonna be Actually I twice as much the week. And once you've got the tempt, you have about five to seven minutes to fill the gel before the colon rises. And now we fill the syringe juice with the solution.So I'm gonna fill it with about 15 the solution. And then to get rid of any air bubbles, I'll turn it upside down and squeeze gently until that top air bubble is gone. Now this little screw here is gonna go into this groove.This adapter is gonna line up with this clamp here, and it's gonna get C clamped in very tightly. And then this tubing is gonna attach to the syringe. And the same thing is done on the other side with the high density matrix where it's time to deliver.And so I'm gonna be turning this wheel in a steady clockwise motion. And first the blue solution is gonna go out first because that's the the most in nature, and it's gonna form the bottom part of the gel. And then after a little while, the clear solution will start filling in the gel and the Gradient will be formed.One moment is the gently on an angle to And as soon as you finish pouring the gel to wash out your tubes immediately because they will polymerize Going, It's the group there. And then press down. So this little, And on the other side, I'll do the same thing.Okay.Hi, my name is Celeste Peterson and I'm a fellow at Harvard University studying microbial bio communities. So I am profiling the bacterial communities by looking at their 60 F sequence and how the sequence changes over time in space. And to do that, I'm using DDGE.So DGE is Dena gel electrophoresis. And basically the idea is that there's a gradient and the DNA, as it runs down the gradient gets de natured. And so different 16 species will stop at different points along the gradient.And so it ends up being a fingerprint of the different sexiness species in the community. So the goal of my experiment is to see who is in the community and how that's changing over time and space. And I can run the sexiness DDD gel and then I can cut out the bands and identify the species that are represented in each community.So one of the biggest issues when, when doing A DDG gel is to figure out the gradient that's the best. And so that is just something that needs to be played around with and figuring out for a particular community which type of gradient. So the one I'm using today is 35 to 55%urea.One of the big problems that can happen with this technique is that smears come up in in the leans. And I found for that, for whatever reason, one of the best things to do is to run the gels for a really long time and then the smears disappear. Well, today I'm just using it for general bacterial communities, but this can also be used for a specific family of bacteria to see how those change over time, and those tend to be very clean gels.You can also look at mutations in single genes with DDGE.

Probing for Mitochondrial Complex Activity in Human Embryonic Stem Cells

Mitochondria are cytoplasmic organelles that have a primary role in cellular metabolism and homeostasis, regulation of the cell signaling network, and programmed cell death. Mitochondria produce ATP, regulate the cytoplasmic redox state and Ca2+ balance, catabolize fatty acids, synthesize heme, nucleotides, steroid hormones, amino acids, and help assemble iron-sulfur clusters in proteins. Mitochondria also have an essential role in heat production. Mutations of the mitochondrial genome cause several types of human disorder. The accumulation of mtDNA mutations correlates with aging and is suspected to have an important role in the development of cancer. Due to their vitally important role in all cell types, the function of mitochondria must also be critical for stem cells. Key advances have been made in our understanding of stem cell viability, proliferation, and differentiation capacity. But the functional activity of stem cells, in particular their energy status, was not yet been studied in detail. Almost nothing is known about the mitochondrial properties of human embryonic stem cells (hESCs) and their differentiated precursor progeny. One way to understand and evaluate the role of mitochondria in hESC function and developmental potential is to directly measure the activity of mitochondrial respiratory complexes. Here, we describe high resolution clear native gel electrophoresis and subsequent in gel activity visualization as a method for analyzing the five respiratory chain complexes of hESCs.

In this video, we will show you how the mitochondrial respiratory chain complexes of human embryonic stem cells can be analyzed using in gel activity assays.

Mitochondria are cytoplasmic organelles that have a primary role in cellular metabolism and homeostasis, regulation of the cell signaling network, and ...

Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their separation in a polyacrylamide gel matrix based on the molecular weight. Fragments between 2 to 500 bases, with length differences as small as a single nucleotide, can be separated using this method1. The migration of the sample is dependent on the chosen acrylamide concentration. A higher percentage of polyacrylamide resolves lower molecular weight fragments. The combination of urea and temperatures of 45-55 &deg;C during the gel run allows for the separation of unstructured DNA or RNA molecules.
In general this method is required to analyze or purify single stranded DNA or RNA fragments, such as synthesized or labeled oligonucleotides or products from enzymatic cleavage reactions.
In this video article we show how to prepare and run the denaturing urea polyacrylamide gels. Technical tips are included, in addition to the original protocol 1,2.

Denaturing Urea Polyacrylamide Gel Electrophoresis Urea PAGE

Denaturing urea polyacrylamide gel electrophoresis is used to separate single-stranded DNA or RNA up to a limit of 500 nucleotides. Urea in combination with heat denatures samples and unstructured single strands migrate within the gel matrix according to their molecular weight.

Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their ...

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other proteins (Sali, Glaeser et al. 2003). Thus, the study of protein-protein interaction networks requires the detailed characterization of MPCs to gain an integrative understanding of protein function and regulation. For identification and analysis, MPCs must be separated under native conditions. In this video, we describe the analysis of MPCs by blue native polyacrylamide gel electrophoresis (BN-PAGE). BN-PAGE is a technique that allows separation of MPCs in a native conformation with a higher resolution than offered by gel filtration or sucrose density ultracentrifugation, and is therefore useful to determine MPC size, composition, and relative abundance (Sch&auml;gger and von Jagow 1991); (Sch&auml;gger, Cramer et al. 1994). By this method, proteins are separated according to their hydrodynamic size and shape in a polyacrylamide matrix. Here, we demonstrate the analysis of MPCs of total cellular lysates, pointing out that lysate dialysis is the crucial step to make BN-PAGE applicable to these biological samples. Using a combination of first dimension BN- and second dimension SDS-PAGE, we show that MPCs separated by BN-PAGE can be further subdivided into their individual constituents by SDS-PAGE. Visualization of the MPC components upon gel separation is performed by standard immunoblotting. As an example for MPC analysis by BN-PAGE, we chose the well-characterized eukaryotic 19S, 20S, and 26S proteasomes.

Blue Native Polyacrylamide Gel Electrophoresis BN-PAGE for Analysis of Multiprotein Complexes from Cellular Lysates

In this video, we describe the characterization of multiprotein complexes (MPCs) by blue native polyacrylamide gel electrophoresis (BN-PAGE). In a first dimension, dialyzed cellular lysates are separated by BN-PAGE to identify individual MPCs. In a second dimension SDS-PAGE, MPCs of interest are further subdivided to analyze their constituents by immunoblotting.

Multiprotein complexes (MPCs) play a crucial role in cell signalling, since most proteins can be found in functional or regulatory complexes with other ...

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits2. During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel&#39;s molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight3. The leading model for DNA movement through an agarose gel is &#34;biased reptation&#34;, whereby the leading edge moves forward and pulls the rest of the molecule along4. The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation5; 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: 
 
1. Understand the mechanism by which DNA fragments are separated within a gel matrix 
2. Understand how conformation of the DNA molecule will determine its mobility through a gel matrix 
3. Identify an agarose solution of appropriate concentration for their needs 
4. Prepare an agarose gel for electrophoresis of DNA samples 
5. Set up the gel electrophoresis apparatus and power supply 
6. Select an appropriate voltage for the separation of DNA fragments 
7. Understand the mechanism by which ethidium bromide allows for the visualization of DNA bands 
8. Determine the sizes of separated DNA fragments 
&#160;

A basic protocol for the separation of DNA fragments using agarose gel electrophoresis is described.

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from ...

Induction and Analysis of Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) is essential for proper morphogenesis during development. Misregulation of this process has been implicated as a key event in fibrosis and the progression of carcinomas to a metastatic state. Understanding the processes that underlie EMT is imperative for the early diagnosis and clinical control of these disease states. Reliable induction of EMT in vitro is a useful tool for drug discovery as well as to identify common gene expression signatures for diagnostic purposes. Here we demonstrate a straightforward method for the induction of EMT in a variety of cell types. Methods for the analysis of cells pre- and post-EMT induction by immunocytochemistry are also included. Additionally, we demonstrate the effectiveness of this method through antibody-based array analysis and migration/invasion assays.

A straightforward method is described for the induction of epithelial to mesenchymal transition (EMT) in a variety of cell types. Methods for the analysis of cells in EMT states by immunocytochemistry are included.

Epithelial  to mesenchymal transition (EMT) is essential for proper morphogenesis during  development. Misregulation of this  process has been implicated ...

Isolation and Functional Analysis of Mitochondria from Cultured Cells and Mouse Tissue

Comparison between two or more distinct groups, such as healthy vs. disease, is necessary to determine cellular status. Mitochondria are at the nexus of cell heath due to their role in both cell metabolism and energy production as well as control of apoptosis. Therefore, direct evaluation of isolated mitochondria and mitochondrial perturbation offers the ability to determine if organelle-specific (dys)function is occurring. The methods described in this protocol include isolation of intact, functional mitochondria from HEK cultured cells and mouse liver and spinal cord, but can be easily adapted for use with other cultured cells or animal tissues. Mitochondrial function assessed by TMRE and the use of common mitochondrial uncouplers and inhibitors in conjunction with a fluorescent plate reader allow this protocol not only to be versatile and accessible to most research laboratories, but also offers high throughput.

Comparison of mitochondrial membrane potential between samples yields valuable information about cellular status. Detailed steps for isolating mitochondria and assessing response to inhibitors and uncouplers using fluorescence are described. The method and utility of this protocol are illustrated by use of a cell culture and animal model of cellular stress.

Comparison between two or more distinct groups, such as healthy vs. disease, is necessary to determine cellular status. Mitochondria are at the nexus of ...

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Silencing of the tumor suppressor protein BRCA2 and its detection by conventional biochemical analyses represent a great technical challenge owing to the large size of the human BRCA2 protein (approximately 390 kDa). We report modifications of standard siRNA transfection and immunoblotting protocols to silence human BRCA2 and detect endogenous BRCA2 protein, respectively, in human epithelial cell lines. Key steps include a high siRNA to transfection reagent ratio and two subsequent rounds of siRNA transfection within the same experiment. Using these and other modifications to the standard protocol we consistently achieve more than 70% silencing of the human BRCA2 gene as judged by immunoblotting analysis with anti-BRCA2 antibodies. In addition, denaturation of the cell lysates at 55 &#176;C instead of the conventional 70-100 &#176;C and other technical optimizations of the immunoblotting procedure allow detection of intact BRCA2 protein even when very low amounts of starting material are available or when BRCA2 protein expression levels are very low. Efficient silencing of BRCA2 in human cells offers a valuable strategy to disrupt BRCA2 function in cells with intact BRCA2, including tumor cells, to examine new molecular pathways and cellular functions that may be affected by pathogenic BRCA2 mutations in tumors. Adaptation of this protocol for efficient silencing and analysis of other &#39;large&#39; proteins like BRCA2 should be readily achievable.

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Gene silencing by siRNA represents a convenient experimental strategy to analyze BRCA2-dependent biological functions with immediate implications to better understand cancer biology. A method to efficiently silence BRCA2, along with the experimental procedure to detect and quantify changes in BRCA2 protein expression by immunoblotting in human cell lines, is presented.

Silencing of the tumor suppressor protein BRCA2 and its detection by conventional biochemical analyses represent a great technical challenge owing to the ...

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes within individual endothelial cells (ECs). These processes are critical for homeostatic maintenance such as wound healing, and are also crucial in promoting tumor growth and metastasis. EC morphology is defined by the organization of the cytoskeleton, a tightly regulated system of actin and microtubule (MT) dynamics that is known to control EC branching, polarity and directional migration, essential components of angiogenesis. To study MT dynamics, we used high-resolution fluorescence microscopy coupled with computational image analysis of fluorescently-labeled MT plus-ends to investigate MT growth dynamics and the regulation of EC branching morphology and directional migration. Time-lapse imaging of living Human Umbilical Vein Endothelial Cells (HUVECs) was performed following transfection with fluorescently-labeled MT End Binding protein 3 (EB3) and Mitotic Centromere Associated Kinesin (MCAK)-specific cDNA constructs to evaluate effects on MT dynamics. PlusTipTracker software was used to track EB3-labeled MT plus ends in order to measure MT growth speeds and MT growth lifetimes in time-lapse images. This methodology allows for the study of MT dynamics and the identification of how localized regulation of MT dynamics within sub-cellular regions contributes to the angiogenic processes of EC branching and migration.

Protocols for Human Umbilical Vein Endothelial Cell (HUVEC) culture, transient transfection of fluorescently-labeled markers of microtubule growth, live-cell imaging and automated analysis of interphase microtubule growth dynamics are detailed.

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes ...

Purification of Native Complexes for Structural Study Using a Tandem Affinity Tag Method

Affinity purification approaches have been successful in isolating native complexes for proteomic characterization. Structural heterogeneity and a degree of compositional heterogeneity of a complex do not usually impede progress in conducting such studies. In contrast, a complex intended for structural characterization should be purified in a state that is both compositionally and structurally homogeneous as well as at a higher concentration than required for proteomics. Recently, there have been significant advances in the application of electron microscopy for structure determination of large macromolecular complexes. This has heightened interest in approaches to purify native complexes of sufficient quality and quantity for structural determination by electron microscopy. The Tandem Affinity Purification (TAP) method has been optimized to extract and purify an 18-subunit, ~ 0.8 MDa ribonucleoprotein assembly from budding yeast (Saccharomyces cerevisiae) suitable for negative stain and electron cryo microscopy. Herein is detailed the modifications made to the TAP method, the rationale for making these changes, and the approaches taken to assay for a compositionally and structurally homogeneous complex.

The Tandem Affinity Purification (TAP) method has been used extensively to isolate native complexes from cellular extract, primarily eukaryotic, for proteomics. Here, we present a TAP method protocol optimized for purification of native complexes for structural studies.

Affinity purification approaches have been successful in isolating native complexes for proteomic characterization. Structural heterogeneity and a degree ...

Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting

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Denaturing Gradient Gel Electrophoresis (DGGE)

Probing for Mitochondrial Complex Activity in Human Embryonic Stem Cells

Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for Analysis of Multiprotein Complexes from Cellular Lysates

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Induction and Analysis of Epithelial to Mesenchymal Transition

Isolation and Functional Analysis of Mitochondria from Cultured Cells and Mouse Tissue

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

Purification of Native Complexes for Structural Study Using a Tandem Affinity Tag Method