We would like to thank all the members of the McMahon laboratory for their assistance and support.&#160;This research was supported by grants from an NIH/NCI R01 CA176839-01 (to MM) and an Institutional Research and Academic Career Development Award (IRACDA to JS).&#160;

1. Preparation of Whole Cell Lysates from Cell Culture
<ol>
	<li>Place cell culture dishes on ice and add cold PBS with 5 mM EDTA (e.g. 5 ml of PBS with 5 mM EDTA/10 cm2 plate). Remove adherent cells from the dish using a cell scraper and then transfer the cell suspension to a cold 15 ml conical tube.</li>
	<li>Pellet the cell suspensions by low-speed centrifugation at 1,000 rpm (230 x g) for 5 min at 4 &#176;C. Place conical tubes on ice and carefully aspirate the supernatant without disrupting the...

<ol>
	<li>Burnette, W. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Western+blotting:+electrophoretic+transfer+of+proteins+from+sodium+dodecyl+sulfate--polyacrylamide+gels+to+unmodified+nitrocellulose+and+radiographic+detection+with+antibody+and+radioiodinated+protein+A.">Western blotting: electrophoretic transfer of proteins from sodium dodecyl sulfate--polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A.</a> Anal. Biochem. 112, 195-203 (1981).</li><li>Renart, J., Reiser, J., Stark, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transfer+of+proteins+from+gels+to+diazobenzyloxymethyl-paper+and+detection+with+antisera:+a+method+for+studying+antibody+specificity+and+antigen+structure.">Transfer of proteins from gels to diazobenzyloxymethyl-paper and detection with antisera: a method for studying antibody specificity and antigen structure.</a> Proc. Natl. Acad. Sci. U.S.A. 76, 3116-3120 (1979).</li><li>Towbin, H., Staehelin, T., Gordon, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrophoretic+transfer+of+proteins+from+polyacrylamide+gels+to+nitrocellulose+sheets:+procedure+and+some+applications.">Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications.</a> Proc. Natl. Acad. Sci. U.S.A. 76, 4350-4354 (1979).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> NuPAGE Technical Guide. Life Technologies Corporation. IM-1001. 60, (2010).</li><li>Laemmli, U. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleavage+of+structural+proteins+during+the+assembly+of+the+head+of+bacteriophage+T4.">Cleavage of structural proteins during the assembly of the head of bacteriophage T4.</a> Nature. 227, 680-685 (1970).</li><li>Kubo, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+incubation+of+solutions+of+proteins+containing+dodecyl+sulfate+on+the+cleavage+of+peptide+bonds+by+boiling.">Effect of incubation of solutions of proteins containing dodecyl sulfate on the cleavage of peptide bonds by boiling.</a> Anal. Biochem. 225, 351-353 (1995).</li><li>Moos, M., Nguyen, N. Y., Liu, T. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reproducible+high+yield+sequencing+of+proteins+electrophoretically+separated+and+transferred+to+an+inert+support.">Reproducible high yield sequencing of proteins electrophoretically separated and transferred to an inert support.</a> J. Biol. Chem. 263, 6005-6008 (1988).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=iBlot+Dry+Blotting+System.">iBlot Dry Blotting System.</a> Life Technologies Corporation. 25-0911, 84 (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Western+Blot+Analysis.">Western Blot Analysis.</a> LI-COR Biosciences. 988-12622, (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Odyssey+Infrared+Imaging+System+Application+Software+Version+3.030.">Odyssey Infrared Imaging System Application Software Version 3.030.</a> LI-COR Biosciences. , (2007).</li><li>Hambaeus, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+Milk+Composition.">Human Milk Composition.</a> Clin. Nutr. 54, 219-236 (1984).</li><li>DenHollander, N., Befus, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Loss+of+antigens+from+immunoblotting+membranes.">Loss of antigens from immunoblotting membranes.</a> J. Immunol. Methods. 122, 129-135 (1989).</li></ol>

The authors have nothing to disclose.

The critical steps in generating high-quality, quantitative Western blots according to this protocol are the following: 1) measuring protein concentrations; 2) sample preparation; 3) blocking the membrane and; 4) quality and caliber of the primary antibody.
The accuracy of measuring total protein concentrations can have a major impact on quantifying protein bands since the exceptional sensitivity of infrared fluorescent detection will amplify any slight differences found in the protein concent...

The technique of Western blotting was first developed between 1977 and 1979 in order to create a better method for detecting proteins using antibodies1-3. This procedure utilized electrophoretic transfer of proteins to membranes from SDS-PAGE gels with target proteins visualized using secondary antibodies and detected by autoradiography, UV light, or a peroxidase reaction product3. Thus, these same basic principles are still widely used in today&#39;s Western blot protocols. However, this classic Western blotting technique does present many disadvantages, such as slow electrophoresis run times, low resolution and artificial protein bands, susceptibility to protein degradation, and limited sensitivity as well as poor data quality4. Therefore, this protocol describes significant advances and improvements to the standard Western blot procedure that generates more accurate qualitative and quantitative data.
The Laemmli system for separating a broad range of proteins using SDS-PAGE is the most widely used gel system for Western blotting5. Despite the popularity of this Western blotting system, this method can result in band distortion, loss of resolution, and spurious bands4. This may be a consequence of the deamination and alkylation of proteins due to the high pH (9.5) of the separating gel, reoxidation of reduced disulfide bonds due to the varying redox state of the gel, and cleavage of aspartyl-prolyl peptide bonds due to heating the protein in Laemmli buffer (pH 5.2)4,6. The Bis-Tris gel system, which operates at a neutral pH (7.0), provides significant benefits over the Lamemmli system. This system improves protein stability, minimizes protein modifications, maintains proteins in their reduced states, prevents aspartyl-prolyl cleavage during electrophoresis, and more importantly, the electrophoresis run time is 35 min4,6,7. In addition, the Bis-Tris gel system also produces sharper bands, higher resolution and separation, and increased sensitivity resulting in more reliable data4.
In conjunction with the Bis-Tris gel system, the iBlot dry blotting system uses high field strength and currents to significantly reduce the transfer time of proteins from gels onto membranes within 7 min8. This transfer system is based on the dry blotting method that generates a more efficient and reliable transfer of proteins8. For a detailed comparison of the efficacy of the iBlot transfer system to the conventional transfer systems please refer to the following website: <a href="http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Western-Blotting/Western-Blot-Transfer/iBlot-Dry-Blotting-System/iBlot-Dry-Blotting-Comparison-to-Semi-Dry-and-Wet.html">http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Western-Blotting/Western-Blot-Transfer/iBlot-Dry-Blotting-System/iBlot-Dry-Blotting-Comparison-to-Semi-Dry-and-Wet.html</a>. It utilizes an anode and cathode stack, which are comprised of a gel matrix that contains the appropriate transfer buffers, that act as ion reservoirs8. During the transfer, water electrolysis helps to prevent the generation of oxygen from the copper anode resulting in a more consistent protein transfer without causing band distortion8. Moreover, this transfer system also increases the transfer speed by reducing the distance between the electrodes8.
Although chemiluminescence is the most common and traditional technique for protein detection of Western blot analyses, two-color infrared fluorescent detection greatly improves the sensitivity, quality, and accuracy of Western blot data. This detection method uses infrared laser excitation in two optimal wavelengths, 700 nm and 800 nm, to generate a clear data image with the greatest signal-to-noise ratio and highest sensitivity9. Thus, two target proteins can be visualized simultaneously on the same membrane using the 700 nm and 800 nm fluorescent detection channels. More importantly, the linearity and dynamic range of infrared fluorescence allows for precise quantitative analysis of both strong and weak protein bands9. Furthermore, this protocol provides tremendous advantages and improvements over the classic Western blotting technique by decreasing the electrophoresis and transfer times of this experiment without compromising the efficacy of these processes and utilizing infrared fluorescent protein detection to produce greater qualitative and quantitative Western blot data.

<table border="0" cellpadding="0" cellspacing="0" width="624">
	<colgroup>
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="19">
			<td height="19" style="height:19px;width:297px;">BCA Protein Assay Kit</td>
			<td style="width:204px;">Thermo Scientific/Pierce</td>
			<td style="width:123px;">23225</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">4x NuPAGE&#174; LDS Sample Buffer&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0007</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">10x NuPAGE&#174; Sample Reducing Agent&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0004</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">20x NuPAGE&#174; MES SDS Running Buffer</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0002</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">20x NuPAGE&#174; MOPS SDS Running Buffer</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0001</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">NuPAGE&#174; Antioxidant</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0005</td>
		</tr>
		<tr height="38">
			<td height="38" style="height:38px;width:297px;">NuPAGE&#174; Novex&#174; 4-12% Bis-Tris Gel 1.5 mm, 10 well&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0335BOX</td>
		</tr>
		<tr height="38">
			<td height="38" style="height:38px;width:297px;">NuPAGE&#174; Novex&#174; 4-12% Bis-Tris Gel 1.5 mm, 15 well</td>
			<td>Invitrogen/Life Technologies</td>
			<td>NP0336BOX</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">SeeBlue&#174; Plus2 Pre-Stained Standard&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>LC5925</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">XCell SureLock&#174; Mini-Cell&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>EI0001</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">iBlot&#174; Transfer Stack, PVDF Regular</td>
			<td>Invitrogen/Life Technologies</td>
			<td>IB4010-01</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">iBlot&#174;Transfer Stack, PVDF Mini</td>
			<td>Invitrogen/Life Technologies</td>
			<td>IB4010-02</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">iBlot&#174; Transfer Stack, Nitrocellulose Regular</td>
			<td>Invitrogen/Life Technologies</td>
			<td>IB3010-01</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">iBlot&#174;Transfer Stack, Nitrocellulose Mini</td>
			<td>Invitrogen/Life Technologies</td>
			<td>IB3010-02</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">iBlot&#174; Gel Transfer Device&#160;</td>
			<td>Invitrogen/Life Technologies</td>
			<td>IB1001</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#946;-Actin</td>
			<td>Sigma</td>
			<td>A2228</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Phospho-BIM (S69)</td>
			<td>BD Biosciences</td>
			<td>N/A</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Total BIM</td>
			<td>Epitomics</td>
			<td>1036-1</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Phospho-ERK1/2 (T202/Y204)</td>
			<td>Cell Signaling Technology</td>
			<td>4370</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Total ERK1/2</td>
			<td>Cell Signaling Technology</td>
			<td>9107</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Odyssey&#174; Blocking Buffer&#160;</td>
			<td>LI-COR Biosciences</td>
			<td>927-40000&#160;</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">IRDye 800CW Goat anti-Rabbit IgG</td>
			<td>LI-COR Biosciences</td>
			<td>926-32211&#160;</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">IRDye 680LT Goat anti-Mouse IgG&#160;</td>
			<td>LI-COR Biosciences</td>
			<td>926-68020&#160;</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Western Incubation Box, Medium&#160;</td>
			<td>LI-COR Biosciences</td>
			<td>929-97205&#160;</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Odyssey&#174; Classic Imaging System</td>
			<td>LI-COR Biosciences</td>
			<td>N/A</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Odyssey&#174; Application Software V3.0.30</td>
			<td>LI-COR Biosciences</td>
			<td>N/A</td>
		</tr>
	</tbody>
</table>

the fastest western in town: a contemporary twist on the classic western blot analysis

The Western blot techniques that were originally established in the late 1970s are still actively utilized today. However, this traditional method of Western blotting has several drawbacks that include low quality resolution, spurious bands, decreased sensitivity, and poor protein integrity. Recent advances have drastically improved numerous aspects of the standard Western blot protocol to produce higher qualitative and quantitative data. The Bis-Tris gel system, an alternative to the conventional Laemmli system, generates better protein separation and resolution, maintains protein integrity, and reduces electrophoresis to a 35 min run time. Moreover, the iBlot dry blotting system, dramatically improves the efficacy and speed of protein transfer to the membrane in 7 min, which is in contrast to the traditional protein transfer methods that are often more inefficient with lengthy transfer times. In combination with these highly innovative modifications, protein detection using infrared fluorescent imaging results in higher-quality, more accurate and consistent data compared to the standard Western blotting technique of chemiluminescence. This technology can simultaneously detect two different antigens on the same membrane by utilizing two-color near-infrared dyes that are visualized in different fluorescent channels. Furthermore, the linearity and broad dynamic range of fluorescent imaging allows for the precise quantification of both strong and weak protein bands. Thus, this protocol describes the key improvements to the classic Western blotting method, in which these advancements significantly increase the quality of data while greatly reducing the performance time of this experiment.

Two-color infrared fluorescence detects both strong and weak bands on the same membrane with enhanced sensitivity and the highest signal-to-noise ratio to produce clear Western blot images. Typical results generated by two-color Western blot detection visualized in both the 700 nm and 800 nm fluorescent channels are exemplified in Figures 1 and 2. The uppermost Western blot in Figure 1 shows the concurrent (overlay) detection of total ERK1/2 in the 800 nm channel (green)...

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The Fastest Western in Town: A Contemporary Twist on the Classic Western Blot Analysis

This protocol explores the latest advancements in performing Western blot analyses.&#160;These novel modifications employ a Bis-Tris gel system with a 35&#160;min electrophoresis run time, a 7&#160;min dry blotting transfer system, and infrared fluorescent protein detection and imaging that generates higher resolution, quality, sensitivity, and improved accuracy of Western data.

The Western blot techniques that were originally established in the late 1970s are still actively utilized today. However, this traditional method of ...

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26.9K Views.  University of California, San Francisco. This protocol explores the latest advancements in performing Western blot analyses. These novel modifications employ a Bis-Tris gel system with a 35 min electrophoresis run time, a 7 min dry blotting transfer system, and infrared fluorescent protein detection and imaging that generates higher resolution, quality, sensitivity, and improved accuracy of Western data.