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The Protein Man's Blog | A Discussion of Protein Research

How to Check Western Transfer before using expensive antibodies

Posted by Protein Man on May 24, 2016 11:30:00 AM

Immunodetection of proteins on a Western blot requires the use of expensive antibodies, but poor or incomplete transfer would result in wasting these antibodies. A Western transferred blot can be checked for success of protein transfer with a protein stain and therefore prevent wasting expensive antibodies. Various options for protein stains for Western blot are available, including, but not limited to, Ponceau S, Amido black 10B, Coomassie brilliant blue R250, India ink or colloidal gold. In addition to checking success and quality of Western transfer, staining blots is also used for semi-quantitative protein estimation. In addition, checking the blot with a stain gives a rough idea to a researcher that the desired protein is present (based on size, mobility etc) and whether to go for immunodetection especially when expensive and limiting amounts of antibodies are available.

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Tags: Western Blotting

How to visualize proteins after electrophoresis

Posted by Protein Man on May 16, 2016 2:07:05 PM

How to visualize proteins after electrophoresis

In-gel visualization of proteins separated by SDS-PAGE or by 2-D gel electrophoresis is achieved by staining gels with dye, metals ions or fluorescent stains. Different staining method are preferred depending upon broad range binding of stain to proteins, the sensitivity to detect low abundant proteins and downstream application desired for a separated protein like mass spectrometry. Sometimes two staining methods are carried out as single staining method cannot achieve everything desired by a researcher. Various staining method for in-gel visualization of proteins are as follows.

Coomassie Brilliant Blue staining

The Coomassie dyes R-250 and G-250 bind to proteins stoichiometrically through their sulfonic acid groups. The interactions between dye and protein are Van der Waals and ionic. The sulfonic acid groups interact with positive amine groups. Therefore coomassie dye binds to wide range of proteins. The most commonly used dye R-250 can detect protein as low as 0.1 µg. Coomassie Brilliant Blue involves staining and destaining step as the gel also turns blue. Coomassie Brilliant blue is compatible with mass spectrometry analysis. Though widely used for staining gels to view proteins, its not a method of choice if higher sensitivity is desired. For analytical purposes other methods like silver staining and fluorescent staining are preferred over classical Coomassie Brilliant Blue staining.

Colloidal Coomassie G-250 staining

In colloidal Coomassie staining G-250 dye is used instead of R-250 due to its colloidal properties. G-250 forms colloidal particles in high alcoholic solutions containing strong acids and high concentration of salts 1, 2. Formation of colloidal G-250 particles reduces free dye in solution and thus the dye does not penetrate and stain gel. This step enhances the sensitivity of staining proteins and removes background staining of gels. With colloidal Coomassie staining detection limit of 1-10 ng of protein in gel is achieved 3.

Silver staining

It offers high sensitivity of less than 1 ng of protein 4. The silver ions bind to the protein and are reduced further with a developing solution to give an image of protein bands. Silver staining involves various steps like protein fixation, sensitization, silver impregnation and image development. Based on solution used there are two methods of silver staining: silver nitrate and silver-ammonia complex method. Silver staining protocols compatible with downstream application like mass spectrometry are available. The downside of silver staining is that it has limited dynamic range and thus do not interact uniformly with all proteins. In addition it involves use of hazardous chemicals.

Fluorescent staining

Fluorescent staining uniformly stains protein, is rapid and offers sensitivity equal to that attained by silver staining method. It involves no destaining step and is compatible with mass spectrometry and microsequencing. Commercially fluorescent stains are available to stain 1D or 2D gels to visualize bands.

Stain free detection of proteins in gel

In stain free method for visualizing proteins, 2, 2, 2-Trichloroethnaol is added to the polyacrylamide solution before casting a gel 5. The principle behind stain free method is that the tryptophan amino acids in protein undergo an ultraviolet light-induced reaction with trihalocompounds to produce fluorescence in visible range (300 nm). This method is fast as one can see bands on transilluminator within 5 minutes and it avoids use of stains.


1. Neuhoff, V. et al (1988). Electrophoresis 9, 255-262
2. Candiano, G. et al (2004). Electrophoresis 25, 1327-1333
3. Kang, D. et al (2002). Bull. Korean Chem. Soc. 11, 1511-1512
4. Chevallet, M. et al (2006). Nat Protoc.1(4): 1852-1858
5. Ladner, C. L. et al (2004). Anal Biochem. 2004 Mar 1, 326(1):13-20
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Tags: Protein Detection

The 3 Types of Crosslinking Reagents and When to Use Them

Posted by Protein Man on May 3, 2016 10:00:00 AM

Crosslinking reagents or crosslinkers are used to covalently bind two or more protein molecules to facilitate the identification of relationships between near-neighbor proteins, ligand-receptor interactions, three-dimensional protein structures, and molecular associations in cell membranes. In the same manner, they can also be used to modify nucleic acids, drugs, and solid surfaces, and in the preparation of antibody-enzyme conjugates and immunotoxins. 

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Using Chaotropic Extraction Buffers to Preserve the Native Charge of Protein

Posted by Protein Man on Apr 26, 2016 10:00:00 AM

chaotrapic.jpgProtein solubility is a key factor for successful 2D gel electrophoresis. Thus, the choice of protein solubilization buffers can greatly affect the results of your experiments. Proteins need to be solubilized during sample preparation and electrophoresis to break the inter- and intra-molecular interactions involved in protein aggregation (e.g. disulfide and/or hydrogen bonds, ionic and/or hydrophobic interactions, and van der Waals forces). Failure to break these interactions may result in sample loss or the formation of experimental artifacts.

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Why Is Lactate Dehydrogenase (LDH) Release A Good Measure For Cytotoxicity?

Posted by Protein Man on Mar 31, 2016 10:00:00 AM

When treated with a cytotoxic compound, living cells may face one of two fates. They could either stop growing and dividing, or die through either of two distinct processes - necrosis or apoptosis. Basically, cells undergoing necrosis (accidental cell death) swell and lose membrane integrity before shutting down and releasing their intracellular contents into the surrounding environment. This type of cell death is usually triggered by external factors such as toxic chemical or traumatic physical events.

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Should I Use A Native Or Denaturing Gel?

Posted by Protein Man on Mar 23, 2016 8:00:00 AM

Gel electrophoresis is a simple, rapid and highly sensitive tool that can be used to separate proteins based on their physical properties (e.g. molecular weight and native charge or isoelectric point) prior to downstream detection or analysis. The separation of proteins by electrophoresis can be explained by the fact that charged molecules will travel through a gel matrix when an electrical current is applied. Proteins are commonly separated in this manner using polyacrylamide gel electrophoresis (PAGE) to identify individual proteins in complex samples or to examine multiple proteins within a single sample.

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Why Today's High School Biology Classes Are Teaching Biotech

Posted by Protein Man on Mar 1, 2016 10:00:00 AM


As you probably know, biotechnology has grown tremendously over the past decade. What you may not know, however, it is now being taught in some high school classes. This post will explore why biotech is being taught as early as high school and how this is paving the way for a new generation of biotech experts.

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Why Does Tyrosine and Tryptophan Have Effect in Protein Determination and to What Degree?

Posted by Protein Man on Feb 17, 2016 10:00:00 AM

Since accurate protein quantitation is essential to all experiments related to protein studies, different methods have been developed to measure the concentration of proteins in a given assay. Some of the more traditional methods of total protein quantitation include the measurement of UV absorbance at 280 nm (A280), Bicinchoninic acid (BCA) and Bradford assays, and other alternative methods such as Lowry and other novel assays.

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How to Safely Use Detergents during Protein Extraction

Posted by Protein Man on Feb 9, 2016 10:00:00 AM

While detergents can be used to extract, solubilize, and manipulate (disrupt or form) membrane proteins from biological membranes for subsequent biochemical and physical characterization, and are useful in controlling protein crystallization and preventing nonspecific binding in affinity purification and immunoassay procedures, they can also be one of your greatest foes in the laboratory.

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Tips for Preparing Phosphate Buffers

Posted by Protein Man on Feb 2, 2016 10:00:00 AM

When doing biological applications in the laboratory, it is essential that you have your phosphate buffers available at all times. This is of extreme importance since most biological applications are very sensitive to changes in pH, and these buffers are very effective in keeping the pH range of cellular fluids within the normal range (6.9 to 7.4).

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