Western Blotting

Adapted from Chapter 7, Gel Electrophoresis of Proteins, by David E. Garfin, Pages 197-268, in Essential Cell Biology, Volume 1: Cell Structure, A Practical Approach, Edited by John Davey and Mike Lord, Oxford University Press, Oxford UK (2003). Used by permission of Oxford University Press.

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Certain synthetic membranes bind proteins tightly enough that they can be used as supports for solid-phase immunoassays. Bound proteins retain their antigenicity and are accessible to probes. Several techniques have been developed for probing proteins bound to synthetic membranes. They are collectively known as “blots”. Only the most common blotting technique is discussed here. In this technique, proteins are transferred from an electrophoresis gel to a support membrane and then probed with antibodies. This technique is called “immunoblotting” or, more popularly, “western blotting”. It combines the resolution of PAGE (1-D or 2-D) with the specificity of immunoassays allowing individual proteins in complex mixtures to be detected and analyzed (1-4). Western blotting complements electrophoretic separations and uses electrophoresis to transfer proteins from gels to membranes.

1. Immunoblotting

The immunoblotting procedure is as follows. (i) Proteins are transferred from an electrophoresis gel to a membrane surface. The transferred proteins become immobilized on the surface of the membrane in a pattern that is an exact replica of the gel. (ii) Unoccupied protein-binding sites on the membrane are saturated to prevent non-specific binding of antibodies. This step is called either “blocking” or “quenching”. (iii) The blot is probed for the protein of interest with a specific primary antibody. (iv) The blot is probed a second time. The second probe is an antibody that is specific for the primary antibody type and is conjugated to a detectable enzyme. The site of the protein of interest is thus tagged with an enzyme through the specificities of the primary and secondary antibodies. (v) Enzyme substrates that are converted into insoluble, detectable products are incubated with the blot. The products leave a colored trace at the site of the band or spot representing the protein of interest (Figure 1).

Figure 1. Specific enzymatic immunodetection of a blotted protein. Depicted are blocked binding sites on the membrane (1), a primary antibody (2) specifically bound to an antigenic protein, and a secondary antibody (3) bound to the primary antibody. The secondary antibody is conjugated to a reporter enzyme (4). Substrate (S) is converted into insoluble product (P).
1.1 Apparatus for blotting

Electrotransfer from a gel to a membrane is done by directing an electric field across the thickness of the gel to drive proteins out of the gel and on to the membrane. There are two types of apparatus for electrotransfer: (i) buffer-filled tanks and (ii) “semidry” transfer devices (Figure 2).

Figure 2. Two types of electrotransfer apparatus. (A) A tank transfer cell is shown in an exploded view. The cassette (1) holds the gel (2) and membrane (3) between buffer-saturated filter paper and buffer pads (4). The cassette is inserted vertically in the buffer-filled tank between the positive and negative electrodes (not shown). A lid with connectors and leads for applying electrical power is not shown. (B) An exploded view of a semidry transfer unit is shown. The gel (4) and membrane (5) are sandwiched between buffer-saturated stacks of filter paper (3 and 6) and placed between the cathode assembly (2) and anode plate (7). The safety lid (1) attaches to the base (9). Power is applied through cables (8).

Transfer tanks are made of plastic with two electrodes mounted near opposing tank walls. A nonconductive cassette holds the membrane in close contact with the gel. The cassette assembly is placed vertically into the tank parallel to the electrodes and submerged in electrophoresis buffer. A large volume of buffer in the tank dissipates the heat generated during the transfer.

In semidry blotting, the gel and membrane are sandwiched horizontally between two stacks of buffer-wetted filter papers in direct contact with two closely spaced solid plate electrodes. The close spacing of the semidry apparatus provides for high field strengths. The term “semidry” refers to the limited amount of buffer that is confined to the stacks of filter paper.

Tanks rather than semidry apparatus should be used for most routine work. With tanks, transfers are somewhat more efficient than with semidry devices. Under semidry electrotransfer conditions, some low-molecular-weight proteins are driven through the membranes and because low buffer capacity limits run times, some high-molecular- weight proteins are poorly transferred.

1.2 Membranes and buffers for immunoblotting

The two membranes most used for protein work are nitrocellulose and polyvinylidene fluoride (PVDF). Both bind proteins at about 100 μg/cm2. Nitrocellulose is the best membrane to use in the initial stages of an experiment. PVDF is used when proteins are to be sequenced. It can withstand the harsh chemicals of protein sequenators, whereas nitrocellulose cannot.

Tank transfers from SDS-PAGE gels are done in modified electrophoresis buffer, 25 mM Tris, 192 mM glycine, 20% (v/v) methanol, pH 8.3. With semidry transfers from SDS-PAGE gels, the buffer is 48 mM Tris, 39 mM glycine, 20% methanol, pH 9. The methanol in the buffers helps remove SDS from protein-detergent complexes and increases the affinity between proteins and the membranes. Methanol is not used in transfers from non-denaturing gels. Nonfat dry milk and Tween 20 detergent are used to block unoccupied sites in membranes and are included as carriers for the antibodies used to probe the membranes.

1.3 Immunodetection

Appropriate primary antibodies can be produced in any convenient animals, such as rabbits or mice. Antibodies to many important proteins can be purchased from a number of commercial vendors. Secondary antibodies (e.g., goat anti-rabbit immunoglobulin) conjugated to enzymes are also commercially available. The most common enzymes used in western blotting are alkaline phosphatase and horeseradish peroxidase. The preferred substrate for alkaline phosphatase is the mixture of 5-bromo- 4-chloro-3-indolyl phsophate (BCIP) and nitroblue tetrazolium (NBT). The substrate BCIP is dephosphorylated by the enzyme and then oxidized in a reaction coupled to reduction of NBT. The resultant highly visible purple product is deposited on the protein bands or spots. With horseradish peroxidase, use 4-(chloro-1-naphthol) or diaminobenzidine as substrate (with added hydrogen peroxide). Chemiluminescent substrates for horseradish peroxidase are based on oxidation of luminol. The luminol substrate provides the most sensitive signal of the blotting substrates but requires photographic exposures or specially configured imaging devices. Protocol 1 gives a procedure for western blotting. For alternative procedures and more detail than can be provided here, consult refs. 1-3.

1.4 Total protein detection

For proper identification of the proteins of interest in a blot, immunodetected proteins must be compared to the total protein pattern of the gel. This requires the indiscriminant staining of all the proteins in the blot. Colloidal gold stain is a very sensitive reagent for total protein staining. It consists of a stabilized sol of colloidal gold particles. The gold particles bind to proteins on the surfaces of membranes. Detection limits are in the low hundreds of picogram range and can be enhanced by an order of magnitude by subsequent treatment with silver.

CBB G-250 is another popular total protein stain. Researchers blotting 2-D PAGE gels particularly favor it since it is compatible with mass spectrometry. Stained blots provide good media for archiving 2-D PAGE separations. A version of SYPRO Ruby, formulated for blots, is a very sensitive total protein stain.

Protocol 1. Immunoblotting
Equipment and reagents
Electrotransfer apparatus, tank or semidry, with filter papers, sponges and power supply Primary antibody
Blotting membrane, nitrocellulose or PVDFSecondary antibody-enzyme conjugated
Transfer bufferaSubstrate for the enzyme conjugated to the secondary antibodye
TBSb and TTBScTotal protein stainf
The formulation given here is for 12 ml of gel solution containing 5% T (3%C) acrylamide, 2% carrier ampholytes, 5% glycerol. The volume needed depends on the casting apparatus that is used; adjust volumes accordingly. This recipe is sufficient for casting one gel of 100 x 125 x 0.8 mm (10 ml) or four 100 x 125 x 0.2 mm (10 ml total). 8 M urea can be substituted for the glycerol if desired (see ref. 16).
1. Prepare transfer buffer appropriate to the electrotransfer apparatus. Refer to the recommendations of the manufacturer of the apparatus or use those given here. Make about 1 liter of buffer more than is required to fill the apparatus. Do not adjust the pH of transfer buffers; just confirm that they are close to the expected pH.
2. Remove the gel from the cassette and soak it in transfer buffer for about 10 min. It is helpful to cut off the stacking gel, if one was used, since the soft gel will stick to the transfer membrane.
3. Follow the manufacturer's instructions for setting up the transfer apparatus. Cut filter paper to size if necessary. Soak filter paper and sponge pads (if used) in transfer buffer.
4. Cut the transfer membrane to size with a clean, sharp scalpel or razor blade. Do not touch the membrane with bare hands. Use gloves and (or) blunt, flat-blade forceps to manipulate the membrane.
5. Completely wet the transfer membrane with transfer buffer. PVDF must be wetted in methanol prior to being placed in aqueous solutions. Avoid air bubbles in the membrane by slowly sliding it into buffer (or methanol) at a slight angle or by floating it on buffer. Immerse the membrane in buffer and let it soak for 15 min. Do not allow the membrane to dry out before beginning the transfer.
6. Place about 1 liter of transfer buffer in a large tray and assemble the transfer array in it. Use the buffer in the tray to keep all elements of the transfer array well wetted during the assembly process.
7. To avoid trapping air bubbles between the gel and the membrane, lay the membrane on the on the gel from the center to the ends then gently roll a test tube or pipette on top of the membrane to push out pockets of air.
8. Put the transfer array into the transfer apparatus. Follow the manufacturer’s instructions for electrotransfer.
9. Wash the membrane for 5-10 min in TBS.
10. Incubate the membrane for 30 min to 1 hr at room temperature in TBS containing 5% (w/v) nonfat dry milk to block excess protein binding sites on the membrane (5 g of nonfat dry milk per 100 ml of TBS).
11. Wash the membrane twice, for 5 min each time, with TTBS.
12. Incubate the membrane for 1 to 2 hr at room temperature with primary antibody or antiserum diluted in TTBS containing 5% nonfat dry milk. Dilutions of primary antibody vary with the source, but are generally of the order of 1:100 to 1: 3,000.
13. Wash the membrane twice with TTBS, for 5 min each time.
14. Incubate the membrane for 1 to 2 hr at room temperature with secondary antibody- enzyme conjugate appropriately diluted (e.g., 1:3,000) in TTBS containing 5% nonfat dry milk.
15. Wash the membrane twice, for 5 min each time, with TTBS.
16. Wash the membrane with TBS to remove the Tween 20.
17. Incubate the membrane with substrate solution for about 1 hr or until the desired intensity is obtained.
18. Wash the completed blot with water. Washed immunoblots can be stored dry.
19. For total protein staining with colloidal gold, do not block excess binding sites with nonfat milk. Rather, soak the membrane for 20 min in TBS containing 0.3% Tween 20, then wash it with an excess of water for 5 min. Immerse the membrane in colloidal gold stain (Bio-Rad) for 4 hr or until desired intensity is obtained. Greater sensitivity is achievable by enhancing the gold stain with silver (Bio-Rad).
20. For total protein staining with SYPRO Ruby Blot Stain (Bio-Rad), do not block the membrane at all. Immerse (nitrocellulose) or float face down (dried PVDF) the membrane in 10% methanol, 7% acetic acid for 15 min, then wash it 4 times for 5 min each. Immerse (nitrocellulose) or float face down (PVDF) the membrane in stain for 15 min, then wash it with water. View the stain with epi-illumination.
a aTransfer buffers. For tanks (25 mM Tris, 192 mM glycine, 20% methanol, pH 8.3), dissolve 3.0 g of Tris and 14.4 g of glycine in 800 ml of water, then add 200 ml of methanol. For semidry apparatus (48 mM Tris, 39 mM glycine, 20% methanol, pH 9), dissolve 5.8 g of Tris and 2.9 g of glycine in 800 ml of water, then add 200 ml of methanol.
b TBS is Tris-buffered saline (0.02 M Tris-Cl, 0.5 M NaCl, pH 7.5). To make TBS, dissolve 2.4 g of Tris and 29.2 g of NaCl in approximately 800 ml of water. Adjust the pH to 7.5 with HCl and bring the volume to 1 liter with water.
c TTBS is TBS containing 0.05% Tween 20. Add 0.5 ml of Tween 20 to 1 liter of TBS.
d The usual enzymes conjugated to antibodies are alkaline phosphatase and horseradish peroxidase.
e Substrates. For alkaline phosphatase, the substrate is 0.15 mg of BCIP and 0.3 mg of NBT per ml of 0.1 ml Tris-Cl, 0.5 mM MgCl2. The buffer consists of 1.2 g of Tris and 10 μl of 4.9 M MgCl2 per 100 ml adjusted to pH 9.5 with HCl. Stock BCIP is 30 mg of BCIP (toluidine salt) per ml of dimethylformamide, and stock NBT is 60 mg of NBT per ml of 70% dimethylformamide. To make the substrate solution, add 50 μl of stock BCIP and 50 μl of stock NBT to each 10 ml of buffer. For horseradish peroxidase, the substrate solution contains 0.015% hydrogen peroxide and 0.05% 4-(chloro-1-naphthol) in TBS containing 16.7% methanol. To make this substrate, dissolve 60 mg of 4-(chloro-1-naphthol) in 20 ml of methanol; protect this solution from light. Add 600 μl of 3% hydrogen peroxide to 100 ml of TBS. Mix the two solutions together and use the resultant solution immediately. An alternative substrate s prepared with 50 mg of diaminobenzidine and 100 μl of 3% hydrogen peroxide in 100 ml of TBS.
f For total protein stain use either colloidal gold stain or SYPRO Ruby Blot Stain (Bio-Rad).