Protocol: Western Blotting with Alkaline Phosphatase Conjugates

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SAMPLE PREPARATION

For Protein Concentration Determination of Cell Culture

1. Decant medium from 10 cm dish of adherent cells and rinse plate rapidly with phosphate-buffered saline (PBS).
2. Aspirate excess PBS.
3. Add 1 ml boiling lysis buffer (1% SDS, 1.0 mM sodium ortho-vanadate, 10 mM Tris pH 7.4).
4. Scrape cells from dish, transfer to a microcentrifuge tube, and boil for an additional 5 minutes. To reduce viscosity, the sample may be sonicated briefly or passed several times through a 26-gauge needle.
5. Centrifuge the sample for 5 minutes to pellet insoluble material, then discard pellet.
6. Dilute an aliquot of the cell lysate sample at least 10-fold for the BCA (Pierce) protein concentration assay (SDS concentration must be below 0.1% to avoid interference with the colorimetric reading).

For Protein Gel Electrophoresis of Cell Culture (without determining protein concentration)

1. Decant medium from 10 cm dish of adherent cells and rinse plate rapidly with phosphate-buffered saline (PBS).
2. Aspirate excess PBS.
3. Add 1 ml boiling 2X concentrated electrophoresis sample buffer (125 mM Tris pH 6.8, 4% SDS, 10% glycerol, 0.006% bromophenol blue, 1.8% b-mercaptoethanol).
4. Scrape cells from dish, transfer to a microcentrifuge tube, and boil for an additional 5 minutes. To reduce viscosity, the sample may be sonicated briefly or passed several times through a 26-gauge needle. Centrifuge the sample for 10 minutes to pellet insoluble material. Discard pellet.
5. The cell lysate sample (supernatant) is now ready for loading onto your gel.

For Protein Concentration Determination of Whole Tissue

1. Rapidly homogenize every 0.25 g tissue in 3.5ml of boiling lysis buffer (1% SDS, 1.0 mM sodium ortho-vanadate, 10 mM Tris pH 7.4).
2. Microwave for 10-15 seconds.
3. Centrifuge the homogenate (16,000 x g, 15°C) for 5 minutes to pellet insoluble material, then discard pellet.
4. Dilute an aliquot of the tissue lysate sample at least 10-fold for the BCA (Pierce) protein concentration assay.

POLYACRYLAMIDE GEL ELECTROPHORESIS

Guidelines for choosing the percent gel to be used for certain molecular weight proteins (based on 37:1 acralyamide: bis acraylamide ratio)

4-5% gels: > 250 kDa

7.5% gels: 250-120 kDa

10% gels: 120-40 kDa

13% gels: 40-15 kDa

15% gels: < 20 kDa

Gel Electrophoresis

1. If not already in electrophoresis sample buffer, add an equal volume of 2X sample buffer (125 mM Tris pH 6.8, 4% SDS, 10% glycerol, 0.006% bromophenol blue, 1.8% b-mercaptoethanol) to all samples and boil for 3-5 minutes.
2. Apply 5-20 µg total protein of cell or tissue lysate to each well of a 0.75-1.0 mm thick gel. For thicker gels (1.5 mm thick), apply up to 25-40 µg in each well.
3. Electrophorese until the bromophenol blue in the samples reaches the bottom of the gel. Turn off power supply. Keep gels in running buffer until ready to transfer.

PROTEIN BLOTTING

Wet Transfer

Note: Since extra negative charges are needed to reach 1 Amp in a wet transfer system, adjust the pH of the transfer buffer to approximately pH 8.0 using NaOH.

1. For transfer of proteins smaller than 20 kDa, transfer proteins from gel to PVDF (polyvinylidene difluoride) membrane at 1 Amp constant current for 45 mins or equivalent (250 mAmp for 3 hours or 500 mAmp for 90 minutes) in transfer buffer (25 mM Tris, 190 mM glycine, 20% MeOH).
2. For transfer of proteins smaller than 120 kDa, transfer proteins from gel to PVDF membrane at 1 Amp constant current for 1 hour or equivalent (250 mAmp for 4 hours or 500 mAmp for 2 hours) in transfer buffer (25 mM Tris, 190 mM glycine, 20% MeOH).
3. For proteins larger than 120 kDa, transfer to PVDF membrane at 1 Amp constant current for 90 minutes or equivalent (250 mAmp for 6 hours or 500 mAmp for 3 hours) in transfer buffer + SDS (25 mM Tris, 190 mM glycine, 20% MeOH, 0.05% SDS).
4. For Proteins larger than 250 kDa, transfer to PVDF membrane at 1 Amp constant current for 1 hour and 45 minutes or equivalent (500 mAmp for 3.5 hours) in transfer buffer + SDS (25 mM Tris, 190 mM glycine, 20% MeOH, 0.05% SDS).

Semi-Dry Transfer

For transfer of proteins from 10% or 13% gels to PVDF membranes semi-dry transfer can also be used. Transfer proteins to PVDF membrane at 1.2 mAmp/cm² for 1 hour and 45 minutes in transfer buffer (25 mM Tris, 190 mM glycine, 20% MeOH).

Optional

If blots are not to be used for colorimetric detection, visualize the transferred proteins by staining the membrane for 15 minutes with India ink (Higgins black India ink, Eberhard Faber) diluted 1:1000 in wash buffer (10 mM Tris pH 7.5, 100 mM NaCl, 0.1% Tween 20). Rinse excess stain with wash buffer before blocking.

BLOCKING

FOR ALL ANTIBODIES EXCEPT PHOSPHOTYROSINE

1. Remove the blot from the transfer apparatus or staining tray and immediately place into blocking buffer (5% non-fat dry milk, 10 mM Tris pH 7.5, 100 mM NaCl, 0.1% Tween 20).
2. Incubate the blot for 30 minutes at 37°C, 1 hour at room temperature, or overnight at 4°C.

FOR PHOSPHOTYROSINE ANTIBODIES

1. Remove the blot from the transfer apparatus or staining tray and immediately place into blocking buffer (1% BSA, 10 mM Tris pH 7.5, 100 mM NaCl, 0.1% Tween 20).
2. Incubate the blot for 30 minutes at 37°C, 1 hour at room temperature, or overnight at 4°C.

INCUBATION WITH ALKALINE PHOSPHATASE CONJUGATED ANTIBODIES

1. Dilute the AP conjugated antibody in the corresponding blocking buffer.
2. Decant the blocking buffer from the blot, add the antibody solution, and incubate with agitation for 30 minutes at 37°C, one hour at room temperature, or overnight at 4°C.

PREPARATION OF CHROMAGEN REAGENTS

Prepare BCIP (bromochloroindolyl phosphate) by dissolving 0.5 grams of the disodium salt in 10 ml of 100% dimethylformamide. Prepare NBT (nitro blue tetrazolium) in a glass vial by dissolving 0.5 grams in 10 ml 70% dimethylformamide. Store separately at 4°C in dark containers.