Tips

WESTERN BLOT TIPS

We are dedicated to helping our customers achieve exceptional results. While the information below can never be an exclusive solution to every problem you may encounter; it is our hope that you will find the information useful and even beneficial in troubleshooting any problems you may have. Of course, if you find you are still having problems you may submit them to us using this Western Blot Troubleshooting Form.

SYMPTOMS

> Wrong band size
> No bands/signal
> High uniform background
> Swirly specked background
> White bands
> Smeared bands/lanes


WRONG BAND SIZE
ISSUERECOMMENDATION
Protein variantsUse the proper control to detect the correct band size. A recombinant protein or overexpression lysate, and/or a peptide competition of the primary antibody may be used.


NO BANDS / SIGNAL
ISSUERECOMMENDATION
Antibody concentrationIncrease the concentration of the primary or secondary antibody.

Non-specific binding of primary antibody Use the blocking step just prior to primary antibody incubation.

Protein concentrationTiter the total protein lysates until the signal appears.

It is best to use a positive control lysate to show expression in the the target protein, or an over-expression lysate, or a recombinant protein.

Use a fraction specific prep to increase the concentration of the protein such as a nuclear prep vs. a whole cell prep.

Make sure that the lysis buffer used was strong enough to disrupt the cell's membrane.

Ensure complete protein transfer to the membrane by Ponceau staining and that the proteins have left the gel by Coomassie staining.
Antibody compatibilityEnsure that the primary antibody reacts with the species of the lysate and it is suitable for western blot.

Make sure the primary antibody reacts with the secondary antibody.
BlockingLower the concentration of the blocking agent or lessen the incubation time.
ECL ReactionAlways use fresh reagents. Test by dot blotting the secondary antibody onto membrane and incubating with ECL.
Image exposureIncrease exposure time of the film.
Native proteinsSome antibodies can not be used on reduced or denatured proteins. Run blot with proteins in native conformation, without SDS.
Small proteinsUse smaller pore size membrane (0.2um instead of 0.45um) to prevent transfer through the membrane.
Large proteins Use lower percent gel and use a lower voltage to transfer overnight at 4C.
Add SDS to transfer buffer and lower the concentration of methanol.
Sodium AzideRemove from all buffers as it inhibits the HRP reaction.


HIGH UNIFORM BACKGROUND
ISSUERECOMMENDATION
Insufficient blockingBlock for one hour at room temp, use 3 % - 5 % BSA instead of milk.
Insufficient washingWash for five minutes three to fives times on a high speed orbital shaker. Use a large volume of wash buffer.
Non-specific bindingLower the concentration of primary and secondary antibodies by diluting in blocking solution.

Incubate primary antibody overnight at 4C.

Confirm secondary is specific by omitting the primary, and running a control blot.
Incompatible blockDo not use milk if you are using a phospho-specific antibody or an avidin/strepavidin secondary. Milk contains biotin and casein.

Do not use milk or BSA if secondary is anti-bovine, anti-goat, or anti-sheep. This will the secondary to recognize the bovine IgG in the block. Use 5 % serum from host animal of the secondary antibody.
Dry membraneDo not allow membrane to dry out after applying the antibody, keep covered with parafilm.
Film exposure Reduce time or wait fifteen minutes before exposing.
ECL incubation Reduce development time by 1-3 minutes.


SWIRLY SPECKED BACKGROUND
ISSUERECOMMENDATION
Mishandling of membrane Try to minimize contact of the membrane and gel. Use clean tools to touch membrane and gel. Do not use hands to directly touch the membrane.
Buffer contamination Use fresh buffers for every experiment. Make sure to filter the buffer before use.
Uneven plastic wrapUse sheet protectors instead of plastic wrap. They are made up of tougher plastic and easier to uniformly flatten.
Air bubblesGently roll out all air bubbles between the membrane and the gel prior to starting the transfer step.
HRP aggregation Filter the secondary antibody with 0.2um filter to remove aggregates.
Insufficent washingWash for five minutes three to fives times on a high speed orbital shaker. Also try to use a larger volume of wash buffer.


WHITE BANDS
ISSUERECOMMENDATION
Too much antibody/proteinWhite bands surrounded by black are caused by intense localized signal that completely exhausts the ECL reaction with a quick burst of light. No light is then produced during development and a white band occurs. Use a more diluted primary, secondary, or protein concentration.


SMEARED BANDS / LANES
ISSUERECOMMENDATION
Protein loadUse less protein and/or try an immunoprecipitation to enrich your target in the lysate.

Antibody concentrationDilute the antibody concentration.