Introduction To Western Blot
Introduction To Western Blot
Western Blotting
Principles
Technical Guidance
Data Analysis
Troubleshooting
Technical Guidance
Data Analysis
Troubleshooting
Chapter
Preface
Introduction
Since Western blotting is one of the most prevalent laboratory procedures
in use today, we have produced this handy reference guide to provide
a basic overview of the key technical considerations that go into performing
successful Western blots. Beyond basic theory, we have included some
typical experiments, as well as troubleshooting advice and time-saving
pointers to make things go more smoothly. We hope you will find this Overview
manual useful, and would greatly appreciate your feedback to Western blotting, also known as immunoblotting or protein blotting,
[email protected]. is a core technique in cell and molecular biology. In most basic terms,
For those who are not already familiar with our products, we specialize it is used to detect the presence of a specific protein in a complex mixture
in antibodies, and have been manufacturing high-quality immunological extracted from cells. The Western blotting procedure relies upon three key
reagents for over 25 years. As a result we think a lot about antibodies, not elements to accomplish this task: the separation of protein mixtures by size
just how they are created, produced and used, but also what is so special using gel electrophoresis; the efficient transfer of separated proteins to
about them. If you can imagine the difficulty of finding a single needle in a solid support; and the specific detection of a target protein by appropriately
haystack, you can begin to appreciate the task accomplished by the antibody matched antibodies. Once detected, the target protein will be visualized
as it successfully finds its corresponding antigen amongst the collection as a band on a blotting membrane, X-ray film, or an imaging system.
of other potential targets present in cellular materials.
Since Western blotting is accomplished rapidly, using simple equipment
If you are choosy about your antibodies and want to find a perfect match for and inexpensive reagents, it is one of the most common laboratory
your experiment, then please give us a try. We focus on antibody production techniques. The results achieved are also easy to interpret, unique,
in small and large scale across a broad range of research areas, and for and unambiguous. Therefore, it is routinely used on its own, or along
a variety of applications. We are so confident in our antibodies and in our with other immunoassays, in research and clinical settings. An overview
ISO-certified production facilities, that we offer a performance guarantee for of the technique is shown in the diagram below:
all the applications listed on our detailed datasheets. We are also available
to help, offering technical support from trained scientists experienced in the
use of antibodies. We can address queries that arise while carrying out your Mr (kDa)
–
1 2 3 Mr (kDa) 1 2 3
experiments, and can also assist in selecting the proper antibodies and
75 75
controls. Please contact our technical team at [email protected].
50 50
Finally, if you do find yourself without access to the antibody you are seeking, 37 37
remember that we are able to identify new specificities using the latest 25 25 target
technology with our parent company MorphoSys. Our HuCAL® recombinant 15 15 protein
antibodies are identified by screening over 45 billion potential specificities
using highly sophisticated techniques to produce new monoclonals faster +
than with traditional methods.
Please visit us at www.abdserotec.com/westernblot to learn more about our
FIGURE 1 Overview of Western Blotting. Separation of protein mixtures by electrophoresis;
Western blotting products, and to search our catalog of over 14,000 antibodies.
transfer to a blotting membrane; and detection of target protein, which only
becomes visible in the final stage as a band similar to that shown in lane 3.
Lane 1: Prestained molecular weight standards. Lanes 2&3: Protein mixtures.
Mr (kDa) 1 2 3
Higher molecular weight
than expected, often due
to glycosylation or
multimer formation.
Antigen
30 Lower molecular weight
22 than expected, usually Recognition sites
due to cleavage or
degradation.
Epitope
FIGURE 2 Expected vs. Actual Molecular Weight. Lane 1: Target protein band Antibody
at the expected molecular weight. Lanes 2&3: Common alterations
that modify the molecular weight.
Western blots are in wide use across a broad range of scientific and clinical
disciplines. Their ability to clearly show the presence of a specific protein both
by size and through the binding of an antibody makes them well-suited for
evaluating levels of protein expression in cells, and for monitoring fractions
during protein purification. Likewise, they are helpful for comparing expression FIGURE 3 Antibody-Antigen Interaction
of a target protein from various tissues, or seeing how a particular protein
responds to disease or drug treatment.
Chapter
Epitope Tags
If there are no antibodies available to the protein of interest, it is still
Samples, Gels, and Blotting
possible to carry out a range of immunodetection techniques, including Western
blotting, by using epitope tags and matched epitope tag antibodies.
This elegant strategy works by adding a small sequence of DNA that codes
for a known antigenic epitope during cloning of the protein of interest.
Since matched antibodies already exist that will specifically bind to this epitope,
the target protein can be detected because it also expresses the appropriate
Overview
epitope. Therefore, immunodetection can be carried out quickly and without the A typical Western blot, or immunoblot, relies upon a purified, semi-purified,
need to wait for the generation of unique antibodies to a newly identified target or crude extract of cellular proteins containing a target protein that can
protein. This technology is also of significant benefit when working in organisms be detected by antibodies. Several key steps are required to take the sample
where few specific antibodies are readily available. One downside to this from the cellular starting point to a detectible band on a Western blot.
technology is that the target protein is altered by the addition of tag, This chapter focuses on the preparative stages that are accomplished prior
and thus it is not identical to native forms of the protein. to immunodetection by antibodies. Throughout these processes it is essential
that the cellular protein is prepared and stored carefully, since this will
There are a wide variety of epitope tag antibodies available, including: significantly impact the experimental results.
His-6 (MCA1396), V5 (MCA1360), c-myc (MCA2200), and others which are
The three key preparative stages are:
supplied by AbD Serotec. Epitope tag antibodies are available with a range
of common antibody labels allowing one to switch experimental techniques • Sample production by lysis or homogenization to solubilize
or detection systems without having to modify the target protein. In the Western and release cellular proteins.
blots shown below, myc-tagged KSR (Kinase Suppressor of Ras) is detected • Separation of protein mixtures using gel electrophoresis.
through the use of either an anti-myc antibody or an anti-KSR antibody. • Transfer of separated proteins to a blotting membrane which
A: B:
can be manipulated more easily than a gel.
Anti-KSR
A B antibody
Mr (kDa) 1 2 3 4
Mr (kDa)
–
1 2 3
160
105 KSR Myc-tag 75
75
50
50 37
Anti-myc
antibody 25
35
15
+
FIGURE 5 Sample Preparation, Electrophoresis, and Transfer
FIGURE 4 Western Blot and Model of Myc-tagged KSR. PANEL A: Myc-tagged murine
KSR expressed in COS cells is detected using either anti-KSR (MCA2106) Western blots are effective in detecting low nanogram to low picogram
in lanes 1&2, or anti-myc epitope (MCA2200) in lanes 3&4. Lanes 1&3: myc-KSR amounts of target protein, depending on the antibodies used and the detection
vector. Lanes 2&4: vector alone control. Note that an identical band is produced substrate chosen. If the target is suspected to be of very low abundance,
with both antibodies. PANEL B: KSR target protein with c-myc epitope tag. or if there is no detectible signal on the blot, then it may be necessary
KSR-myc fusion is detectible by both anti-KSR antibodies and anti-myc antibodies. to concentrate, immunoprecipitate, or fractionate the starting material.
10 C hapte r 1 Your fi rs t choi ce for anti bodi es ! www.abds erot e c . c om Chapter 2 11
Sample Preparation The amount of lysis buffer is determined based upon a cell count,
or else it is estimated based upon the size of the tissue culture vessel.
Cell Lysates The accompanying table provides some suggested starting points. Sometimes
mechanical disruption, such as with sonication or dounce homogenization,
Crude cellular lysates are the most common direct source of starting material is required to fully release proteins from certain cell and tissue samples.
used in Western blotting. They can be prepared from immortalized cell lines Sonication is also used to break down cellular DNA which can interfere either
known to express the target protein, or from transfected cells carrying a protein due to its high viscosity or via non-specific binding. After lysis and
expression vector. Many different cell types (mammalian, insect, yeast, centrifugation, the amount of protein in each lysate is measured.
or bacteria) can be used to supply the protein needed with slight variations
in the preparation procedure. In most cases, the cells are harvested, washed, Cell Lysis Volume Recommendations
and lysed to release the target protein. For best results, all these steps should
be carried out in a cold room, or on ice. This will minimize proteolysis,
Type of cells Amount of material Volume of lysis buffer
dephosphorylation, and denaturation, since all begin to occur once the cells
are disrupted. It is possible to simply lyse cells directly in gel loading buffer Tissue Culture 107 cells or 1 ml
if a quick check is all that is required. However, sonication may be neccessary 100 mm dish
to disrupt the highly viscous cellular DNA. Usually, 20-50 mg of cellular lysate
is loaded per lane for gel electrophoresis.
Whole Tissue 100 mg Add 2 ml and sonicate or
dounce homogenize
Harvest and wash Lyse cells on ice
cells on ice to release proteins
Bacteria Spin sample, estimate volume Add 10 volumes and vortex
Tissue Samples
Tissue samples display a higher degree of structure than cultured cells and
FIGURE 6 Cells are Harvested, Washed, and Lysed to Release Proteins thus may require higher levels of mechanical intervention in order to release
the protein of interest. They may also contain multiple cell types which are
Choosing the proper lysis buffer and determining an appropriate volume is often
differentially responsive to the lysis buffer chosen. Smaller solid tissue samples
a trial and error process that is affected by the type of protein being isolated
(up to 100 mg) are placed in ice cold extraction buffer and homogenized
as well as the particular cells used as a source. Lysis buffers vary from very gentle
on ice, usually with sonication or a douncing rod to facilitate cellular disruption.
ones with no detergent to harsher solutions such as RIPA (Radio Immuno
Alternatively, and more often with larger tissue samples, a blender is used
Precipitation Assay) buffer, which is denaturing and contains multiple detergents.
to homogenize the tissue in PBS, and then cell lysis buffer is added. Once the
Typically, NP-40 (Nonidet P-40) lysis buffer, with a milder non-ionic detergent,
tissue has been homogenized and lysed, the solubilized cellular components
is used for the isolation of soluble cytoplasmic proteins. At other times, RIPA
are clarified by centrifugation and tested for protein concentration prior
buffer is chosen because it reduces background, and because sometimes multiple
to loading on a gel.
detergents are required to fully release membrane bound or nuclear proteins.
Consideration should also be given to the antibody-antigen interaction which
may be affected by the changes to the target protein during lysis.
purification. These samples rarely require any further manipulation and are Denaturing & + + Removes all higher order structure,
simply mixed with gel electrophoresis loading buffer (Laemmli sample buffer). Reducing including disulfide bonds
When using a purified or semi-purified protein preparation, it is possible to
Denaturing + - Higher order structure is disrupted,
load a much smaller amount of total protein onto the gel. Usually 0.5-1 mg
but disulfide bonds are retained
of purified or semi-purified protein is sufficient to observe a strong signal.
If unsure, results can be improved by loading several dilutions of the sample. Reducing - + Disulfides are removed, but most
higher order structure remains
Most often the gel is made and run under denaturing conditions (25 mM Tris Mr (kDa)
base, 192 mM glycine, 0.1% SDS, at pH 8.3). However, alternative gel conditions Mr (kDa)
can be used, depending upon the protein under investigation and the aims of
260
260
the experiment. Options include: non-denaturing, non-reducing, native, two- 160
160
dimensional separations (by size and by isoelectric point), and buffer variations 110
110
80
80
that are more suited to the separation of smaller or larger proteins. It is 60
60
important to make sure that the buffer used is compatible with later steps in 50
50
the procedure and the blotting materials. 40
40
30
30
SDS-PAGE gels (commercially supplied or made in-house) usually consist
of a main gel, which is poured between two glass or plastic plates, and which 20
20
is sometimes topped by a short stacking gel. Gels can be made with a uniform 15
15
Acrylamide Concentration (%) Separation Range (kDa) FIGURE 7 HeLa Cell Lysates (LYS001) Separated on a 4-12% Gradient Gel
5 60-210
7.5 35-95
10 15-70
15 4-45
Blotting Membranes
The solid support onto which the separated proteins are transferred is usually
of two types, nitrocellulose or polyvinylidene fluoride (PVDF) membrane, both
of which bind proteins with high affinity. Nitrocellulose has been in use for
a long time, and is sometimes preferred because of its excellent protein binding
and retention capabilities. However, nitrocellulose is brittle and thus it is usually
less effective when blots need to be reused. PVDF demonstrates superior
mechanical strength making it suitable for stripping/reprobing and for further
protein characterization techniques, such as sequencing and proteolysis
Sometimes higher background staining is seen with PVDF membranes, FIGURE 8 Western Transfer Methods
and extra care must be taken to prevent this from occurring.
60
60
The size of the target protein should be considered when choosing transfer
conditions. Generally, smaller proteins will transfer out of the gel faster, 50
50
40
40
and may actually transfer through the blotting membrane into the filter papers
beyond. Blotting membranes with a smaller pore size can be used for small 30
30
proteins and peptides, and SDS can be reduced or eliminated from the transfer
buffer to improve binding to the membrane. If there is a suspicion that the 20
20
Chapter
Blocking
Blocking is a very important step in the immunodetection phase of Western
blotting because it prevents non-specific binding of antibody to the blotting
membrane. The most commonly used blocking solutions contain 3-5% BSA
or non-fat dried milk (also known as Blotto or BLOTTO) in a solution of PBS
(phosphate buffered saline) or TBS (tris buffered saline). Often, a small
Overview amount of Tween®20 detergent is added to blocking and washing solutions
to reduce background staining, and the buffer is known as PBST or TBST.
After blotting, the target protein will be detected using appropriately matched When choosing between these buffers, it is important to note that TBS/TBST
and labeled antibodies. The typical immunodetection stage involves a few is preferred with AP (Alkaline Phosphatase) labeled antibodies because PBS
basic steps: will interfere with the AP signal.
• Blocking - The blot containing the transferred protein bands is incubated Non-fat dried milk is considered to be a good starting point when selecting
with a protein or detergent solution which covers the entire surface a blocking solution because it is inexpensive and in very wide use. However,
so that antibodies do not bind non-specifically to the membrane. milk proteins are not compatible with all detection labels, so care must be
• Antibody incubation - Labeled antibody binds to the target protein taken to choose the appropriate blocking solution for the antibodies, buffers,
band present on the blot in a one-step or two-step procedure. and detection reagents. For example, BSA blocking solutions are preferred
with biotin and AP antibody labels, and anti-phosphoprotein antibodies.
• Detection with substrate - The label attached to the antibody, This is because milk solutions contain casein, which is itself a phosphoprotein,
usually an enzyme such as HRP (Horseradish Peroxidase), is detected and biotin, thus it will interfere with the assay results. Commercially supplied
using a substrate which produces a visible signal corresponding blocking solutions, such as Block Ace (BUF029) from AbD Serotec, are very
to the position of the target protein. convenient to use and can improve consistency of results, especially when
non-specific background signal is an issue. After blocking, the blot is rinsed
Mr (kDa) 1 2 3 in wash buffer, usually TBST, with gentle agitation and in sufficient volume
Add Add to keep the blot submerged. Please refer to Chapter 5 for detailed protocols.
antibodies substrate 75
50 Antibody Incubation
37
After blocking and washing, the blot will be incubated in a dilute solution
25 target
of antibody, usually for a few hours at room temperature or overnight
15 protein
at 4°C. The antibody is diluted in wash buffer (PBST or TBST) or a diluted
blocking solution, the choice depends upon the antibody. At AbD Serotec,
we offer a HISPEC assay diluent (BUF049A) which can be used with primary
and or secondary antibodies to reduce cross-reactivity and minimize
FIGURE 10 Immunodetection Overview. The Western blot is blocked, incubated with non-specific binding. Since antibody preparations vary in their levels of
antibodies, and treated with substrate to make the target protein visible. Wash purity and specific binding properties, there will be differences in the level
steps are carried out between incubations to remove excess unbound material of dilution required. For example, purified antibodies are usually diluted
and to minimize non-specific signal on the immunoblot. to a 1-10 mg/ml final concentration. The manufacturer’s datasheet should
provide dilution recommendations for a particular preparation. However,
it is best to test a range of dilutions with each new antibody, optimizing
conditions for the samples under consideration. Dot blots, slot blots,
or test blots (see the end of this chapter) can be used for checking various
Indirect vs. Direct Detection Faster overall, since there are fewer steps. Often gives a stronger signal because
multiple secondary antibodies bind
Antibody detection of the target protein is accomplished using a one-step Less chance of non-specific signal. to each primary antibody.
or two-step protocol. The one-step procedure, direct detection, relies upon
a single antibody which has been covalently joined to an easily detected label Easy to change label type or detection
molecule (biotin, an enzyme, or a fluorescent dye). Labeled primary antibodies methods for a new experiment
can be ordered directly from AbD Serotec or other commercial antibody suppliers. by swapping secondaries.
In addition, it is possible to directly label an antibody by using a commercially Saves labeling time and expense, especially
supplied labeling kit such as our LYNX Rapid Conjugation Kits®, or with when all primary antibodies are made in the
in-house reagents. same species.
With indirect detection, two different antibodies are used in sequence Provides access to a wider range of labels.
for the detection step. First, the Western blot is incubated with an unlabeled
primary antibody directed against the target protein. After washing,
a labeled secondary antibody is used to detect the presence of the primary Disadvantages Disadvantages
antibody, and thus the target protein. The labeled secondary antibody is typically
oupling of label to the primary antibody may
C More non-specific signal can arise from
directed against the immunoglobulin class or subclass of the primary antibody’s affect the antibody’s ability to bind to the the binding of the secondary antibody
species. For example, one of our popular secondaries is STAR88P, a purified target protein. to other proteins on the blot.
donkey antibody raised against goat/sheep immunoglobulin (IgG) which
is coupled to an HRP label. Biotinylated primary antibodies also require L abeling every primary antibody adds Extra incubation and wash steps add time
time and cost. to the experiment.
a two-step detection procedure; however, the second step involves incubation
with streptavidin, a bacterial protein, conjugated to HRP (or AP), rather than with
a labeled antibody.
Dot blots and slot blots are also a very useful variation on the typical Western
blot. They do not require gel electrophoresis, so there is no separation
of proteins by size. Instead, the target protein or cell lysate mixture is added
FIGURE 13 Detection of the Antibody Label. The antibody label is exposed to substrate directly onto the surface of the nitrocellulose or PVDF membrane. Protein
in the final stages, creating a visible band either on the surface of the blot solutions can be applied directly in a small volume, or with a vacuum
(colorimetric substrates), or as light emission (ECL substrate) captured manifold to produce an orderly grid of samples similar to that seen in Figure
on X-ray film or with a CCD camera. 14. Each dot or slot blot would contain known amounts of target protein
Chapter
or cell lysate. Once dry, dot blots and slot blots are subjected to the same
immunodetection steps used for Western blotting, i.e. blocking, antibody
incubation, and target detection with substrate. Grey and black spots on the
figure below indicate which samples are positive for the target protein and
correspond roughly to the bands produced on a Western blot.
Overview
The data produced with a Western blot is usually quite easy to interpret.
In the majority of cases, bands corresponding to the target protein will
become visible upon treatment of the blot with substrate. Their identity
is confirmed by comparison to molecular weight markers (for size)
and a positive control (size and signal). In some cases the data may
1. Block
be more complex, showing unexpected sizes, multiple bands,
2. Antibody Incubation
3. Target Detection or alteration in bands following a particular treatment. The focus of this
chapter is analysis and as such the data itself will be discussed along
with examples of different types of Western blot data from research
and clinical settings to demonstrate the flexibility of the technique.
If there are no bands on the blot, or if there are unexplained blotches
or uneven signal, troubleshooting advice is offered in Chapter 6.
Data
FIGURE 14 Dot Blots and Slot Blots. The dot blots at the left represent a dilution series Quantitation
of a sample, with smaller lighter dots corresponding to lower concentrations It is very important to be aware that the data produced with a Western
of target protein. The slot blots represent a group of random samples, blot is typically considered to be semi-quantitative. That is, it provides
the intensity of the signal corresponds to the concentration of the target a relative comparison of protein levels, but not an absolute measure
protein in that sample. of quantity for a specific target protein in a particular experiment.
The reason for this is two-fold: first, there will be variations in loading
By making a number of identical dots or slots of a single known protein
and transfer rates between the samples in separate lanes and on
sample, or a range of sample dilutions, one can quickly test several
separate blots that will need to be normalized before a more precise
combinations and concentrations of primary and secondary antibodies.
comparison can be made; second, the signal generated will not be
Dot blots and slot blots are also beneficial when screening a large number
linear across the concentration range of samples due to substrate
of samples, or if a simple answer will suffice. The main downside to slot
availability and linear responsiveness of the detection method. Since
blots/dot blots is that they provide no information about molecular weight.
the signal produced is not linear, it should not be used to attach
Thus, it is harder to detect false positive signals, or to tell whether modified
a precise concentration to a particular sample. ELISAs are more
forms of a protein are present.
suitable for this purpose and generally more sensitive.
Densitometers and Analysis Software FIGURE 16 Detection of Rat Homer Protein Isoforms. Western blot of Homer isoforms
In order to make a permanent record, or to get an objective measure of the probed with anti-Homer [177-366] (AHP737) which detects the control and
signal generated on a Western blot, a densitometer is used to scan the blot isoform 1c. Lane 1: control, 30 mg rat cortical extract. Lane 2: untransfected
or film. Imaging software is then used to compare the signal generated control. Lane 3: Isoform 1a. Lane 4: Isoform 2b. Lane 5: Isoform 1c.
by the bands detected on the Western blot.
102
81 30
46 25
33
30 12
Chapter
Confirmation of HIV
In the diagnosis of HIV infection in patients, an ELISA is used first because
it demonstrates 99.5% specificity and is quick and easy to perform on
a large number of samples. Western blotting is used as a supplementary
assay because the ELISA is subject to false positives. In order to perform this
assay, patient serum samples are used as the source of antibodies for
immunodetection, and blots containing HIV antigens, proteins, viral lysates, Overview
or peptides are used as the source of target antigen on the Western blot.
The following buffers and methods provide a general starting point for use
If the HIV target proteins on the blot are detected by the patient serum then
with the majority of AbD Serotec reagents in Western blotting. When specific
it indicates that the patient sample is a true positive for HIV infection, since
recommendations are provided on product datasheets, those instructions
an immune response has been mounted by the patient. A similar strategy
should always be used instead of the general guidance offered here.
is also used in tests for Lyme disease and autoimmune disease.
With specialized laboratory equipment, such as for gel electrophoresis
and electroblotting, it is advisable to follow the manufacturer’s instructions.
If difficulties arise with any of our antibodies or related products, please feel
free to contact [email protected], as we may have additional
information on file and can assist with troubleshooting.
Buffers
N.B. Azide should not be added to any buffers that will be used with
HRP-labeled antibodies because it will inactivate the HRP enzyme.
PBS
8.0 g NaCl
0.2 g KCl
1.15 g Na2HPO4
0.2 g KH2PO4
Dissolve in 800 ml distilled water, adjust pH to 7.4, and then add more dH20
to a final volume of 1 liter. Sterilize by autoclaving and store at room
temperature (RT).
TBS
8.0 g NaCl
0.2 g KCl
3.0 g Tris base
Dissolve in 800 ml distilled water, adjust pH to 8.0 with 1 M HCl, and then
add more dH20 to a final volume of 1 liter. Sterilize by autoclaving and store at RT.
Suspension cells:
1. Pipet cells into a fresh conical tube and place on ice.
2. Spin cells on low speed at 4°C, and aspirate off media.
3. Add 10 ml ice cold PBS, and gently invert tube to wash cells.
4. Spin cells on low speed, and aspirate off supernatant.
5. Repeat wash and aspiration. Resuspend cells in 5 ml ice cold PBS.
6. Count cells, and centrifuge on low speed at 4°C to form a cell pellet.
Aspirate off liquid.
7. Gently resuspend the cell pellet in ice cold cell lysis buffer (with fresh
protease inhibitors), use 1 ml buffer for 107 cells.
8. Incubate cells for 30 minutes on ice. If needed, sonicate the lysates
on ice for 15-30 seconds to disrupt genomic DNA and cellular components.
9. Transfer to a microfuge tube and clarify the lysate by spinning at 4°C,
for 10 minutes at 12,000 RPM.
Gel Electrophoresis & Protein Transfer by Electroblotting 7. Drain excess PBS/TBS from the membrane and transfer to appropriate
enzyme substrate solution and incubate for time period recommended
* Detailed instructions for making gels in-house can be found in Sambrook et al. by manufacturer to visualize protein bands.
1. For standard denaturing and reducing conditions, mix sample 1:1 by volume
with Laemmli 2x sample buffer. Immunodetection – Direct
2. Heat to 100oC for 5 minutes or 70oC for 10 minutes. 1. Place membrane into blocking solution for at least 2 hours at RT,
3. Load 20-50 mg sample per lane, along with suitable positive or overnight at 4°C. Use a sufficient volume to keep the blot fully covered,
and negative controls. with gentle agitation throughout.
4. Run the gel and transfer to PVDF or nitrocellulose membrane according 2. Rinse the membrane briefly in washing buffer and then incubate
to the manufacturer’s instructions for the equipment and materials in use. with labeled primary antibody diluted in wash buffer or blocking buffer
5. Confirm protein transfer by staining for 1 minute with Ponceau S, followed (a concentration of 1-10 µg/ml is generally acceptable). Incubate overnight
by complete destain in distilled water. at 4°C, or for 2 hours at room temperature. Use a sufficient volume to keep
6. Mark position of molecular weight standards if they are unlabeled. the blot fully covered, with gentle agitation throughout.
3. Wash the membrane in a sufficient volume and with gentle agitation
(For our in-house Western blotting, we use NuPAGE® Novex® precast 4-12%
as follows: 4x5 minutes in wash buffer and 2x5 minutes in PBS or TBS.
gradient gels run in Tris-Acetate buffer and transferred to nitrocellulose using
the Xcell SureLockTM II blot module from Invitrogen, as per the manufacturer’s 4. Drain excess PBS/TBS from the membrane and transfer to appropriate
instructions.) enzyme substrate solution and incubate for time period recommended
by manufacturer to visualize protein bands.
Chapter
Difference seen Possible Cause Action/Solution
Band(s) at lower T arget protein has been cleaved Use a fresh sample which has been
molecular weight than or digested kept on ice
expected Splice variants exist Add fresh protease inhibitors
Another protein bearing the to the lysis buffer
Overview same/similar epitope has been Try alternate antibody
detected by antibody
While Western blotting is a relatively simple and straightforward technique,
Band(s) at slightly Protein may be glycosylated Use enzymes to remove suspected
it does not always yield results that meet with expectations. When this higher molecular or otherwise modified at one modification returning molecular
occurs, it is useful to be able to quickly isolate the possible causes and weight than expected, or more amino acid residues weight closer to expected
to formulate an effective solution by troubleshooting the experiment. In this and may be blurred Check amino acid sequence
chapter, suggestions are offered to assist in identifying and resolving some and literature
frequently encountered problems that arise during the course of Western Band(s) at significantly Dimers, multimers, or protein- Add fresh DTT or bME to samples and
higher molecular protein interactions may be reheat before repeating experiment
blotting. Many of these problems can be avoided with careful attention
weight than expected occurring because samples Prepare new samples with fresh
to experimental protocols, and with optimization at key stages throughout have not been fully reduced and loading buffer
the procedure. As mentioned at the end of Chapter 3, the proper antibody denatured
concentration can be determined with the use of dot blots and slot blots, Multiple bands Primary antibody concentration Use an affinity-purified primary
significantly reducing the need for future troubleshooting. Additionally, at various molecular may be too high, or there antibody
the use of negative and positive controls are of great help in assessing where weights is a cross-reactivity with similar Optimize primary antibody
epitopes on other proteins concentration
things have gone wrong, and eliminating some possible sources of error Try another antibody
under consideration. Check antibody specificity with
blocking peptide
Since one issue that commonly arises during Western blotting is the presence Secondary antibody Decrease/optimize the concentration
of unusual or unexpected bands on the blot, our troubleshooting section concentration is too high leading of the secondary antibody
begins with a table describing some common reasons and potential solutions to non-specific binding Use an affinity-purified secondary
for addressing and evaluating this type of problem. antibody
Repeat immunodetection with
In most cases, the rest of the troubleshooting issues can be grouped into secondary antibody alone to check
for non-specific binding
three major types: no bands, faint bands, and signal on Western blots that
Protein exists in several different Check literature
interferes with bands. Therefore, the potential causes and solutions have been
isoforms
organized in this manner, and also with regard to potential problem sources, Bands are blurry Gel was run at too high a voltage Repeat gel at lower voltage
i.e. antibody, antigen, technique, or buffer related where applicable. For Incorrect running buffer Prepare fresh running buffer
further assistance when using our products in Western blotting, contact composition
[email protected]. Trapped air bubble present Carefully remove air bubbles between
during transfer the gel and the membrane before
protein transfer
Bands are smile Running conditions were too fast Check and optimize gel
shaped, not flat so gel became over heated electrophoresis conditions
Run gel at 4°C
White (negative) bands Too much protein has been Load less sample
on the film when using loaded Repeat with dilution series of sample
ECL detection Antibody concentration Reduce/optimize the antibody
is too high concentrations
Antibody related Inappropriate secondary Retrace steps to check compatibility Antibody related Primary or secondary antibody Repeat using higher concentration
antibody used between primary and secondary antibodies concentrations were too low of antibody
Reprobe with correct secondary or strip blot Optimize antibody concentration with
and reprobe if necessary dot blots
Repeat experiment with the correct
antibody combination Low antigen-antibody Reduce the number of wash steps
Wrong concentration of Increase the antibody concentration binding affinity to a minimum
antibody or low affinity to the 2-4 fold higher than initially recommended Increase the antibody concentration
target protein Increase length of incubation 2-4 fold higher than the recommended
Test/optimize antibody on dot blots starting dilution
Try another antibody
Antigen related Insufficient sample loaded on Check concentration of sample
Antibody not suitable C
heck datasheet for recommended conditions the gel Increase the amount of source material
for Western blotting Test/optimize antibody on dot blots Immunoprecipitate, fractionate,
Try alternate antibody or concentrate sample
Antibody has lost activity Test on a dot blot at several concentrations
due to long term or improper Use fresh aliquot of antibody that has been Blot has been stripped Redo blot since antigen may have been
storage stored at -20°C or below and reprobed stripped off or damaged by stripping
Antigen related Antigen not expressed Use another source of target protein process
in the source material Technique related Low transfer efficiency Confirm transfer with Ponceau S staining
Not enough antigen loaded Check concentration of sample Optimize transfer conditions for target
on the gel Increase the amount of source material protein size
Immunoprecipitate, fractionate, Optimize transfer buffers for methanol
or concentrate the sample and SDS concentrations
Technique related Transfer did not work properly onfirm protein transfer by staining the
C Film exposure time (ECL Test different exposure times
membrane with Ponceau S and/or the gel detection) was too short
with Coomassie dye.
N
ote how well any prestained molecular Buffer related Non-fat dry milk may mask Decrease % of milk in the blocking
weight markers have transferred onto the blot some antigens and antibody solutions
Optimize/check transfer conditions and set Try alternate blocking solution
up (especially orientation to electrodes)
Repeat using two membranes in case
protein has transferred through the first
Washes are too stringent Use fewer washers
Reduce washing time
Buffer related Blocking agent is interfering Try lower concentration
with signal Try alternate blocking agent
Buffers may contain sodium Use azide free buffers
azide which inactivates HRP
Peroxide may be inactive Add fresh peroxide to substrate buffer
reducing activity of peroxidase
ECL detection reagents have Use fresh detection reagents
been contaminated
Antibody related Concentration of primary and/or Reduce/optimize the antibody Antibody related HRP-linked secondary antibody Spin secondary antibody and filter
secondary antibody too high concentrations has aggregated to remove aggregates
Reduce/optimize incubation times
Use affinity purified antibodies Technique related Not enough solution used during Make sure the membrane is fully
Primary and/or secondary binds Use alternate blocking solution incubation and/or washing immersed and agitated throughout
to the blocking agent incubations
Antibody has reduced activity due U
se a fresh aliquot of antibody that Trapped air bubbles Carefully remove air bubbles between
to long term or improper storage has been stored at -20°C or below the gel and the membrane before
Phospho-specific antibody U
se alternate blocking solution- BSA protein transfer
has reacted with casein or Block Ace (AbD Serotec BUF029)
(a phosphoprotein) in nonfat Uneven agitation during Use a shaker for all incubations
milk blocking agent incubation
Secondary antibody is binding Try another blocking agent Buffer related Antibodies are binding to the Filter the blocking agent
to blocking agent Reduce protein concentration blocking agent Try another blocking agent
of blocking agent
Test secondary antibody alone on blot
Try alternate form of secondary,
such as F(ab’)2
Antigen related Non-specific interaction with Sonicate the lysates
genomic DNA in samples Add DNAse to lysis buffer
Technique related Membrane blocking is C
onfirm concentration matches
not sufficiant that recommended in the protocol
Try other blocking agents
Try alternate incubation temperatures,
including room temperature
Membrane has dried out Repeat procedure taking care that the
blot does not dry out during any step
by using sufficient volumes and
agitation throughout
PVDF membrane has higher Try nitrocellulose instead
background
Inadequate washing between Increase the length of washing steps
incubations Use a larger volume of wash buffer
Incubation temperature too high Try alternate incubation temperatures
such as 4°C
Film over-exposed or blot Wait 5-10 minutes and then re-expose
developed for too long blot to film
Reduce exposure and/or development
times
Buffer related Insufficient concentration Use TBS containing >0.1% Tween® 20
of detergent in the buffers Try stronger detergent, such as NP-40
Transfer, incubation, or blocking Use fresh buffers
solutions are contaminated
HuCAL® and LYNX Rapid Conjugation Kit® are registered trademarks of MorphoSys UK Ltd.
HuCAL® products are for in vitro use only. All AbD Serotec reagents are for research purposes
only, not for therapeutic or diagnostic use.
DyLight® dyes are a registered trademark of Thermo Fisher Scientific and its subsidiaries. LI-COR®
and Odyssey® Blocking Buffer are registered trademarks of LI-COR Biosciences. NuPAGE®
and Novex® are registered trademarks of Invitrogen.
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LIT.CMR.2009.1 © MorphoSys UK Ltd 2009. All rights reserved. Published by MorphoSys UK Ltd. Endeavour House, Langford Business
Park, Langford Lane, Kidlington, Oxford OX5 1GE, UK.