SDS PAGE, WESTERN BLOTTING, AND ELISA

Presented by
Parul Sharma
PGD20225872
M.Pharm Pharmacology
1
SDS PAGE, WESTERN BLOTTING, AND
ELISA

SDS PAGE
(Sodium dodecyl sulfate
Polyacrylamide Gel
Electrophoresis)
SDS-PAGE is widely used to analyze the proteins in complex extracts. The most used
methods are derived from the discontinuous SDS-PAGE system first described by
Laemmli (1970).
The system consists of two gels - a resolving (aka running) gel in which proteins are
resolved based on their molecular weights (MWs) and a stacking gel in which proteins
are concentrated prior to entering the resolving gel. Differences in the compositions of
the stacking gel, resolving gel and electrophoresis buffer produce a system that is
capable of finely resolving proteins according to their MWs.
2

Chemistry of
acrylamide
polymerization
• The polyacrylamide gels are used to
separate proteins.
• Polyacrylamide is inert, and hence,
shows no interaction with the protein
being separated and forms a matrix.
• Size of the pores in the gel can be
controlled by adjusting the
concentration of acrylamide.
• Acrylamide undergoes polymerization
in order to form a gel. Hence, APS
(ammonium per sulphate) & TEMED
(N,N,N’,N’-
tetramethylethylenediamine) are
added to initiate the process of
polymerization.
3

• APS & TEMED are added to the very last step of gel preparation
because the process of polymerization of acrylamide starts as soon
as TEMED is added to the preparation.
• APS generates acrylamide free radicals so that free radical
polymerization can be initiated.
• TEMED is a free radical stabilizer and is added to promote
polymerization.
4

Proteins are
denatured prior to
electrophoresis
• Proteins show tremendous variation in
their amino acid compositions and in
the distribution of amino acids in their
folded structures, features with
important implications for
electrophoresis.
• Because proteins are so diverse with
respect to their surface charges and
geometries, the molecular weights of
folded proteins cannot be simply
determined by their migration rate in
an electric field. Positively and
negatively charged proteins would
migrate in different directions.
5

6
• To resolve the proteins in a sample
according to their size, proteins are
converted to a uniform geometry by binding
to amino acids in protein and imparting a
uniform charge/mass ratio to the proteins.
• In SDS-PAGE, the solution is to denature the
proteins by boiling them with the anionic
detergent, sodium dodecyl sulfate (SDS),
and 2-mercaptoethanol.
• The combination of heat and detergent is
sufficient to break the many noncovalent
bonds that stabilize protein folds, and 2-
mercaptoethanol breaks any covalent bonds
between cysteine residues.
• SDS being an anionic surfactant when
dissolved in water gives a net negative
charge to the denatured protein. One
molecule of SDS binds every 2 amino acids
of the protein.

Discontinuities between the stacking and running gels
underlie the resolving power of the SDS-PAGE gels
• The stacking and running (resolving) gels have
different pore sizes, ionic strengths and pHs.
• Stacking gel contains less concentration of acrylamide
and is prepared using Tris HCl buffer with pH 6.8
• Resolving/separating gel contains higher
concentration of acrylamide and is prepared using Tris
HCl buffer with pH 8.8
• SDS PAGE electrophoresis buffer is made using Tris
glycine buffer with pH 8.3.
• Role of stacking gel is to ensure the movement of all
loaded sample to be concentrated in one tight band
before entering resolving gel.
7

Steps involved in SDS
PAGE electrophoresis
8

1. Gel Preparation
• Gel glass plates are prepared in the glass frame and placed in
the casting frame.
• Comb is placed in between these glass plates. (mark approx.
1cm below the comb, the resolving gel is prepared up to this
mark).
• To ensure that there is no leakage between the plates, we pour
water in between.
• Components for gel preparation includes:
• Polyacrylamide
• Tris HCl buffer
• Sodium dodecyl sulfate (SDS)
• Distilled water
• APS & TEMED
• Prepared gel is then poured in between the glass plates, the
comb is placed, and the gel is left undisturbed for solidification.
9

2. Preparation of running buffer and sample
• Running buffer is prepared using Tris-glycine (pH – 8.3)
• Sample preparation includes the following components
• Protein mixture
• Tris HCl (pH – 6.8)
• SDS
• Beta-mercaptoethanol
• Bromophenol blue
• Glycerol
• Distilled water
10

• Tris HCl buffer is used to maintain the pH
• SDS maintains the primary structure of protein and provides a negative charge to the
protein.
• Beta mercaptoethanol is the reducing agent that breaks –SH bonds between proteins.
• Bromophenol blue dye is used to aid visualization.
• Glycerol provides viscosity to the sample so that it does not come out of wells.
• Distilled water is used for volume makeup.
• Running buffer is then poured in between the gel and the sample is loaded in the wells.
• The whole apparatus is closed and connected to an electrical circuit.
11

3. Supply of electric current
• Once a voltage is applied, the chloride ions in the sample buffer
and stacking gel move rapidly toward the positive pole, forming
the leading edge of a moving ion front.
• Glycine molecules have a very little charge in the stacking gel, so
they migrate at the rear of the moving ion front. This difference in
chloride and glycine mobility sets up a steep voltage gradient in
the stacking gel that sweeps along the negatively charged protein-
SDS complexes.
• The large pores of the stacking gel present very little resistance to
the movement of protein-SDS complexes, which then “stack up”
into a very concentrated region at the interface between the
running and stacking gels.
• Protein-SDS complexes remain concentrated at the interface until
the slowly migrating glycine molecules reach the boundary
between the two gels
12

• Dramatic changes occur as the glycine ions enter the running gel. The
pH of the running gel is closer to the pKa of the glycine amino groups, so
a significant fraction of the glycine molecules assume a negative charge.
• Negatively charged glycine molecules begin to move at the same rate as
the chloride ions, thereby eliminating the voltage difference that
controlled protein mobility through the stacking gel.
• The pores in the running gel are much smaller than those of the stacking
gel, so the pores present frictional resistance to the migration of
proteins.
• Proteins begin to migrate at different rates, because of the sieving
properties of the gel. Smaller protein-SDS complexes migrate more
quickly than larger protein SDS complexes.
• Within a certain range determined by the porosity of the gel, the
migration rate of a protein in the running gel is inversely proportional to
the logarithm of its MW.
• Commonly used dyes for protein visualization are Coomassie blue and
silver stain.
13

• Western blotting, also known as
immunoblotting or protein blotting, is
a core technique in cell and molecular
biology.
• In most basic terms, it is used to
detect the presence of a specific
protein in a complex mixture
extracted from cells.
• The Western blotting procedure relies
upon three key elements to
accomplish this task:
the separation of protein
mixtures by size using gel
electrophoresis;
the efficient transfer of
separated proteins to a solid
support;
and the specific detection of a
target protein by appropriately
matched antibodies.
• Once detected, the target protein will
be visualized as a band on a blotting
membrane, X-ray film, or imaging
system. 16

One of the critical features of any
successful Western blot is the
highly specific interaction between
an antibody and an antigen. The
antigen, usually a protein or
peptide, is the target of the
antibody.
The precise point of interaction is
between a small region of the
antigen, an epitope, and the
recognition sites found on the
arms of the antibody molecule.
Usually, Western blot-positive
antibodies recognize a short linear
sequence of amino acids found
within the target protein that
remains intact, or becomes visible,
when the target protein is fully
unraveled.
This is because most Western blots
are carried out under denaturing
and reducing conditions which
remove all higher-order protein
structures.
17

Monoclonal
and
Polyclonal
Antibodies
18

Genetically Engineered Antibodies
• In addition to traditional monoclonal and
polyclonal antibodies targeted against specific
proteins, there are other means of antibody
generation and protein detection available as
the result of numerous advances in genetic
engineering technology.
• It is now possible to create and produce
antibodies using fully in vitro techniques such as
phage display in conjunction with highly
complex libraries which represent the vast array
of potential antibody binding regions
19

Epitope Tags
20
• If there are no antibodies available to the protein of
interest, it is still 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
the 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
epitope.
• Therefore, immunodetection can be carried out quickly
and without the need to wait for the generation of
unique antibodies to a newly identified target protein.

• A typical Western blot, or
immunoblot, relies upon a
purified, semi-purified, or crude
extract of cellular proteins
containing a target protein that
can be detected by antibodies.
• Several key steps are required to
take the sample from the cellular
starting point to a detectible
band on a Western blot.
21

The three key preparative stages
are:
• Sample production by lysis or
homogenization to solubilize and
release cellular proteins.
• Separation of protein mixtures
using gel electrophoresis.
• Transfer of separated proteins to
a blotting membrane which can be
manipulated more easily than a gel
22

• Western blots are effective in
detecting low nanogram to low
picogram amounts of target
protein, depending on the
antibodies used and the
detection substrate chosen. If
the target is suspected to be of
very low abundance, or if there
is no detectible signal on the
blot, then it may be necessary
to concentrate,
immunoprecipitate, or
fractionate the starting
material
23

Sample
Preparation
Crude cellular lysates are the most common direct
source of starting material used in Western
blotting.
They can be prepared from immortalized cell lines
known to express the target protein, or from
transfected cells carrying a protein expression
vector.
For best results, all these steps should be carried
out in a cold room, or on ice. This will minimize
proteolysis, dephosphorylation, and denaturation
since all begin to occur once the cells are disrupted.
Cell lysis takes place with the help of different
detergents and lysis buffers are used (e.g. NP 40
lysis buffer, RIPA buffer, Protease inhibitors etc.)
A blender is used to homogenize the tissue in PBS,
and then cell lysis buffer is added. Once the tissue
has been homogenized and lysed, the solubilized
cellular components are clarified by centrifugation
and tested for protein concentration prior to
loading on a gel.
24

SDS PAGE
protein
separation
• After the samples have been prepared, they are separated
by size using SDS-PAGE (sodium dodecyl sulpate-
polyacrylamide gel electrophoresis). Since the samples
have been denatured in a gel loading buffer containing SDS
detergent, the protein is uniformly negatively charged and
will now migrate in an electric field through the gel and
towards the positive electrode.
• Since the charge-to-mass ratio is equalized by the binding
of SDS consistently along the length of the proteins, and
higher structure has been removed, the proteins will be
separated primarily by size.
• The key is to effect a separation such that the target
protein will be properly resolved from the other
components of the mixture. This makes it possible to
clearly identify the target protein later through
immunodetection with a specific antibody.
25

Transfer of
protein to
membrane
• We need to transfer protein from the gel into a
membrane. Usually, nitrocellulose or PVDF
(polyvinylidene difluoride) is used.
• 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
• Why protein transfer??
Because in order to detect protein we are going to add
probes. And probes can bind to different regions of the
gel making alterations in our result interpretation. So
the probe should attach only to the target protein.
Another reason is that gel is very fragile because of its
composition and hence rest of the blotting process of
probing and reactions can not be done using gel.
26

27
• While it is possible to use diffusion or vacuum-
assisted transfer, electroblotting (Towbin et
al.,1979) is the method relied upon in most
laboratories, due to the speed and efficiency of
transfer.
• Electrophoretic transfer can be accomplished
under wet or semi-dry conditions.
• In a wet transfer, the gel/blotting paper/filter
paper sandwich is placed into a cassette along
with protective fiber pads. The cassette is then
immersed in a buffer tank and subjected to an
electrical field.
• With semi-dry transfer, the gel/blotting
paper/filter paper sandwich is assembled on large
electrode plates which generate the electric field,
and buffer is confined to the stack of wet filter
papers.

• This prepared membrane is placed in a gel holder cassette, and this whole set
is placed in a buffer tank with gel facing the cathode.
• Transfer buffer is generally composed of –
• Tris base (pH 8.3)
• Glycine
• Methanol
• Methanol removes SDS from protein and helps the protein to bond with the
membrane to interact with antibodies.
28

• Once the blotting step has been
completed, the apparatus is carefully
disassembled and the success of the
transfer is evaluated. The simplest
method of confirming the transfer
involves noting the appearance of
prestained markers on the blot as
compared to the gel.
• However, this is only a crude measure
since it provides results for a single lane. A
more reliable method of confirming
transfer is through the use of a reversible
stain which identifies the presence of
protein bands directly on the membrane
29

After blotting, the target protein will be detected using appropriately matched and labeled antibodies. The
typical immunodetection stage involves a few basic steps:
• Blocking - The blot containing the transferred protein bands is incubated with a protein or detergent
solution which covers the entire surface so that antibodies do not bind non-specifically to the membrane.
• Antibody incubation - Labeled antibody binds to the target protein band present on the blot in a one-
step or two-step procedure.
• Detection with substrate - The label attached to the antibody, usually an enzyme such as HRP
(Horseradish Peroxidase), is detected using a substrate that produces a visible signal corresponding to the
position of the target protein.
30

Blocking of nonspecific sites
• Blocking is a very important step in the immunodetection phase of Western blotting
because it prevents the non-specific binding of antibodies 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 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 blocking, the blot is rinsed in wash buffer.
31

Incubation of membrane with antibodies
• After blocking and washing, the blot will be incubated in a
dilute solution of antibody, usually for a few hours at room
temperature or overnight at 4°C. The antibody is diluted in
wash buffer (PBST or TBST) or a diluted blocking solution,
the choice depends upon the antibody.
• In the first step, Primary antibodies are incubated with the
protein.
• Then a secondary antibody specific to the primary antibody
is used with conjugated enzymes (HRP or alkaline
phosphatase) or any other detecting compound. The
secondary antibody shows no interaction with the protein
itself.
• Washing is done to remove excess or unbound secondary
antibodies.
32

Detection with
Substrate
• The most common antibody label used in
Western blots is HRP, a small, stable enzyme with
high specificity and rapid turnover. HRP is
deactivated by sodium azide, so it is imperative
that no azide is present in the blocking, dilution,
or washing solutions.
• The HRP label is detected when it is exposed to a
substrate solution in the final step of the
immunodetection procedure. Substrate solutions
for Western blotting are chemical reagents that
are acted upon by the enzyme to yield a signal
that can be easily measured. HRP label is
typically detected with either colorimetric or
chemiluminescent substrates.
33

What kind of
studies can
be done
using
western blot
technique??
• Study cell signalling pathways
• Cell cycle pathways
• Drug action pathways
• Protein-protein interaction
35

ELISA
(enzyme-linked
immunosorbent
assay)
• ELISA (enzyme-linked immunosorbent
assay) is a plate-based assay technique
designed for detecting and quantifying
peptides, proteins, antibodies, and
hormones.
• In an ELISA, an antigen must be
immobilized to a solid surface and then
complexed with an antibody that is
linked to an enzyme.
• Detection is accomplished by assessing
the conjugated enzyme activity via
incubation with a substrate to produce a
measurable product.
• The most crucial element of the
detection strategy is a highly specific
antibody-antigen interaction.
36

• ELISA begins with a coating step, in which the first
layer, consisting of a target antigen or antibody, is
adsorbed onto a 96-well polystyrene plate.
• This is followed by a blocking step in which all
unbound sites are coated with a blocking agent.
• Following a series of washes, the plate is
incubated with enzyme-conjugated antibody.
• Another series of washes removes all unbound
antibody.
• A substrate is then added, producing a
calorimetric signal. Finally, the plate is read. 37

ELISA Types
ELISAs can be
performed with
several
modifications to
the basic
procedure: direct,
indirect, sandwich
or competitive.
The antigen is then
detected either directly
(enzyme-labeled
primary antibody) or
indirectly (enzyme-
labeled secondary
antibody). The
detection antibodies are
usually labeled with
alkaline phosphatase
(AP) or horseradish
peroxidase (HRP).
A large selection
of substrates is
available for
performing the
ELISA with an HRP
or AP conjugate.
The choice of
substrate depends
upon the required
assay sensitivity
and the
instrumentation
available for
signal-detection
(spectrophotomet
er, fluorometer or
luminometer).
38

1. Direct ELISA
The direct detection method uses a primary antibody labeled with a
reporter enzyme or a tag that reacts directly with the antigen.
Direct detection can be performed with an antigen that is directly
immobilized on the assay plate or with the capture assay format.
Direct detection, while not widely used in ELISA, is quite common
for immunohistochemical staining of tissues and cells.
Advantages
• Quick because only one antibody and fewer steps are used.
• Cross-reactivity of secondary antibody is eliminated.
Disadvantages
• Immunoreactivity of the primary antibody might be adversely
affected by labeling with enzymes or tags.
• Labeling primary antibodies for each specific ELISA system is time-
consuming and expensive.
• No flexibility in the choice of primary antibody label from one
experiment to another.
• Minimal signal amplification.
39

2. Indirect
ELISA
For indirect detection, the antigen coated to a multi-well plate is detected in
two stages or layers.
First, an unlabeled primary antibody, which is specific to the antigen, is
applied.
Next, an enzyme-labeled secondary antibody is bound to the first antibody.
The secondary antibody is usually an anti-species antibody and is often
polyclonal.
Advantages
• A wide variety of labeled secondary antibodies are available commercially.
• Versatile because many primary antibodies can be made in one species and
the same labeled secondary antibody can be used for detection.
• Maximum immunoreactivity of the primary antibody is retained because it
is not labeled.
• Sensitivity is increased because each primary antibody contains several
epitopes that can be bound by the labeled secondary antibody, allowing for
signal amplification.
Disadvantages
• Cross-reactivity might occur with the secondary antibody, resulting in a
nonspecific signal.
• An extra incubation step is required in the procedure.
40

3. Sandwich
ELISA
Sandwich ELISAs typically require the use of matched
antibody pairs, where each antibody is specific for a
different, non-overlapping part (epitope) of the antigen
molecule.
A first antibody (known as capture antibody) is coated to the
wells. The sample solution is then added to the well.
A second antibody (known as detection antibody) follows
this step in order to measure the concentration of the
sample.
This type of ELISA has the following advantages:
• High specificity: the antigen/analyte is specifically captured
and detected
• Suitable for complex (or crude/impure) samples: the
antigen does not require purification prior to measurement
• Flexibility and sensitivity: both direct or indirect detection
methods can be used
41

4. Competitive
ELISA
The key event of competitive ELISA (also known as
inhibition ELISA) is the process of competitive reaction
between the sample antigen and antigen bound to the
wells of a microtiter plate with the primary antibody.
First, the primary antibody is incubated with the sample
antigen, and the resulting antibody–antigen complexes are
added to wells that have been coated with the same
antigen.
After an incubation period, any unbound antibody is
washed off.
The more antigen in the sample, the more primary antibody
will be bound to the sample antigen.
Therefore, there will be a smaller amount of primary
antibody available to bind to the antigen coated on the
well, resulting in a signal reduction.
The main advantage of this type of ELISA arises from its
high sensitivity to compositional differences in complex
antigen mixtures, even when the specific detecting
antibody is present in relatively small amounts.
42

Applications
of ELISA
• Serum Antibody Concentrations
• Detecting potential food allergens (milk,
peanuts, walnuts, almonds and eggs)
• Disease outbreaks – tracking the spread of
disease. E.g. HIV, bird flu, common colds,
cholera, STD etc
• Detections of antigens E.g. pregnancy
hormones, drug allergen, GMO, man cow
disease
• Detection of antibodies in blood sample for
past exposure to disease E.g. Lyme disease,
trichinosis, HIV, bird flu.
44

Reference
1. “ELISA Handbook Principle, Troubleshooting, Sample
Preparation and Assay Protocols” by Boster antibody and
ELISA experts.
2. Kurien, B. T., & Scofield, R. H. (2006). Western
blotting. Methods, 38(4), 283-293.
3. Fido, R. J., Tatham, A. S., & Shewry, P. R. (1995). Western
blotting analysis. Plant gene transfer and expression
protocols, 423-437.
4. Singh, N., Shepherd, K., & Cornish, G. (1991). A simplified
SDS-PAGE procedure for separating. J. Cereal Sci, 14, 203-
208.
5. Simpson, R. J. (2006). SDS-PAGE of proteins. Cold Spring
Harbor Protocols, 2006(1), pdb-prot4313.
45

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