SDS-PAGE is a technique used to separate proteins by molecular weight. Proteins are denatured and given a negative charge by SDS detergent before running through a polyacrylamide gel matrix by electrophoresis. Smaller proteins migrate faster through the gel, allowing separation by size. After electrophoresis, proteins bands can be visualized using stains like Coomassie blue or silver stain to analyze characteristics like molecular weight, purity, and subunit composition.

2.  Sodium dodecyl sulphate polyacrylamide gel
electrophoresis(SDS-PAGE) is an analytical
technique used to separate proteins based on
their molecular weight.
 Electrophoresis is a technique used to
separate macromolecules in an electrical
field.
 This technique employs discontinuous
polyacrylamide gel for support and SDS for
denaturation.

3.  SDS (also called lauryl sulfate) is an anionic
detergent.
 Its molecules have a net negative charge
within a wide pH range.
 A polypeptide chain binds amounts of SDS in
proportion to its relative molecular mass.
 The negative charges on SDS masks all the
charges present on protein molecules giving
the protein a net negative charge.

4. SDS molecule
12 carbon tail attached to a sulphate group

5.  Polyacrylamide is a polymer formed from
acrylamide subunits.
 It is highly water-absorbent, forming a
soft gel when hydrated.
 Polyacrylamide is ideal for protein separations
because it is chemically inert and electrically
neutral.
 It forms a mesh like matrix which allows for
separation based on weight.

6.  When proteins are separated by electrophoresis
through a gel matrix, smaller proteins migrate
faster due to less resistance from the gel matrix.
 SDS is a detergent with a strong protein-
denaturing effect and binds to the protein
backbone in ratio to its mass. In the presence of
SDS and a reducing agent(mercaptoethanol) that
cleaves disulfide bonds critical for proper
folding, proteins unfold into linear chains with
negative charge proportional to the polypeptide
chain length.

7.  Polyacrylamide gels restrain larger molecules
from migrating as fast as smaller molecules.
Because the charge-to-mass ratio is nearly
the same among SDS-denatured
polypeptides, the final separation of proteins
is dependent almost entirely on the
differences in relative molecular mass of
polypeptides

9.  Gel is polymerized between two glass plates
in a gel caster or casting frame, one is short
plate and the other is spacer plate.
 Clamping frame to hold gel cassettes inside
the tank.
 Electrode assembly.
 Combs for well formation.
 Power supply.

10.  The gel used in SDS may or may not be a
discontinuous system.
 Discontinuous system comprises of a 5% stacking
and 4-15% resolving gel based on the
concentration of TEMED.
 Typical components of these gels are:
o SDS
o APS (ammonium per sulphate)
o TEMED(tetra methyl ethylene diamine)
o Acrylamide bis
o Tris (Molarity varies between resolving and
stacking gels).

11.  Hand cast gels can be made in laboratory by the researchers
themselves.
 Align the short plate and stacker plate such that their
bottoms are at exactly the same level and clamp them into
casting frame.
 Place casting frame upon casting stand.
 As a non standard step, water can be poured in between the
two plates, to check for a leak which can later be removed by
filter paper.
 Add all the ingredients into a beaker except for TEMED.
 When the performer is ready to pour the ingredients between
the two plates only right before then the TEMED should be
added to the rest of ingredients.

12.  Resolving buffer is poured between the plates first and
allowed to stand until solidified.
 Butanol can be added upon it to produce a straight bubble
free layer which can later be removed by filter paper.
 Once resolving buffer solidifies Remove butanol and start
pouring the stacking buffer.
 Fill until the mixture reaches the top of short plate
 Ensure absence of air bubbles and insert comb.
 Allow it to stand until solidified.

13.  The sample loaded on a SDS gel usually contains:
o Laemlli buffer
o DI water
o Protein sample
 Laemlli buffer contains:
o SDS
o  Mercaptoethanol
o Tris Hcl pH 6.8
o Bromophenol blue
o glycerol

14.  Add all the ingredients to a centrifuge
eppendorf.
 Centrifuge for1 Minute for run down.
 Heat on thermal cycler or in Hot water at 95
C for 5 minutes.

15.  Assemble the electrophoresis assembly.
 Place the gel cassette in the electrode
assembly with the short plate facing inside of
the electrode assembly.
 For running a single gel place dummy
plate(buffer dam) on the other end of
electrode assembly.
 Remove the comb from gel cassette.
 Load sample in the well produced by combs
using micropipette tips.

16.  Add running buffer into gel box and fill up to
the mark stating two gels or four gels as per
requirement.
 Also add running buffer in between assembly
holding two gel cassettes.
 Place the cap of gel box aligning the color coded
electrodes(red to red and black to black).
 insert the switch into power supply, select the
desired current or voltage and press run.
 Alllow it to run until the sample reaches bottom
end of the gel.

17. Visualization through
Coomassie stain
Visualization through
Silver staining

18. Coomassie stain Silver stain
 Less sensitive
 Less complicated
 Require less steps
 Stain is poured over
gel and left for almost
90 minutes.
 Later de-staining is
done to reveal protein
bands.
 Highly sensitive
 Complex to perform
 Requires various steps
to produce the final
result.

19.  As the electrophoresis completes gel is removed
from the cassette and is placed in fixative
solution for 20 minutes.
 After this fixative is replaced by water which is
left for 10 minutes
 Water is replaced by fresh water which is again
left for 10 minutes.
 Image developing solution then replaces water,
which takes 15-20 minutes to visualize protein
bands present in sample.
 Stopping solution(5% acetic acid) then replaces
developing solution to stop the reaction.

20.  Highly sensitive method
 Very small amount of sample is required.
 Estimation of protein size.
 Estimation of protein purity
 Comparison of polypeptide composition of
different samples.
 Analysis of number and size of polypeptide
subunits.
 Determination of molecular weight.