Electrophoresis- Analytical techniques

1. ELECTROPHORESIS
1
Esha Bhavin Shah
Assistant Professor
Department of Pharmaceutical Chemistry and Quality Assurance
Babaria Institute of Pharmacy
Bits Edu Campus
Email: eshahshah.bip@bitseducampus.ac.in

2. INTRODUCTION
 In practical terms a positive electrode(anode)
and negative electrode(cathode) are placed in a
solution containing ions.
Then voltage is applied across the electrodes, so
solute ions of different charge for example,
anions (negative) and cations (positive) will
move through the solution towards the electrode
of opposite charge.

3. -+
ELECTROPHORESIS
The migration of electrically charged particles or ions in
solutions due to an applied electric field.
+ -
3

4. THEORY
 Electrohoresis is the movement of ions under the
influence of electrical field. So, separation in
electrophoresis relies on differences in the speed of
migration (migration velocity) of ions or solutes.
• Migration Velocity (ν) =μe E
Where, μe=elecrophoretic mobility E=electrical field
strength
 Electrophoretic mobility is a factor that determines
how fast ion or solute moves in a given medium.
• μe = q/ 6Лήr
• where, q=charge of ion ή=viscosity of solution
r=radius of ion

5.  The instrumentation of capillary electrophoresis is very similar to
that of HPLC.
 Power supply of E is equivalent to HPLC pump and capillary
equivalent to column.
COMPARISON OF ELECTROPHORETIC AND
CHROMATOGRAPHIC TERMS
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6. ELECTROPHORESIS APPARATUS

7. Principle of Electrophoresis
• Electromigration :
– Ions migrating in electric field
Cations cathode (-ve)
Anions  anode (+ve)
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-+

8. Structure and Properties of Protein
• PROTEINS - polymers of amino acids
• STRUCTURE of Amino Acids
– aa's have a carboxyl group (-COOH) & amino group (-NH2) and
are often ionized at physiological pH
• Proteins are amphoteric compounds and are therefore either positively
or negatively charged.
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9. Migration of proteins in electric field
negatively charged proteins move towards the
positive pole
directly proportional to the overall charge of
proteins
inversely proportional to protein size (molecular
weight)

10. Electropherogram
An Electropherogram is the
result of an electrophoresis
which gives the movement of
charged particles over time in
a gel, paper or another
medium.
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11. PROCEDURE FOR
ELECTROPHORESIS

12. 12
Melting the agar…

13. 13
Pouring the gel…

14. Solidification of gel

15. Creation of lanes

16. Formation of lanes

17. Preparation of sample

18. Buffer solution added to the tank
This ensures that the electric current goes through the whole tank and that maintains
that ions can move in the solution

19. samples loaded into wells

20. Electrical current applied to the chamber
Safety cover is put over the top and the current is switched on.
The dye will migrate through the gel toward the positive electrode, as will the DNA
Depending on how much voltage is applied and how warm the gel is and size and shape
of molecules will depend on how fast the ions move through the gel
Smaller fragments will move easier so they will be closer to the positive electrode
Once the dye has moved through the gel to the buffer, the electrical current is switched
off and gel is removed from the tray

21. VISUALISATION
• After the electrophoresis is complete, the molecules in the
gel can be stained to make them visible.
• Ethidium bromide, silver, or coomassie blue dye may
be used for this process.
• If the analyte molecules fluoresce under ultraviolet light,
a photograph can be taken of the gel under ultraviolet
lighting conditions.
• If the molecules to be separated contain radioactivity
added for visibility, an autoradiogram can be recorded of
the gel.

22. 22
There are molecular weight size
markers available that contain a
mixture of molecules of known
sizes. If such a marker was run on
one lane in the gel parallel to the
unknown samples, the bands
observed can be compared to
those of the unknown in order to
determine their size. The distance
a band travels is approximately
inversely proportional to the
logarithm of the size of the
molecule.

23. Quantification of separated protein band by Densitometer
Densitometer is a device that measures
the degree of darkness in photographic
or semi-transparent material.

24. Types of Electrophoresis:
Zone Electrophoresis:
a) Paper electrophoresis
b) Gel electrophoresis
c) Cellulose acetate electrophoresis
d) Thin layer electrophoresis
 Moving boundary electrophoresis:
a) Capillary electrophoresis
b) Isoelectric focussing
c) Immuno electrophoresis

25. Zone electrophoresis:
The term Zone electrophoresis is applied to those systems in which ionic
mobilities are studied on strips of paper, cellulose acetate or acrylamide.

26. Zone electrophoresis
It involves the migration of the charged particle on the supporting media, paper ,
cellulose acetate membrane, starch gel, polyacrylamide.
The components separated are distributed into discrete zone on the support media.
Supporting media is saturated with buffer solution, small volume of the sample is
applied as narrow band.
On application of potential difference at the ends of a strip ,components migrate at the
rate determined by its electrophoretic mobility.
Advantages:
Useful in biochemical investigations.
Small quantity of sample can be analyzed
Low cost and easy maintenance
Disadvantages:
Unsuitable for accurate mobility and isoelectric point determination.
Due to the presence of supporting medium, technical complications such as capillary
flow, electrosmosis, adsorption and molecular sieving are introduced.

27. Paper Electrophoresis
Paper Electrophoresis is one of the zone electrophoresis. This is very important method
in all laboratories.
Paper of good quality should contain at least 95% α-cellulose and should have only a very
slight adsorption capacity.
This technique is useful for the separation of small charged molecules such as amino
acids and small proteins. A strip of filter paper is moistened with buffer and the ends of the
strip are immersed into buffer reservoirs containing the electrodes. The samples are
spotted in the center of the paper, high voltage is applied, and the spots migrate according
to their charges. After electrophoresis, the separated components can be detected by a
variety of staining techniques, depending upon their chemical identity.

28. Applications:
Serum analysis for diagnostic purpose is routinely carried about by paper
electrophoresis.
Muscle proteins, egg white proteins, milk proteins & snake, insect venom analysis
done by this technique.

29. Capillary electrophoresis
By using capillaries as distinct from
flat bead systems, it was possible to:
 minimize zone spreading,
 improve heat dissipation,
shorten separation times and
increase efficiency.
Applications:
Separation of steroids and complex drug mixtures within 10 to 15 minutes.
analysis of proteins found in serum, urine, CSF and body fluids, immunosubstraction
electrophoresis, hemoglobin variants, lipoproteins, carbohydrate-deficient transferrin (CDT)
forensic and therapeutic drug screening, and molecular diagnostics.

30. Gel electrophoresis:

31. Gel electrophoresis is a method for separation and analysis of macromolecules (DNA,
RNA and proteins) and their fragments, based on their size and charge.
Applications:
It is used in clinical chemistry to separate proteins by charge and/or size (IEF agarose,
essentially size independent).
In biochemistry and molecular biology to separate a mixed population of DNA and RNA
fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins
by charge.
Estimation of the size of DNA molecules following restriction enzyme digestion, e.g. in
restriction mapping of cloned DNA.
Analysis of PCR products, e.g. in molecular genetic diagnosis or genetic fingerprinting
Separation of restricted genomic DNA prior to Southern transfer, or of RNA prior to
Northern transfer.
Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and
biochemistry.
The results can be analyzed quantitatively by visualizing the gel with UV light and a gel
imaging device. The image is recorded with a computer operated camera, and the intensity
of the band or spot of interest is measured and compared against standard or markers
loaded on the same gel. The measurement and analysis are mostly done with specialized
software.
Depending on the type of analysis being performed, other techniques are often
implemented in conjunction with the results of gel electrophoresis, providing a wide range of
field-specific applications.

32. ISOELECTRIC
FOCUSING (IEF)

33. Principle
• Isoelectric focusing is an electrophoretic
method in which proteins are separated on the
basis of their pIs. (isoelectric pH) (1-12).
• It makes use of the property of the protein that
their net charges are determined by the pH of
their local environment.
• Proteins carry positive, negative or zero net
electrical charge, depending on the pH of their
surroundings.

34. • The net charge of any particular protein is the sum
of all its positive and negative charges.
• They are determined by the ionizable acidic and
basic side chains of the constituent amino acids
and prosthetic groups of the protein.
• If no. of acidic groups >> no. of basic groups, the
pI of that protein will be at a low pH value and
the protein is classified as acidic.
• If no. of basic groups >> no. of acidic groups, the
pI of that protein will be at a high pH value and
the protein is classified as basic.
• Proteins show variations in isoelectric points, but
pI values usually fall in between pH 3-12, mostly
between pH 4-7.

35. • Proteins are positively charged in solutions at pH
values below their pI and negatively charged
above pI.
• So,
pH<<pI ----> proteins carry net positive charge-
migrate towards cathode
pH>>pI ----> Proteins carry net negative charge-
migrate towards anode
• At pI  a protein will not move in an electric
field.

37. Mechanism
• When protein is placed in a medium with linear
pH gradient and subjected to electric field, it will
initially move towards the electrode with opposite
charge.
• During migration through pH gradient, the protein
will either pick up or lose protons.
• So, this results in change in its net charge and
mobility.
• Eventually, it will arrive at a point in the pH
gradient equaling to its pI.
• There being uncharged, it will stop migrating
results in sharp bands.

38. +pI
acidic
basic
Anode (+) Cathode (-)
0
0 -
pH

39. • Focusing is the steady state mechanism with
regard to pH.
• Proteins approach their respective pI values at
differing rates but remain relatively fixed at those
pH values for extended periods.
• This type of motion is in contrast to conventional
electrophoresis in which proteins continue to
move through the medium until electric field is
removed.
• In IEF, proteins migrate to their steady state
positions from any where in the system.
• Thus, sample application point is arbitary.

40. Establishing pH gradients
• Establishment of stable, linear pH gradients is
accomplished in two ways using
1. Carrier ampholytes
2. Acrylamido buffers

41. 1. Carrier ampholytes
• CA (amphoteric electrolytes) are mixtures of molecules
containing multiple aliphatic amino and carboxylic
groups.
• They are small (300-1000 Da) multi charged organic
buffer molecules with closely spaced pI values and high
conductivity.
• CA are included directly in IEF gels.
• In electric fields, CA partition in to smooth pH gradient
that linearly increase from anode to cathode.
• This is the most common and simplest way to obtain
pH gradients.

42. 2. Acrylamido buffers
• AB are derivatives of acrylamide containing both
reactive double bonds and buffering groups.
• Their general structure is CH2=CH-CO-NH-R, where
R contains either a carboxyl or 30 amine group.
• They are incorporated into PAGE at time of casting.
• Because the buffering compounds are fixed in place in
the separation medium, the gels are called
“immobilized pH gradients” or IPGs.
• IPGs have more stability but are cumbersome and
expensive.

43. • IEF is a high resolution technique that can resolve
proteins differing in pI value of less than 0.05pH
unit.
• Antibodies, antigens and enzymes retain their
activities during IEF.
• The pH range chosen should be centered on pI of
the proteins of interest.
• With CA, 2%w/v is best
• <1% -- unstable pH gradients
• >3% -- ampholytes difficult to remove at time
of staining
• With AB, conc of 3 meq is appropriate.

44. Gels for IEF
• The most common composition of gels for IEF
are
• Poly acrylamide gels with 5%T and 3%C
• Ammonium persulfate
• Urea
• 0.05% TEMED
• Now a days, pre cast IEF mini gels and IPG
sheets are also available.

45. Power conditions and resolution
• The pH gradient and applied electric field
determine the resolution of IEF run.
• pI = sqrt of pH gradient/ sqrt of voltage gradient
• Narrow pH range and high voltage = better
resolution.
• High voltage leads to shorter run time but has dis
adv of generating heat. (joule effect)
• So electric fields of order 100V/cm are preffered.

46. Protein solubilization at pI
• Some proteins tend to precipitate out at pI
values.
• To prevent this, most commonly Urea is used,
especially for those proteins that tend to
aggregate at their pI values.
• Urea works by disrupting hydrogen bonds. (7-
8 M).
• Membrane proteins require detergent
solubilizing agents like CHAPS and CHAPSO,
triton X-100.

47. Detection
• Mostly dyes like amidoblack and coomassive
blue and silver staining are used.
• Autoradiography, liquid scintillation counting
and Flourography can also be used for
radioactive proteins.

48. Capillary Isoelectric Focusing (CIEF)
 It separates analytes according to differences in their isoelectric points or pI values.
 Capillary filled with a solution of carrier ampholytes and sample.
 Anode end of the capillary is placed into an acidic solution and cathode end into a
basic solution.
 When electric field is applied, due to presence of ampholyte cause the pH gradient
into capillary.
 Charged sample components then migrate through the capillay untill they reach a
region of pH equal to their pI, where they become neutral and therefore, cease to
migrate.
E
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49. Applications of Electrophoresis
1. Forensics
DNA fingerprint of a criminal.
2. Molecular Biology To separate and organize DNA and RNA by
size
3. Genetics Provide clearer picture of DNA, it also helps prepare
DNA for cloning and genetic engineering.
4. Microbiology Information out about the organisms. Virology : to
help diagnose different strains of viruses.
5. Biochemistry Mapping of cellular components, particularly
proteins and nucleic acids.
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50. 5. Protein and peptide determination:
(1) To check Purity
(2) Physical properties like MW, pI
(3) Binding studies
(4) Identification (CE-MS)
(5) Quantitation
(6) Immunoassays
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6. Determination of additives in food and drug.
For example, Separation of Tartazine, Sunset yellow, amaranth,
indigo carmine
7. Separation and Quantification of Vitamins in fruits and
vegetable.
For example, Separation and quantification of Ascorbic acid in
vegetable and fruits
8. Used for separation of enatiomer from racemic mixture.

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52. 9. Determination of minerals, fatty acids and carbohydrates.
10. Determination of various organic acids like Hippuric acid,
Oxalic acid, Tartaric acid, Malic acid, Lactic acid in food.
11. Pharmaceutical assay
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