Electrophoresis is the migration of charged molecules in solution in response to an electric field. The rate of migration depends on: the strength of the field (Voltage); the net charge, size and shape of the molecules The ionic strength, viscosity and temperature of the medium in which the molecules are moving.
Electrophoresis is a technique used to separate molecules based on their size and charge, according to the following equation
where v = the rate (velocity) of migration, E = strength of the electrical field, z = charge on the molecule and = frictional force on the molecule. =6r where is the viscosity of the medium and r is the stokes radius of the molecule.
Electrophoresis
As an analytical tool, electrophoresis is simple, rapid and highly sensitive. It is used to Study the properties of a single charged species, and as a separation technique.
Electrophoresis
The sample is run in a support matrix e.g. paper, cellulose acetate, starch gel, agarose gel polyacrylamide gel. At the end of the run, the matrix can be stained and used for scanning, autoradiography or storage.
Agarose and polyacrylamide also separate molecules by size Dilute agarose gels are generally more rigid and easy to handle at low concentration, used to separate larger macromolecules Nucleic acids, Large proteins and protein complexes. A polyacrylamide gel contains long linear polymers of acrylamide cross-linked to each other by bis-acrylamide. It is easier to handle at higher concs, used to separate most proteins and small oligonucleotides
Proteins vs Nucleic Acids Proteins are amphoteric, their net charge determined by the pH of the medium. The net charge carried by a protein is independent of its size, the charge carried per unit mass differs from protein to protein. At a given pH under non-denaturing conditions, the electrophoretic separation of proteins is determined by size and charge of the molecules.
Proteins vs Nucleic Acids Nucleic acids however, Remain negative at any pH used for electrophoresis and Carry a fixed negative charge per unit length of molecule, provided by the PO4 group of each nucleotide of the nucleic acid. Electrophoretic separation of nucleic acids is strictly according to size.
Polyacrylamide gels
Started as disc elerctrophphoresis Then thin slab electrophoresis
Polyacrylamide gels
Started as disc elerctrophphoresis Then thin slab electrophoresis
Advantages Less heat generated during electrophoresis Easy diffusion of dyes during staining/destaining
Simple/native PAGE
Done at pH where protein remains stable in native form Mobility dependent on both charge and size
Simple/native PAGE
Acrylamide and Methylene Bisacrylamide (polylinker)
SDS-PAGE: Separation of Proteins under Denaturing conditions SDS an anionic detergent Denatures proteins by specific binding in a mass ratio of 1.4:1. SDS confers a negative charge to the polypeptide in proportion to its length It is usually necessary to reduce disulphide bridges in the proteins 2- mercaptoethanol or dithiothreitol. In denaturing SDS-PAGE separations therefore, migration is determined by molecular weight.
Denaturation ensures that the proteins no longer have any secondary, tertiary or quaternary structure
SDS-PAGE separates proteins based on their primary structure or size but not the amino acid sequence!
For most applications, the ratio of crosslinker (bis-acrylamide) to monomer (acrylamide) is kept at 37.5 to 1. The gel pore size is then dependent on the total acrylamide concentration.
% Acrylamide
7.5 10 12 15
SDS-PAGE Standards Phosphorylase B Serum albumin Ovalbumin Carbonic Anhydrase Trypsin Inhibitor 97,400 66,200 45,000 29,000 21,500
MW
Lysozyme
14,400
MB 701: Electrophoresis
Urea Gels
Suitable for proteins that are insoluble at the low ionic strength characteristic of electrophoretic conditions
Gradient gels
Used to separate native proteins Separation by size only
Isoelectric focusing
Gels run in a pH gradient Protein moves until it reaches its pI 5-6% acrylamide or 2% agarose used The gel is used as a stabilizing medium rather than a filter Pre-cast gels more commonly used