Typically, a DNA molecule is digested with restriction enzymesand the agarose gel electrophoresis is used as a diagnostic tool to visualize the fragments. An electric current is used to move the DNA molecules across an agarose gel, which is a polysaccharide matrix that functions as a sort of sieve. The matrix helps "catch" the molecules as they are transported by the electric current. This technique has lots of applications.
Properties of agarose gel[ edit ] An agarose gel cast in tray used for gel electrophoresis Agarose gel is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can pass.
Low-melting and low-gelling agaroses made through chemical modifications are also available.
Agarose gel has large pore size and good gel strength, making it suitable as an anticonvection medium for the electrophoresis of DNA and large protein molecules.
Agarose gel has lower resolving power than polyacrylamide gel for DNA but has a greater range of separation, and is therefore used for DNA fragments of usually 50—20, bp in size. The limit of resolution for standard agarose gel electrophoresis is around kb, but resolution of Electrophoreses using electricity to separate molecules 6 Mb is possible with pulsed field gel electrophoresis PFGE.
Higher concentration gel would have higher electroosmotic flow. Low EEO agarose is therefore generally preferred for use in agarose gel electrophoresis of nucleic acidsbut high EEO agarose may be used for other purposes. The lower sulphate content of low EEO agarose, particularly low-melting point LMP agarose, is also beneficial in cases where the DNA extracted from gel is to be used for further manipulation as the presence of contaminating sulphates may affect some subsequent procedures, such as ligation and PCR.
Zero EEO agaroses however are undesirable for some applications as they may be made by adding positively charged groups and such groups can affect subsequent enzyme reactions.
The removal of agaropectin in agarose substantially reduce the EEO, as well as reducing the non-specific adsorption of biomolecules to the gel matrix. However, for some applications such as the electrophoresis of serum proteins, a high EEO may be desirable, and agaropeptin may be added in the gel used.
Gel electrophoresis of nucleic acids Factors affecting migration of nucleic acid in gel[ edit ] Gels of plasmid preparations usually show a major band of supercoiled DNA with other fainter bands in the same lane. A number of factors can affect the migration of nucleic acids: This relationship however breaks down with very large DNA fragments, and separation of very large DNA fragments requires the use of pulsed field gel electrophoresis PFGEwhich applies alternating current from two different directions and the large DNA fragments are separated as they reorient themselves with the changing current.
High concentrations gel however requires longer run times sometimes days. The rate at which the various forms move however can change using different electrophoresis conditions,  and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.
The resolution of large DNA fragments however is lower at high voltage. The mobility of DNA may also change in an unsteady field — in a field that is periodically reversed, the mobility of DNA of a particular size may drop significantly at a particular cycling frequency.
Migration anomalies[ edit ] "Smiley" gels - this edge effect is caused when the voltage applied is too high for the gel concentration used.
Contamination - presence of impurities, such as salts or proteins can affect the movement of the DNA. Mechanism of migration and separation[ edit ] The negative charge of its phosphate backbone moves the DNA towards the positively charged anode during electrophoresis.
However, the migration of DNA molecules in solution, in the absence of a gel matrix, is independent of molecular weight during electrophoresis. A widely accepted one is the Ogston model which treats the polymer matrix as a sieve. A globular protein or a random coil DNA moves through the interconnected pores, and the movement of larger molecules is more likely to be impeded and slowed down by collisions with the gel matrix, and the molecules of different sizes can therefore be separated in this sieving process.
For DNA molecules of size greater than 1 kb, a reptation model or its variants is most commonly used. This model assumes that the DNA can crawl in a "snake-like" fashion hence "reptation" through the pores as an elongated molecule. A biased reptation model applies at higher electric field strength, whereby the leading end of the molecule become strongly biased in the forward direction and pulls the rest of the molecule along.
Casting of gel[ edit ] Loading DNA samples into the wells of an agarose gel using a multi-channel pipette. The gel is prepared by dissolving the agarose powder in an appropriate buffer, such as TAE or TBE, to be used in electrophoresis. The melted agarose is allowed to cool sufficiently before pouring the solution into a cast as the cast may warp or crack if the agarose solution is too hot.
A comb is placed in the cast to create wells for loading sample, and the gel should be completely set before use.
The concentration of gel affects the resolution of DNA separation. For a standard agarose gel electrophoresis, a 0. High percentage gels are often brittle and may not set evenly, while low percentage gels 0.
Low-melting-point LMP agarose gels are also more fragile than normal agarose gel. Low-melting point agarose may be used on its own or simultaneously with standard agarose for the separation and isolation of DNA. Loading of samples[ edit ] Once the gel has set, the comb is removed, leaving wells where DNA samples can be loaded.
Loading buffer is mixed with the DNA sample before the mixture is loaded into the wells. The loading buffer contains a dense compound, which may be glycerol, sucrose, or Ficollthat raises the density of the sample so that the DNA sample may sink to the bottom of the well.
The loading buffer also includes colored dyes such as xylene cyanol and bromophenol blue used to monitor the progress of the electrophoresis.
The DNA samples are loaded using a pipette. Electrophoresis[ edit ] Agarose gel slab in electrophoresis tank with bands of dyes indicating progress of the electrophoresis.
The DNA moves towards anode. Agarose gel electrophoresis is most commonly done horizontally in a submarine mode whereby the slab gel is completely submerged in buffer during electrophoresis.
It is also possible, but less common, to perform the electrophoresis vertically, as well as horizontally with the gel raised on agarose legs using an appropriate apparatus.Gel electrophoresis of large DNA or RNA is usually done by agarose gel electrophoresis. See the "Chain termination method" page for an example of a polyacrylamide DNA sequencing gel.
In the early days of DNA manipulation, DNA fragments were laboriously separated by gravity. In the s, the powerful tool of DNA gel electrophoresis was developed. This process uses electricity to separate DNA fragments by .
Gel electrophoresis refers to the separation of particles on the basis of their charge and size across a gel when an electric current is applied Charged particles can include DNA, amino acids, peptides, etc A method of separating DNA in a gelatin-like material using an electrical field DNA is negatively charged.
Gel electrophoresis is a technique commonly used in laboratories to separate charged molecules like DNA, RNA and proteins according to their size. Charged molecules move through a gel when an electric current is passed across it. Gel Electrophoresis. In the early days of DNA manipulation, DNA fragments were laboriously separated by gravity.
In the s, the powerful tool of DNA gel electrophoresis was developed. This process uses electricity to separate DNA fragments by size as they migrate through a gel matrix. By Rene Fester Kratz. Scientists use gel electrophoresis to separate molecules based on their size and electrical charge.
Gel electrophoresis can separate fragments of DNA that were cut with restriction enzymes, creating a visual .