page_title: Agarose
section_title: Agarose gel electrophoresis
hierarchical_section_title: Agarose / Applications / Agarose gel electrophoresis
caption_attribution_description: English: Photo taken by User:Kjaergaard. A size exclusion column.
context_page_description: Agarose is a polysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose. Agarose is one of the two principal components of agar, and is purified from agar by removing agar's other component, agaropectin.
  Agarose is frequently used in molecular biology for the separation of large molecules, especially DNA, by electrophoresis. Slabs of agarose gels for electrophoresis are readily prepared by pouring the warm, liquid solution into a mold. A wide range of different agaroses of varying molecular weights and properties are commercially available for this purpose. Agarose may also be formed into beads and used in a number of chromatographic methods for protein purification.
context_section_description: Agarose gel electrophoresis is the routine method for resolving DNA in the laboratory. Agarose gels have lower resolving power for DNA than acrylamide gels, but they have greater range of separation, and are therefore usually used for DNA fragments with lengths of 50–20,000 bp (base pairs), although resolution of over 6 Mb is possible with pulsed field gel electrophoresis (PFGE). It can also be used to separate large protein molecules, and it is the preferred matrix for the gel electrophoresis of particles with effective radii larger than 5-10 nm.
  The pore size of the gel affects the size of the DNA that can be sieved. The lower the concentration of the gel, the larger the pore size, and the larger the DNA that can be sieved. However low-concentration gels (0.1 - 0.2%) are fragile and therefore hard to handle, and the electrophoresis of large DNA molecules can take several days. The limit of resolution for standard agarose gel electrophoresis is around 750 kb. This limit can be overcome by PFGE, where alternating orthogonal electric fields are applied to the gel. The DNA fragments reorientate themselves when the applied field switches direction, but larger molecules of DNA take longer to realign themselves when the electric field is altered, while for smaller ones it is quicker, and the DNA can therefore be fractionated according to size.
  Agarose gels are cast in a mold, and when set, usually run horizontally submerged in a buffer solution. Tris-acetate-EDTA and Tris-Borate-EDTA buffers are commonly used, but other buffers such as Tris-phosphate, barbituric acid-sodium barbiturate or Tris-barbiturate buffers may be used in other applications. The DNA is normally visualized by staining with ethidium bromide and then viewed under a UV light, but other methods of staining are available, such as SYBR Green, GelRed, methylene blue, and crystal violet. If the separated DNA fragments are needed for further downstream experiment, they can be cut out from the gel in slices for further manipulation.
caption: Agarose-based gel filtration columns used for protein purification on an AKTA FPLC machine.
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