Do you know what agarosa is? Surely you will not be familiar with terms like this if you often visit the laboratory. Well, agarosa is a gel used in biochemistry and biotechnology for electroforesis and special size chromatography which is a method of sorting large molecules by size and electric charge.

Agarosa gels are three-dimensional matrices formed from helical agarosa molecules in supercoil bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can be passed. The 3-D structure is combined with hydrogen bonds and can, therefore, be disturbed by heating back to a liquid state. Melting temperature differs from gel temperature, depending on the source, agarosa gel has a gel temperature of 35-42°C and a melting temperature of 85-95°C. Low agarosa melts and low gels made through chemical modification are also available.

Agarosa gel has a large pore size and good gel strength, making it suitable as an anticonvection medium for electroforesis of DNA and large protein molecules. The pore size of the 1% gel has been estimated from 100 nm to 200-500 nm, and the strength of the gel allows a 0.15% dilute gel to form a slab for gel electroforesis. [6] Low concentration gels (0.1-0.2%) are fragile and therefore difficult to handle. Agarosa gels have a lower finishing power than polyacrylamide gels for DNA but have a greater separation range, and are therefore used for DNA fragments that are typically 50-20,000 bp in size. The resolution limit for standard agarosa gel electroforesis is around 750 kb, but a resolution of more than 6 Mb is possible with pulsed-field gel electroforesis (PFGE). [7] This can also be used to separate large proteins, and it is the preferred matrix for electroforesis of gel particles with effective radii greater than 5-10 nm. 0.9% agarosa gel has pores large enough for the entry of T4 bacteriophages.

Agarosa polymers contain charged groups, specifically pyruvate and sulfate. This negatively charged group creates a flow of water in the opposite direction to the movement of DNA in a process called electroendosmosis (EEO), and can, therefore, slow down the movement of DNA and cause blurred bands. Higher concentration gels will have a higher electroosmotic flow. Therefore, low EEO agarosa is preferred for use in agarosa gel electroforesis from nucleic acids, but high EEO agarosa can be used for other purposes. Lower sulfate content of low EEO agarosa, especially low melting point agarosa (LMP), is also useful in cases where DNA extracted from the gel will be used for further manipulation because the presence of contaminated sulfate can affect several subsequent procedures, such as ligation and PCR. However, zero agarosa EEO is undesirable for some applications because they can be made by adding positively charged groups and these groups can influence subsequent enzyme reactions. Electroendosmosis is the reason agarosa is used in preference for agar because the agaropectin component in agar contains large amounts of negatively charged sulfate and carboxyl groups. The removal of agaropectin in agarosa substantially reduces EEO, as well as reducing the adsorption of non-specific biomolecules to the gel matrix. However, for some applications such as serum protein electroforesis, high EEO may be desired, and agaropectin can be added to the gel used.

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