Taking a Look at Agarose

530 Words Feb 24th, 2018 2 Pages
Agarose is a linear polysaccharide unit made up of the basic repeat unit agarobiose, which comprises alternating units of galactose and 3,6-anhydrogalactose. Agarose is one of the components of agar that is a mixture of polysaccharides isolated from certain seaweeds. Agarose is usually used in concentration between 1% and 3%. The pore size in the gel is controlled by the initial concentration of agarose; large pore sizes are formed from low concentrations and smaller pore sizes are formed from the higher concentratins. [1][2][5]

For the majority of DNA samples, electrophoretic separation is carried out in agarose gels. This is because most DNA molecules and their fragments that are analysed routinely are considerably larger than proteins and therefore, because most DNA fragments would be unable to enter a polyacrylamide gel, the larger pore size of an agarose gel is required. DNA size is referred to in terms of base-pairs (bp) or kilo base-pairs (kbp) though it has now become the accepted nomenclature to abbreviate kbp to simply kb.
Since the charge per unit length (owing to the phosphate groups) in any given fragment of DNA is the same, all DNA samples should move towards the anode with the same mobility under an applied electrical field. However, separation in agarose gels is achieved because of resistance to their movement caused by the gel matrix. The largest molecules will have the most difficulty passing through the gel pores (very large molecules may even be blocked…
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