Question

Why would agorose gel will be inert in gel electrophoresis ?

Answer 1

Agarose is a polysaccharide derived from certain seaweeds such as Gelidium, Gracilaria etc. It's a linear polymer of agarobiose, a disaccharide, which again is composed of D-galactose and 3,6-anhydro-L-galactopyranose. Agarose has a different melting and gelling temperature. Usually standard agarose derived has a typical melting temperature of 90-95 degree celsius and gelling temperature of 35-40 degree celsius. These gelling and melting temperatures depend on the concentration of agarose used for different molecular biology experiments. Each chain of agarose contains almost around 800 galactose molecules and these agarose polymer chains form helical fibres due to the alternating (13) and (14) glycosidic linkage bonding of galactose and anhydrogalactopyranose (also known as L-galactose). These helical fibres then aggregate to make a supercoiled structure which upon solidifcation, form a 3D mesh of channels. This meshwork contains pores depending on the concentration used (High concentration: less and small pores available, Low concentration: highly pourous). As they gell up, they are placed in the electrophoretic chamber in buffer solution for the molecule under study to run for absolute separation. This is the sole reason why agarose gels, upon solidifcation, becomes inert or immobile.