Agarose

Slabs of agarose gels (usually 0.7 - 2%) for electrophoresis are readily prepared by pouring the warm, liquid solution into a mold.

Agarose is a linear polymer with a molecular weight of about 120,000, consisting of alternating D-galactose and 3,6-anhydro-L-galactopyranose linked by α-(1→3) and β-(1→4) glycosidic bonds.

Agarose exhibits the phenomenon of thermal hysteresis in its liquid-to-gel transition, i.e. it gels and melts at different temperatures.

[9] These negatively charged groups can slow down the movement of DNA molecules in a process called electroendosmosis (EEO).

Zero EEO agaroses are also available but these may be undesirable for some applications as they may be made by adding positively charged groups that can affect subsequent enzyme reactions.

However, for some applications such as the electrophoresis of serum protein, a high EEO may be desirable, and agaropectin may be added in the gel used.

[16] The exact temperature is determined by the degree of substitution, and many available low-melting-point (LMP) agaroses can remain fluid at 30–35 °C (86–95 °F) range.

[19] 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.

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.

Agarose gels are cast in a mold, and when set, usually run horizontally submerged in a buffer solution.

These agarose-based beads are generally soft and easily crushed, so they should be used under gravity-flow, low-speed centrifugation, or low-pressure procedures.

Agarose is a useful material for chromatography because it does not absorb biomolecules to any significant extent, has good flow properties, and can tolerate extremes of pH and ionic strength as well as high concentration of denaturants such as 8M urea or 6M guanidine HCl.

For affinity chromatography, beaded agarose is the most commonly used matrix resin for the attachment of the ligands that bind protein.

[23] The ligands are linked covalently through a spacer to activated hydroxyl groups of agarose bead polymer.

It may be used for the culture of strict autotrophic bacteria, plant protoplast,[24] Caenorhabditis elegans,[25] other organisms and various cell lines.