What Is Agarose Gel?
Agarose gel is a substance that is used in science for gel electrophoresis and size exclusion chromatography. These processes use agarose gel to separate and analyze proteins and DNA. The medium is composed of a purified agarose powder that has been boiled in a buffer solution and then cooled into a gel.
Agarose gel is most commonly associated with gel electrophoresis. In this procedure, scientists use an electrical charge to move deoxyribonucleic acid, more commonly known as DNA, or ribonucleic acid (RNA) through a gel matrix toward a positive pole. Because the molecules have to move through small holes in the lattice bonds in the agarose gel, smaller molecules move much faster than larger molecules. Using ultraviolet imaging of the molecules' movement and a formula that relates molecular weight to the speed of travel through the gel, scientists can determine the size of the molecules.
Agarose is extracted in the form of agar from several species of red marine algae, or seaweed, found in California and eastern Asia. Agar, a term derived from the Malay word agar-agar, meaning jelly, is typically derived from the Gelidium genera of seaweed. It is composed of both agarose and agaropectin molecules and provides support to the cell walls within the marine algae. Removed from the plant, the agarcan be used as a food thickener, much like gelatin, a laxative, or a medium for growing bacteria, fungus, or other microorganisms, when purified.
It is fairly easy to separate agarose from agaropectin in agar because the agarose molecules bond strongly to one another, while the agaropectin gels poorly. There are several methods to achieve the isolation of agarose gel. In one method, carrageenan, another molecule found in red seaweed, and a salt are added to the agar. This causes the agaropectin to precipitate, or form a solid that can be removed from the agar solution. Another method adds the enzyme pectinase, a chemical that breaks down the agaropectin, to the solution, allowing the agaropectin to dissolve in water.
Isolated agarose can then be ordered by laboratories, usually in the form of an expensive powder. Preparing the agarose gel from this powder depends on the quality of image and the size of the DNA fragments needed for the electrophoresis. The gel is prepared in different concentrations, typically 1.2%, 1%, 0.8%, 0.7%. If one wished to make a 0.7% gel, she should add a ratio of 0.7 grams (g) of agarose powder to 100 milliliters (mL) of a buffer solution, such as Tris-Acetate-EDTA, or TAE. The ratio can be multiplied or divided to adjust the amount of agarose and buffer proportionately to yield smaller or larger amounts of gel.
Once the correct amounts of the components have been combined in a flask, it should be microwaved until the contents are completely melted. While the solution is still liquid, ethidium bromide (EtBr), a chemical that allows the DNA or RNA to be seen in UV light, should be added in a ration of 1/1000, if the EtBr solution is at a concentration of 0.5mg/mL. The solution should be allowed to cool for a few minutes and then poured into the wells in the electrophoresis tray, where it should be allowed to harden into a gel.
Written by Caitlin Kenney
