An agarose gel is a semi‑solid matrix formed by dissolving agarose, a purified polysaccharide derived from certain red algae, in buffer and allowing it to cool. The gel creates a network of pores that enables the separation of nucleic acids or proteins by size when an electric field is applied.
Explanation
Agarose is a linear polymer composed of repeating units of agarobiose extracted from seaweed genera such as Gelidium and Gracilaria. When heated in buffer, the chains dissolve; upon cooling, hydrogen bonds form between polymers, creating a three‑dimensional network. The concentration of agarose determines the pore size: low concentrations (0.5–1 %) produce large pores suitable for separating large DNA fragments, while higher concentrations (2–4 %) yield tighter meshes for small fragments. During gel electrophoresis, DNA or RNA samples mixed with a tracking dye are loaded into wells. When an electric current is applied, the negatively charged molecules migrate toward the positive electrode. Smaller fragments navigate the pores more easily and travel farther than larger ones, allowing separation by size. After electrophoresis, the gel is stained with a fluorescent dye and visualized under ultraviolet or blue light.
Uses and Practical Notes
Agarose gel electrophoresis is a fundamental tool in molecular biology for checking PCR products, restriction digests, and plasmid preparations; estimating fragment size; and purifying DNA for cloning or sequencing. The gel can be made with different buffers such as TAE or TBE, which influence migration speed and buffering capacity. Because agarose gels are thermoreversible, melted gels may be reused, though repeated heating can lead to degradation. For very small DNA fragments or proteins, polyacrylamide gels provide higher resolution. Proper handling includes wearing gloves when using ethidium bromide or other intercalating dyes and disposing of gels according to laboratory safety protocols.
Related Terms: Gel electrophoresis, Agarose, DNA ladder, Polyacrylamide gel, Restriction enzyme