Final answer:
The percentage of agarose in a gel determines its pore size, which is crucial for separating molecules using gel electrophoresis based on their size. Smaller pores separate smaller molecules, while larger pores are used for larger molecules. Dyes and molecular weight standards are used to visualize and compare the sizes of the separated molecules.
Step-by-step explanation:
The type (DNA, RNA, protein) and size (MW) of molecule to be separated will determine the percentage of agarose used in the gel electrophoresis, which in turn dictates the pore size of the gel matrix.
Gel electrophoresis is a powerful technique used to separate biological molecules like DNA, RNA, and proteins. This separation occurs based on the size and charge of these molecules. Since nucleic acids carry a negative charge at neutral or basic pH in an aqueous environment, they migrate towards the positive electrode when an electric field is applied. Different sizes of molecules traverse the gel at different rates due to the size exclusion effect created by the pores in the gel. Smaller molecules move through these pores more swiftly than larger molecules, facilitating separation. The agarose percentage in the gel can be adjusted to alter the pore size, allowing for the separation of either larger or smaller molecules. For example, a higher concentration of agarose results in a denser gel with smaller pores, which is more suitable for the separation of small fragments of DNA.
Gel electrophoresis can be visualized with the use of fluorescent or colored dyes, revealing distinct bands corresponding to different molecular weights. To provide a reference for size, a molecular weight standard or ladder is typically run alongside the samples.