Final answer:
Agarose gel electrophoresis is best suited for separating large nucleic acids based on size, while SDS-PAGE allows for the separation of proteins based on size, by denaturing proteins and giving them a uniform negative charge.
Step-by-step explanation:
The relative benefits of agarose gel electrophoresis compared to sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (SDS-PAGE) relate to the different properties of the gels and the types of biological molecules they are best suited to separate. Agarose gels are typically used for the separation of large nucleic acid fragments, as the pore size of the gel can be controlled by the percentage of agarose used, which ranges from 0.6 to 2%. This makes them ideal for analyzing DNA or RNA molecules of various sizes, where size is the primary factor for separation.
In contrast, PAGE provides a finer gel matrix when polyacrylamide is used, and it can be further modified with SDS to separate proteins. The presence of SDS denatures proteins and imparts a uniform negative charge, which allows for separation based on size rather than charge or conformation. This is particularly useful when analyzing the molecular weight of proteins or comparing the protein expression between samples. With its finer matrix, PAGE can also be used to separate smaller RNA molecules when a higher crosslinking ratio of acrylamide to methylenebisacrylamide is used.
Using different stains such as Coomassie blue or silver stain, proteins can be visualized after electrophoresis, providing valuable information on protein abundance and purity in a given sample.