Final answer:
Polyacrylamide gel electrophoresis (PAGE) has a finer matrix than agarose gel, making it suitable for separating smaller molecules such as proteins, whereas agarose gel is better for larger nucleic acids.
Step-by-step explanation:
The type of banding in polyacrylamide gel (PAGE) compared to agarose gel is primarily due to the difference in their pore sizes and consequent separating capabilities. Polyacrylamide, which is a polymer of acrylamide and methylenebisacrylamide, offers a finer matrix due to its adjustable crosslinking, which can be tailored for separating smaller molecules like proteins and smaller RNAs. In contrast, agarose gel, a polysaccharide extracted from seaweed, has larger pores suitable for separating larger nucleic acids, such as DNA fragments greater than 500 base pairs.
PAGE is used extensively for protein analysis; it can separate proteins based on net charges or by mass if proteins are denatured using SDS. More complex separations such as two-dimensional PAGE allow for analysis based on both charge at different pH levels and size. After electrophoresis, proteins can be visualized with stains such as Coomassie blue or silver stain.
In summary, polyacrylamide gel's finer matrix is suitable for more detailed separation, such as discerning differences of a single nucleotide in polynucleotides, while agarose is better for larger molecules, without denaturing them.