Which type of gel electrophoresis is primarily used for protein separation based on size?

Polyacrylamide gel electrophoresis (PAGE) is the preferred method for separating proteins based on their size due to the unique properties of polyacrylamide as a gel matrix. The polymerization of acrylamide creates a network of pores that can be fine-tuned by varying the concentration of acrylamide, allowing for the effective separation of proteins of different sizes. This means that smaller proteins can travel through the gel more easily, while larger proteins experience more resistance, resulting in the size-based separation seen in PAGE.

Additionally, PAGE can be used under denaturing conditions (such as with SDS, sodium dodecyl sulfate) which further aids in the separation process by giving all proteins a similar charge-to-mass ratio, promoting accurate size-based resolution. This makes it an ideal choice for many biochemical applications, including protein analysis and characterization, compared to other methods like agarose gel electrophoresis, which is generally used for larger biomolecules like DNA rather than proteins.