What happens to smaller, highly charged particles in a polyacrylamide gel during electrophoresis?

During electrophoresis, smaller, highly charged particles experience a greater electrophoretic mobility compared to larger particles. This phenomenon occurs due to several factors.

First, the charge-to-mass ratio is a key aspect; smaller particles, particularly those with high charges, will have a higher charge-to-mass ratio, which causes them to be more responsive to the electric field applied during electrophoresis. They move more quickly through the gel matrix, which consists of a network of polymer chains that create pores.

Additionally, the gel's pore size affects how particles travel through it. Smaller molecules can navigate through these pores more easily than larger molecules, which may experience more resistance due to their size. As a result, during electrophoresis, smaller, highly charged particles migrate faster toward the electrode of opposite charge compared to their larger counterparts in the gel. Understanding this behavior is essential in biological research, particularly in the separation and analysis of proteins and nucleic acids.