In-gel electrophoresis the matrix forces sample components to separate by size, as they move through its porous structure. The matrix provides greater resistance to the movement of larger molecules. It also performs additional functions including the reduction of convection currents and the inhibition of sample diffusion, encouraging the separated components to remain as sharp, distinct bands. Furthermore, the matrix serves as a solid medium upon which samples can be fixed and detected in the post-electrophoretic analysis.

A suitable matrix should be chemically inert during electrophoresis. It should be easy to prepare and modify. Two materials, polyacrylamide, and agarose, have proven themselves to satisfy these requirements very well, performing all the above functions, each having advantages within a specific set of applications.

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