What is the difference between agarose and polyacrylamide gels?

There are 3 major differences between these gels, which lead to their distinct uses in the research lab.

The first difference is toxicity; agarose is considered entirely non-toxic, whereas polyacrylamide powders and gels are considered moderately hazardous and require protection during handling.

The second difference between the two substances is molecular complexity. Agarose is complex and has wide gaps between the many differently-sized molecules that make up the gel matrix. Polyacrylamide is made up of only one large molecular type, which has far smaller gaps, although band sizes may vary.

The third difference is in gel preparation, namely the orientation of pour. Agarose is poured horizontally, and polyacrylamide is poured vertically. Since vertical pouring is difficult to do well, gels are typically ordered premade. Agarose preparation is slightly more forgiving, and it can be melted and re-poured if necessary.

Agarose gels are used with DNA, due to the larger size of the biomolecules (DNA fragments are often thousands of kDa). For protein gels, polyacrylamide gives good resolution, as the far smaller size (50 kDa is typical) is more suited for the tighter intermolecular gaps of the gel.

There are variations on preparation for both of these common gels, and the correct selection and type should be selected carefully for each experiment. Selection of the correct gel stain will also depend on which substance is chosen, as some dyes, though not all, work differently in each media.