Why aren’t SDS-PAGE gels horizontal?

Instead of running in horizontal system like agarose gel electrophoresis, SDS-PAGE gels are usually horizontal. A few reasons are responsible for this:

• SDS-PAGE have two component gels: the stacking gel and the resolving gel. The vertical system allows sequential preparation for these gels. For example, the resolving gel can be added first, and once it is set, the stacking gel can be added.
• The SDS-PAGE gel is prepared via free-radical initiated vinyl polymerization. The oxygen in air can react with the free radicals and thus inhibit the polymerization reaction. Therefore, this reaction would not proceed efficiently in an open, horizontal system. Sandwiching the reagents between two plates in a vertical way can effectively keep the oxygen away from the gel mix, thus ensuring the polymerization.
• SDS-PAGE gels are relatively expensive. It is more cost effective to make them thinner. Therefore, the vertical setup is more feasible because gels usually don’t need to be as thick as the ones in a horizontal system.