What is the Difference Between Agarose and Polyacrylamide Gel Electrophoresis?

Agarose and polyacrylamide are two support matrices commonly used in gel electrophoresis, a technique used to separate molecules based on their size and charge. They have different properties and are used for different purposes:

1. Pore Size: Agarose has a larger pore size and is suitable for separating nucleic acids and large protein complexes, while polyacrylamide has a smaller pore size, making it ideal for separating most proteins and smaller nucleic acids.
2. Toxicity: Agarose is considered non-toxic, whereas polyacrylamide powders and gels are considered moderately hazardous and require protection.
3. Gel Preparation: Agarose gels are poured horizontally, while polyacrylamide gels are poured vertically. Agarose preparation is more forgiving, and it can be melted and re-poured if necessary.
4. Resolving Power: Polyacrylamide gels have a greater resolving power than agarose gels, allowing them to separate molecules of DNA whose lengths differ by a single base pair in 1000 base pairs.
5. Sample Quantity: Polyacrylamide gels can accommodate much larger quantities of DNA than agarose gels, with up to 10 µg of DNA being applied to a single slot of a typical polyacrylamide gel.
6. Purity: DNA recovered from polyacrylamide gels is extremely pure and can be used for demanding applications such as microinjection of mouse embryos.

In summary, agarose gels are typically used for separating large molecules like DNA and large protein complexes, while polyacrylamide gels are used for separating smaller proteins and nucleic acids. Polyacrylamide gels have a higher resolving power and can accommodate larger sample quantities compared to agarose gels.

Comparative Table: Agarose vs Polyacrylamide Gel Electrophoresis

Here is a table comparing the differences between agarose and polyacrylamide gel electrophoresis:

Agarose gel electrophoresis is more suitable for separating large DNA fragments, while polyacrylamide gel electrophoresis is better for separating shorter nucleic acids. The choice of gel type depends on factors such as the desired resolution, the size of the nucleic acids, and the apparatus being used.