What is the Difference Between Agarose and Polyacrylamide?

The main differences between agarose and polyacrylamide gels are their porosity, toxicity, and molecular complexity, which lead to distinct uses in research laboratories. Here are the key differences:

1. Porosity: Agarose gels have a larger pore size compared to polyacrylamide gels. This makes agarose suitable for separating large protein complexes and nucleic acids, while polyacrylamide gels with smaller pore sizes are ideal for separating most proteins and smaller nucleic acids.
2. Toxicity: Agarose is considered entirely non-toxic, whereas polyacrylamide gels and powders are considered moderately hazardous, requiring proper protection when handling.
3. Molecular Complexity: Agarose is composed of a complex structure with wide gaps between differently-sized molecules, while polyacrylamide is made up of a single large molecular type with smaller gaps, although band sizes may vary.

In summary, agarose gels are used for separating large molecules, such as DNA fragments and large protein complexes, while polyacrylamide gels are used for separating smaller molecules, such as proteins and shorter nucleic acids. The choice of gel depends on the type and size of the molecules being studied.

Comparative Table: Agarose vs Polyacrylamide

Here is a table summarizing the differences between agarose and polyacrylamide gels:

Agarose gels are used to separate large DNA fragments, while polyacrylamide gels are used to separate shorter nucleic acids, generally in the range of 1-1000 base pairs. Additionally, agarose gels have a lower resolution compared to polyacrylamide gels, and they are run horizontally, whereas polyacrylamide gels are run vertically.