Basis of differentiation | Agarose | Polyacrylamide |
Definition | Is a natural gel and the main constituent of agar used especially in gels for electrophoresis | Is a synthetic resin made by polymerizing acrylamide - a water-soluble polymer used to form a stabilized gel |
Synthesis | Is a complex polysaccharide derived from seaweed | Is produced by the digestion of acrylonitrile by nitrile hydratase |
Composition | Is composed of many molecules | Is composed of one large molecule |
Gap size between molecules | Has wide gaps between the differently-sized molecules | Has smaller gaps between the uniformly-sized molecules |
Gels | Agarose gel is natural and composed of long chains of interlinked sugars to form a meshwork | Polyacrylamide gel is synthetic and composed of chemical crosslinking of acrylamide and bis-acrylamide, producing a molecular sieve |
Pore Size | The pores of the agarose gel become smaller in size with the increasing concentration of agarose in the gel | The pore size of the polyacrylamide gel is determined by the ratio of acrylamide to bis-acrylamide |
Setting | Sets as it cools – this is purely a physical change | Sets after crosslinking occurs – this is a chemical change |
Orientation of pour | Is poured horizontally | Is poured vertically |
Typical concentrations of the gel | 0.5% to 2% | 6% to 15% |
Application | Used for separating much larger DNA fragments such as the products of PCR | Used for separating proteins and small nucleic acids such as miRNA, oligonucleotides, tRNAs, etc |
DNA fragment size | Separate DNA about 50 – 20,000 bp in size | Separate DNA about 5 – 500 bp in size |
Resolving power | Have a comparatively low resolving power | Have a high resolving power |
DNA configuration | Separate DNA in the double-stranded form | Separate DNA in the single-stranded form |
Toxicity | Is considered entirely non-toxic | moderately hazardous and require protection during handling |