What are the differences between agarose and polyacrylamide?

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