Summary of the key differences between agarose and polyacrylamide gel electrophoresis

Name: Summary of the key differences between agarose and polyacrylamide gel electrophoresis
Creator: AAT Bioquest
License: https://www.aatbio.com/tou.html

Electrophoretic Method ▲ ▼	Agarose Gel Electrophoresis ▲ ▼	Polyacrylamide Gel Electrophoresis ▲ ▼
Gel Type	Agarose	Polyacrylamide
Gel Composition	Agarose is a polysaccharide extracted from seaweed. The gel contains long chains of interlinked sugars to form a meshwork.	Polyacrylamide is a synthetic resin made by digesting acrylonitrile with nitrile hydratase. The gel is made by the chemical crosslinking of acrylamide and bis-acrylamide to produce a molecular sieve.
Gel Casting Method	Gel sets as it cools. Agarose powder is mixed in a buffer and microwaved. The mixture is then poured into a gel frame and allowed to set.	Gel sets by a chemical reaction once crosslinking occurs.
Pore Properties	Concentration dictates pore size. Pore size becomes smaller as the concentration increases. (Typical concentration is 0.5-2%).	The ratio of acrylamide to bis-acrylamide dictates pore size. (Typical concentration is 6-15%)
Run Configuration	The gel is run horizontally.	The gel is run vertically.
Application	Separates nucleic acid fragments 50-20,000 base pairs in length.	Separates proteins and nucleic acid fragments 5-500 base pairs in length (e.g., oligonucleotides, miRNA, tRNAs, etc.).
Advantages	Nontoxic gel medium Gels are simple to cast and set quickly Good for separating large DNA molecules, such as PCR products and double-stranded DNA Samples can be recovered from the gel either by melting the gel, digesting with enzymes agarose, or treating with chaotropic salts	Stable chemically cross-linked gel Pores are uniform in size High resolving power, sharp bands Good for separating low molecular weight fragments such as single-stranded DNA
Disdvantages	Agarose is costly Comparatively low resolving power, fuzzy bands Poor separation of low molecular weight fragments No uniform pore size	Toxic monomers (i.e., acrylamide is a potent neurotoxin) Gels are tedious to prepare and are prone to leakage Each experiment requires a new gel

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MLA	"Quest Database™ Summary of the key differences between agarose and polyacrylamide gel electrophoresis." AAT Bioquest, Inc., 26 Apr. 2025, https://www.aatbio.com/data-sets/summary-of-the-key-differences-between-agarose-and-polyacrylamide-gel-electrophoresis.
APA	AAT Bioquest, Inc. (2025, April 26). Quest Database™ Summary of the key differences between agarose and polyacrylamide gel electrophoresis. AAT Bioquest. https://www.aatbio.com/data-sets/summary-of-the-key-differences-between-agarose-and-polyacrylamide-gel-electrophoresis.
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Summary of the key differences between agarose and polyacrylamide gel electrophoresis

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