Agarose vs. Polyacrylamide — What's the Difference?
By Fiza Rafique & Maham Liaqat — Updated on May 8, 2024
Agarose and polyacrylamide are both used to make gels for electrophoresis, but agarose is best for larger DNA fragments while polyacrylamide excels at resolving smaller molecules and proteins.
Difference Between Agarose and Polyacrylamide
Table of Contents
ADVERTISEMENT
Key Differences
Agarose gels are generally used for the electrophoretic separation of DNA fragments ranging from 100 bp to over 20,000 bp. The gels are relatively easy to prepare and handle. On the other hand, polyacrylamide gels are more suited for separating smaller DNA fragments and proteins, particularly those between 1 to 500 bp for DNA, and as low as a few kDa up to hundreds of kDa for proteins.
The pore size in agarose gels is larger and more variable, which makes them less effective at resolving smaller molecules. Conversely, polyacrylamide gels can be cast with uniform and smaller pore sizes, providing superior resolving power for smaller molecules due to the tighter and more controlled network.
Agarose is less toxic and easier to work with compared to polyacrylamide. Polyacrylamide, especially before polymerization, involves the use of acrylamide monomer, which is neurotoxic and requires careful handling. Agarose gels are generally considered safer for routine use.
While agarose gels are ideal for routine DNA checking and preparative gel electrophoresis due to their ability to easily recover larger fragments, polyacrylamide gels are preferred in applications requiring high-resolution, such as in the analysis of STRs in forensic tests or the separation of proteins in SDS-PAGE.
The chemical stability also varies; agarose gels are more biodegradable and less chemically stable compared to polyacrylamide gels, which can be used for a variety of chemical manipulations post-electrophoresis, such as in western blotting, due to their robustness.
ADVERTISEMENT
Comparison Chart
Best Use
Larger DNA fragments (100 bp to 20 kb)
Smaller DNA fragments and proteins
Pore Size
Larger, variable
Smaller, uniform
Toxicity
Less toxic, safer to use
Toxic before polymerization, requires care
Ease of Preparation
Easier to prepare and handle
More complex and time-consuming
Applications
DNA checking, size separation
High-resolution needs, protein analysis
Compare with Definitions
Agarose
A polysaccharide used primarily for gel electrophoresis of DNA.
The lab technician poured melted agarose into a casting tray to prepare the gel.
Polyacrylamide
A polymer used in the formation of fine-pored gels for electrophoresis.
For precise protein measurement, the researcher prepared a polyacrylamide gel.
Agarose
Forms gels that are easy to handle and manipulate.
After running the DNA samples, the agarose gel was easily removed from the tray.
Polyacrylamide
Requires careful handling due to its toxicity.
Gloves and a mask were mandatory while handling the acrylamide solution.
Agarose
Known for its larger pore sizes.
Due to its larger pores, agarose was the preferred medium for separating large DNA fragments.
Polyacrylamide
Offers high resolution and chemical stability.
The biochemist used a polyacrylamide gel to perform a subsequent western blot test.
Agarose
Used in routine laboratory procedures involving nucleic acids.
The geneticist used an agarose gel to verify the size of cloned DNA inserts.
Polyacrylamide
Used in applications requiring detailed molecular analysis.
Polyacrylamide gels are a staple in forensic labs for analyzing DNA from crime scenes.
Agarose
Safer and less toxic than polyacrylamide.
Universities prefer using agarose in undergraduate labs due to its lower toxicity.
Polyacrylamide
Ideal for resolving very small DNA fragments and proteins.
The polyacrylamide gel was essential for separating the closely sized protein subunits.
Agarose
Agarose is a polysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose.
Polyacrylamide
Polyacrylamide (abbreviated as PAM) is a polymer with the formula (-CH2CHCONH2-). It has a linear-chain structure.
Agarose
A polysaccharide obtained from agar that is the most widely used medium for gel electrophoresis procedures.
Polyacrylamide
A synthetic resin made by polymerizing acrylamide, especially a water-soluble polymer used to form or stabilize gels and as a thickening or clarifying agent
Polyacrylamide gels
Linear polyacrylamide is a very efficient neutral carrier
Agarose
A polymeric cross-linked polysaccharide extracted from the seaweed agar; used to make gels that are used in electrophoresis.
Polyacrylamide
A water-soluble white solid polyamide, (-CH2CHCONH2-), related to acrylic acid.
Polyacrylamide
(organic compound) Any of a range of cross-linked polymers of acrylamide; used to form soft gels for making contact lenses etc.
Common Curiosities
What is the primary use of agarose in labs?
Agarose is primarily used for separating medium to large DNA fragments in gel electrophoresis.
Why choose polyacrylamide over agarose for protein analysis?
Polyacrylamide provides finer resolution necessary for the complex separation required in protein analysis.
Can you recover DNA from both types of gels?
Yes, but recovery is easier and more common from agarose gels due to their larger pore size and gentler handling of DNA.
Is agarose suitable for protein electrophoresis?
Agarose is generally not suitable for protein electrophoresis; polyacrylamide gels are preferred due to their finer pore structure.
What safety precautions are needed when working with polyacrylamide?
Handling polyacrylamide, especially in its monomeric form, requires gloves, goggles, and proper ventilation to avoid exposure to toxic substances.
Which gel type would you use for very small DNA fragments?
Polyacrylamide gels would be used for very small DNA fragments due to their ability to provide higher resolution.
Can agarose be used for high-resolution electrophoresis?
Agarose is not typically used for high-resolution electrophoresis due to its larger, more variable pore sizes.
What makes polyacrylamide more complex to prepare than agarose?
The polymerization process and the handling of toxic materials make polyacrylamide more complex and time-consuming to prepare than agarose.
Which gel type is better for quantitative analysis of biomolecules?
Polyacrylamide is generally better for quantitative analysis due to its uniform pore size and higher resolution.
How do the physical properties of these gels affect their laboratory applications?
The physical properties, like pore size and chemical stability, directly influence what types of samples can be effectively separated with each gel type.
What is a key advantage of using polyacrylamide in forensic science?
Its ability to separate very small DNA fragments with high resolution is critical for forensic applications like DNA fingerprinting.
Can both types of gels be stained to visualize the separated components?
Yes, both agarose and polyacrylamide gels can be stained using various dyes to visualize DNA, RNA, or proteins after electrophoresis.
Why is agarose considered safer for student labs?
Agarose does not involve toxic components in its handling and is easier to prepare, making it safer for educational environments.
What are the environmental considerations for disposing of these gels?
Polyacrylamide, due to its toxicity, requires careful disposal compared to the more biodegradable agarose.
How do the preparation times compare between agarose and polyacrylamide gels?
Agarose gels can be prepared more quickly and easily, while polyacrylamide gels require more careful timing and conditions for polymerization.
Share Your Discovery
Previous Comparison
Abaya vs. Hijab
Next Comparison
Hoblin vs. GoblinAuthor Spotlight
Written by
Fiza RafiqueFiza Rafique is a skilled content writer at AskDifference.com, where she meticulously refines and enhances written pieces. Drawing from her vast editorial expertise, Fiza ensures clarity, accuracy, and precision in every article. Passionate about language, she continually seeks to elevate the quality of content for readers worldwide.
Co-written by
Maham Liaqat
