What is the Difference Between Agarose and Polyacrylamide Gel Electrophoresis

The key difference between agarose and polyacrylamide gel electrophoresis is that agarose gel electrophoresis uses horizontally poured agarose gels to separate comparatively larger fragments of DNA, while polyacrylamide gel electrophoresis uses vertically poured polyacrylamide gels to separate shorter nucleic acid fragments.

Electrophoresis is a type of technique that uses an electric field applied across a gel matrix to separate biomolecules like DNA, RNA, and proteins. This separation of biomolecules such as DNA, RNA, and proteins through electrophoresis is based on charge and size. Samples are loaded into the wells of the gel. Later, the electric field is applied across the gel. The field causes negatively-charged molecules to move towards the positive electrode. The gel matrix acts as a molecular sieve through which the smallest molecules pass or travel rapidly while larger molecules move slowly. This enables the separation of molecules based on charge and size. Therefore, agarose and polyacrylamide gel electrophoresis are two types of gel electrophoresis techniques that mainly help to separate molecules based on their size and charge.

CONTENTS

1. Overview and Key Difference
2. What is Agarose Gel Electrophoresis
3. What is Polyacrylamide Gel Electrophoresis
4. Similarities – Agarose and Polyacrylamide Gel Electrophoresis
5. Agarose vs Polyacrylamide Gel Electrophoresis in Tabular Form
6. Summary – Agarose vs Polyacrylamide Gel Electrophoresis

What is Agarose Gel Electrophoresis?

Agarose gel electrophoresis is a technique that uses agarose gels to separate out biomolecules such as DNA and RNA. It is a technique used to separate nucleic acids primarily by size. The main compound called agarose used in this technique is a polysaccharide. It comes from seaweeds. Agarose can be dissolved in boiling buffer and then can be poured into a tray that is kept horizontally. In the tray, it becomes solidified when it cools down to form a slab. Agarose gels are poured with a comb in place to make wells into which nucleic acids such as DNA or RNA are loaded once the gel has solidified.

The gel is later immersed in an appropriate buffer, and a current is applied across the gel. DNA has a uniform negative charge that is independent of the sequence composition of the molecule. Therefore, DNA molecules will migrate from the cathode (-) toward the anode (+). The rate of migration is directly dependent on the size of the molecule. The largest macromolecules have the most difficult time navigating through the gel. On the other hand, the smaller macromolecules slip through the gel rapidly and quite easily.

What is Polyacrylamide Gel Electrophoresis?

Polyacrylamide gel electrophoresis (PAGE) is a technique that uses polyacrylamide gels to separate out biomolecules. It is a technique that is widely used to separate biological macromolecules, usually proteins and nucleic acids, according to their electrophoretic mobility. The hydration of acrylonitrile results in the formation of acrylamide molecules by nitrile hydratase. Acrylamide is soluble in water, and upon the addition of free radical initiators, acrylamide polymerizes, resulting in the formation of polyacrylamide gel. Normally, increased concentrations of acrylamide result in decreased pore size in the gel. Polyacrylamide gels are poured vertically, unlike agarose gels.

In polyacrylamide gel electrophoresis, the molecules may run in their native state, preserving the higher-order structure of molecules. This method is called native PAGE. Alternatively, a chemical denaturant can also be added to remove the higher-order structure and turn the molecule into an unstructured molecule whose mobility depends only on its length. This type is called SDS-PAGE.

What are the Similarities Between Agarose and Polyacrylamide Gel Electrophoresis?

• Agarose and polyacrylamide gel electrophoresis are two types of gel electrophoresis techniques.
• In fact, they are molecular biological techniques.
• Both techniques are used to detect biological macromolecules like DNA and proteins.
• These techniques are done by skilled technicians or researchers.
• In both techniques, the separation of macromolecules is based on the charge and the size.
• Both techniques allow the separation of nucleic acids like DNA and RNA.

What is the Difference Between Agarose and Polyacrylamide Gel Electrophoresis?

Agarose gel electrophoresis is a technique that uses horizontally poured agarose gels to separate out biomolecules, while polyacrylamide gel electrophoresis is a technique that uses vertically poured polyacrylamide gels to separate out biomolecules. This is the key difference between agarose and polyacrylamide gel electrophoresis. Furthermore, agarose gel electrophoresis is used for the separation of DNA and RNA, while polyacrylamide gel electrophoresis is used for the separation of nucleic acids such as DNA, RNA, or proteins.

The following table summarizes the difference between agarose and polyacrylamide gel electrophoresis.

Summary – Agarose vs Polyacrylamide Gel Electrophoresis

Agarose and polyacrylamide gel electrophoresis are two types of gel electrophoresis techniques used in molecular biology laboratories. Agarose gel electrophoresis uses an agarose gel to separate out biomolecules. Agarose is generally not toxic to humans, while polyacrylamide is toxic to humans. Moreover, agarose gel electrophoresis shows a low resolution while polyacrylamide gel electrophoresis shows a more resolution. Polyacrylamide gel electrophoresis uses a polyacrylamide gel to separate out biomolecules. This summarizes the difference between agarose and polyacrylamide gel electrophoresis

 Reference:

1. “Agarose Gel Electrophoresis.” An Overview | ScienceDirect Topics.
2. “Polyacrylamide Gel Electrophoresis.” An Overview | ScienceDirect Topics.

Image Courtesy:

1. “Agarose Gel Electrophoresis” By PlaxcoLab (CC BY 2.0) via Flickr
2. “Polyacrylamide gel electrophoresis of Proteins” By Jean-Etienne Minh-Duy Poirrier from Bruxelles, Belgium – Proteins in a 1D gel electrophoresis (CC BY-SA 2.0) via Commons Wikimedia