Agarose gel electrophoresis

Agarose gel electrophoresis is used to separate DNA or RNA molecules by size. Nucleic acids are negatively charged and are moved through an agarose matrix by an electric field (electrophoresis). Shorter molecules move faster and migrate further.

General Procedure

1. Cast a gel
2. Place it in gel box in running buffer
3. Load samples
4. Run the gel
5. Image the gel

Buffers

• TAE - better resolution of fragments >4kb;
• TBE - better resolution of 0.1-3kb fragments; TBE is better suited for high-voltage (>150V) electrophoresis than TAE because of its higher buffering capacity and lower conductivity;

Loading dyes

dye	0.5-1.5% agarose	2.0-3.0% agarose*
xylene cyanol	4000-5000 bp	750 bp
bromophenol blue	400-500 bp	100 bp

*sieving agarose

for recipes see: Agarose gel loading dye

Notes

• If you are getting unexpected bands on your gel you may want to look at the common issues in agarose gel electrophoresis page.
• If you have no experience with gel electrophoresis or are explaining it to someone new, here is a cute java demo of what happens.

See also

• Agarose gel loading dye

Specific Protocols

• Endy:Agarose gel
• Knight:Agarose gel electrophoresis

External links

• Wikipedia entry on agarose gel electrophoresis
• Colorado state has an excellent page with detailed instructions and photos
• Methodbook.net has a nice primer on agarose gel electrophoresis
• CSH Protocols (~Molecular Cloning) protocol on agarose gel electrophoresis but restricted access