Science Fundamentals: Agarose Gel Electrophoresis 

Science Fundamentals: Agarose Gel Electrophoresis 

Science Fundamentals is a series on foundational concepts in science. My goal is to give you the tools to critically think and discuss scientific concepts in everyday language and without the grind of actually getting a Ph.D. 

Be sure to check out the other installments in the series. I have done DNA, and Polymerase Chain Reaction so far. 

Intro

This is a quick follow up to the PCR article, to flesh out the end of that line of thought. After you run a PCR, you have to determine if the PCR amplified the DNA you wanted. To do this, we typically run agarose gels. 

Agarose is modified agar, which is jello made from seaweed. You can actually buy this in stores these days, usually as vegan jello. I have even seen cakes made out of it, which are usually very pretty, but lack taste. If you want to check these out, I believe they are called dew drop cakes. 

These agarose gels are used to separate DNA by size. An electric current is run through the gel, pushing the DNA through the gel. This works as DNA is a charged molecule, and so it responds to electrical currents. As the electricity pulls the DNA through the gel, the agarose acts like an obstacle course for the DNA. Larger pieces of DNA move more slowly through the obstacle course, but smaller pieces are more nimble and can move faster. Thus the smaller bits of DNA move further in the gel, and the larger ones stay near the top of the gel. 

Procedure

• Mix the agarose and a salt water mixture called TAE. TAE is made of Tris (a special salt), acetic acid (vinegar) and EDTA (a preservative).

• Boil this solution in a microwave 

• After cooling the solution slightly, pour it into a casting tray with teeth.

  • These casting trays allow consistent gels, and the teeth makes partial holes in the gel to allow you to load the DNA, we call these ‘wells’

• Once the gel is cast, mix the DNA with a loading dye

  • This allows you to see the DNA, and the dye makes the DNA heavy. This way it will stay in the wells of the gel

• Then place the gel in the TAE salt water, and load the DNA

• Next, connect the electricity and let the gel run for 20-30 minutes 

• Once the gel has run, you soak the gel in Ethidium Bromide. 

  • Ethidium Bromide is a small chemical that gets in between the DNA

  • As a side note, because it can get in between DNA, it is highly toxic. Science has slowly replaced this with less harmful chemicals. 

• After the Ethidium Bromide, the DNA can be seen under UV light. 

Application 

The application of agarose gel electrophoresis is rather limited. Mostly it is used in science laboratories to visually see the DNA. 

Hopefully this brief introduction to agarose gel electrophoresis is helpful. If you find it useful, please let me know. Drop me a line. If you have any suggestions for future Science Fundamentals, then let me know. I’ll be happy to look at specific topics for you. The next Science Fundamental will be on Antigens.. This is another step on the way to writing about the PCR test versus the antigen test for COVID. So please, stay tuned.