Technique Tuesday: Gel Electrophoresis

Sep 01, 2020

Welcome to our first installment of “Technique Tuesdays”!

With these posts about methods and tools, we hope to give you a window into what day-to-day life is like working in science. 


By Anna Wheless

Technique Name: Gel Electrophoresis

Fun Rating: 

What is the general purpose? Gel electrophoresis separates charged molecules based on their sizes.

Why do we use it? Performing gel electrophoresis, or “running a gel,” is a common way to analyze samples of biological molecules, like DNA, RNA, or protein. Running a gel can help you determine whether there is a mixture of different molecules in your sample, as well as the masses or sizes of the sample’s components. It’s kind of like a weird way of taking attendance: imagine if your teacher counted the number of students in your class every day, and then asked you how tall you are–instead of asking your name–to figure out who might be present or absent. This is similar to what we do to get more information about the molecules in our samples. To truly figure out the sample’s identity, or “name” in this analogy, more steps are required. These steps often include purifying, quantifying, and then sequencing the sample to know for certain its exact identity. 

How does it work? Let’s say you’re working in the lab one day and you have a sample of DNA that you’d like to analyze. You decide that you would like to see the different sizes of the DNA molecules in your sample, because that will help you confirm their identities. Your first choice to do this would probably be gel electrophoresis.

Electrophoresis (pronounced electro-for-EE-sis) is defined as the movement of charged particles through a medium due to an electric field. In gel electrophoresis, this “medium” the particles move through is a type of gel that’s very similar to Jell-O. Jell-O, the dessert product, is essentially a combination of gelatin, flavorings, and food coloring. The gelatin in Jell-O and the gel we use in the lab for gel electrophoresis are both polymers, which are substances made up of linked molecules that form a net-like structure. This net-like molecular structure is critical for the function of gels in gel electrophoresis. 

The key to separating the pieces in your mixed sample of DNA is that the larger the molecule is, the more slowly it will move through the gel. This happens because larger molecules have a harder time moving through the holes in the “net” of the gel’s molecules. After a given amount of time has passed, the smaller pieces of DNA will have traveled farther in the gel than the larger pieces because they fit more easily through the mesh-like structures.

Above: Khan Academy illustration of DNA gel electrophoresis. Required Notice: All Khan Academy content is available for free at

We’ve decided the gel will separate the pieces of DNA by size, but then how exactly do we get the molecules to move through the gel? The answer is in the name: electrophoresis–you’ll use an electric field. DNA is a negatively charged molecule (when it’s in an environment with a pH near 7) due to the phosphate groups in the backbone (see below). After loading the DNA into your gel, you’ll run an electric current through the gel and this will cause the negatively charged DNA to move toward the positively charged electrode. This movement is often called “migration.”

Above: Structure of DNA molecule showing the phosphate groups in the backbone. Although this picture does not show charges, the single-bonded oxygens sticking out on the left all carry a charge of -1. Source

So it’s settled: gel electrophoresis should work on your DNA sample and give you the information you want. The first step to actually running the gel, after preparing the DNA samples, is to cast or “pour” the gel–which is, again, very much like making Jell-O. Then you can load the DNA samples into the gel and submerge it into a buffer solution*. When you pass an electric current through the buffer, the negatively charged DNA will slowly migrate to the positively charged electrode. After some time has passed, you can see where the bands of DNA molecules are in the gel by exposing it to a certain type of light. Then the analysis begins! 

The process is shown by the pictures below:

Top left: Pouring molten agarose gel into mold. Top right: Solidified gel (forbidden Jell-O…NOT edible). Bottom left: Gel submerged in buffer solution. Bottom right: Loading DNA + dye into gel.


Above: A time-lapse video taken over 35 minutes showing DNA and multiple dyes migrating through the gel. The larger dye molecules travel the slowest, and the smaller dye molecules travel more quickly. The DNA is invisible to the naked eye.

Above:  The same gel in the above video and images.  When the gel is illuminated with light, the DNA is visible as bright bands.  The leftmost lane with a bunch of bands contains a mixture of DNA fragments of known sizes, called a ladder. We can figure out how big our DNA fragments are by comparing their bands to the bands on the ladder.

You can use gel electrophoresis to analyze samples of other types of molecules too, like proteins and RNA. The same principles apply, but the gels are typically made out of different substances. The typical choice to analyze protein is to use polyacrylamide gels (pronounced polly-akRIL-amide), and RNA is usually analyzed with another type of agarose gel. A polyacrylamide gel is shown below. You’ll notice it’s much thinner and more transparent than the agarose gels, and uses slightly different equipment: 


Top left: Polyacrylamide gel sandwiched between two glass plates. Top right: Gel submerged in buffer solution. Bottom left: Gel removed from glass plates. Protein is not visible before staining. Bottom right: The same gel after staining, showing bands of protein in blue that were previously invisible.



Above: Protein mixed with dye being loaded into the polyacrylamide gel.

Below: A time lapse video taken over 45 minutes showing a protein+dye sample migrating through a polyacrylamide gel. The blue line you see moving is the dye. Protein is not visible until after staining.

The whole process of running a gel can take varying lengths of time– usually at least around 1-2 hours, or more depending on the circumstances. Gel electrophoresis is a highly versatile technique that’s used daily in my lab at UNC, either for DNA or protein separation. If you ever choose to study the life sciences, you’ll probably end up learning how to run gels too. 


Just in case you were thinking of trying this technique at home: DON’T! Electricity can be dangerous, and it’s easy to shock yourself with a makeshift set-up. 

*Quiz yourself: Why do you think the gel electrophoresis won’t work if you submerge the gel in regular water instead of a buffer solution? Hint: Will pure water carry an electric current? 

Acknowledgements: Thank you to Ben Roberts (Neher Lab, UNC) for letting me photograph his agarose gel process and helping with the video set-up.

Edited by Emma Goldberg and Zoe Terwilliger