What is Gel Electrophoresis Used for

What is Gel Electrophoresis Used for?

An astonishingly high percentage of high school and college biology students are familiar with the crime scene detective series CSI. Every week about 20 million people tuned into CSI, about 11 million of them in your students’ demographic, when new episodes were coming out weekly. CBS is bringing back new episodes of CSI in 2021, so it’s likely your students will have some knowledge of what CSI is and what CSIs do.

With gel electrophoresis, your students can learn a very basic technique for preliminary investigations of crime scenes.

Gel electrophoresis is a method of “sorting” DNA, RNA, and other protein molecules. As you will introduce gel electrophoresis to your class with your tools from Modern Biology, it empowers your students to compare the length and to impute the molecular weight of isolated DNA to known samples. This testing only reveals similarities and dissimilarities at a gross level, but it can be and is a screening tool for directing CSI resources. Of course, you would have to teach your class how to purify a DNA sample first.

There is a great deal more to electrophoresis than its applications in crime scene investigation. It’s a fundamental tool for identifying DNA, RNA, and other macromolecules against known standards. And thoroughly understanding gel electrophoresis opens an abundance of educational opportunities for your AP Bio and college biology classes.

How Would You Explain Gel Electrophoresis to Your Students?

Most biology teachers are familiar with the basics and sometimes with advanced applications of gel electrophoresis. But teachers need to reach their students on a more basic level, perhaps something like the following:

Let’s suppose you have several vials of DNA samples. You want to begin to understand the DNA in each sample. You can’t really take DNA out of the vial and physically examine it.

That’s because even the largest molecules of DNA are incredibly small. Suppose you had a strand of DNA consisting of 100,000 base pairs. This strand of DNA would be 20 to 40 microns long. A micron is a little under 4 one-hundred thousandths of an inch, so this long and large strand of DNA would be around a thousandth of an inch long, more or less.

You aren’t likely to be dealing with many strands of DNA that long. More typically, you will be working with strands of DNA that have 1,000 base pairs or less. This means that even after you stretch out a curled or looping or circular strand of DNA, it will only be about one hundred-thousandth of an inch long. Its width would be in the billionths of an inch.

There’s no way to manipulate DNA with hand-held tools. So, how do we start finding out the basics about our purified DNA samples like comparative length and molecular weight?

Gel electrophoresis gives us a visual tool for measuring microscopic strands of DNA

This technique is called gel electrophoresis because:

  1. It involves a gel.
  2. DNA or other test molecules migrate across the gel toward an electrical charge.
  3. Phoresis is a process of migrating together. The test molecules migrate across the gel.

This process wouldn’t be very useful if there were no way to see the microscopic or submicroscopic molecules of DNA, RNA, or other proteins moving across the gel. Fortunately, protein molecules can be dyed in with a fluorescent chemical called ethidium bromide. We can see different samples move across the electrified gel at different rates under ultraviolet light.

What do you use for the gel?

What is the purpose of gel electrophoresis - How to read gel electrophoresis

The most common material for making the gel for electrophoresis is agarose. It’s a polysaccharide extracted from seaweed. When it’s properly mixed with water, it makes material that is very similar to Jell-O. The agarose is poured over a matrix of wells, tiny divots into which the test DNA and standard DNA are poured (separately).

DNA, RNA, and other proteins carry a very, very small negative charge. The opposite end of the agarose gel is electrified to become an anode, with a positive charge. Of course, to do that, you have to give the nearby end of the gel a negative charge.

Gel electrophoresis operates on the principles of attraction and repulsion

Opposite electrical charges attract, but longer molecules will move more slowly than shorter molecules. Once the test substance has been placed in its well and the control substances have been placed in their wells (and the good experimenter has taken notes of which substance is where), the charge is turned on and the substances begin to move from well to well across the gel.

There is a negative charge on the side of the gel where you have placed the test substances. It repels the substances you are testing. There is a positive charge at the other side of the gel. It attracts the substances you put on the other side of the gel.

One the shortest molecule has reached the positively charged end of the gel, the current is turned off. The distance substances have traveled across the gel tells you proportionally how much shorter or longer they are than the control sample.

When you are doing gel electrophoresis in the lab, you will always add a buffer to the agarose gel. The buffer is basically a saltwater solution. It dilutes the solutions, so there aren’t any big swings in pH that can affect the charge on the control or the samples.

Your students will always have some basic questions

If ethidium bromide makes any kind of DNA glow in ultraviolet light, how will I know which strand of DNA is the test DNA?

You will add control DNA of known length, five thousand base pairs, ten thousand base pairs, and so on. You will put all of these control substances in the same well. You will have your test substance in another well beside it. Electrophoresis will out DNA from control well, so it looks like a ruler, or ladder. Just look where the test DNA lands on the gel to estimate how many base pairs it has.

It’s a fair question to ask why heavier DNA molecules don’t move faster than lighter DNA molecules. After all, heavier molecules have a greater total electrical charge. The reason gel electrophoresis tells us which molecules are longer and which molecules are shorter, instead of which molecules are heavier and which are lighter, is that both kinds of molecules have the same density. They get the same amount of electrical attraction or repulsion per base pair. It’s just easier for short things to go through sticky things than long things.

Of course, students will always ask what they can do with this technique. The answer is that electrophoresis can give you an idea of what your sample is from. More importantly, you can cut the test sample out of the gel, isolating it for further testing. Gel electrophoresis can give you clean samples from mixtures of DNA.

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