Am I running gels or are the gels running me?

Previous to my current experiences in the wet lab, I had envisioned the gel electrophoresis to only be a smaller part of the big picture of the paper I was reading. But after a month of lab, I would argue otherwise. The gel electrophoresis is a method used to visualize DNA based on molecular weight. Molecules with higher molecular weight travel more slowly through agarose gel than low molecular weight counterparts. The movement of DNA through the gel is powered by an electric current.

With flaviviridae (the family of viruses that are frequently carried by mosquitoes), the genome is often small enough to easily edit. This makes them an ideal candidate for a host of creative projects attempting to document their cytopathic effect. The cytopathic effect (CPE) is the resulting structural changes in a host cell brought on by a viral infection. So, we can alter the viral genome and observe the effect of induced “breakages” on CPE. But how do we even prove we made the gene editing change? In steps the gel electrophoresis.

The first step to gene editing is to isolate a gene is to clone the sequence you wish to edit on a plasmid. To determine if the plasmid we wish to replicate is pure, you run a gel to determine its purity. Then, after you’ve transformed your plasmid into your bacteria, cloned it, and reharvested it, you digest it with restriction enzymes. Then, to make sure your plasmid was cut, you then run another gel to confirm it was cut by your restriction enzymes.

Running a gel is also an important step in PCR (short for polymerase chain reaction) quality control. A PCR is a method used to clone a segment of DNA. By running a gel with your PCR product and control, you can figure out how good your primers are, if there was any contamination, and whether your PCR actually worked. But that’s not all. After running a PCR, your product often contains impurities such as primers and DNA polymerases. To purify your product, you can load the crude product into a gel. Only the DNA will move through the gel. Then you can just cut out your band, dissolve the surrounding gel, and obtain a purified DNA product.

So next time you see a gel while reading a paper, take some time to figure it out instead of moving on to the more interesting figures. After all, it’s been the backbone of modern molecular biology since 1950 and will only become more important as gene editing becomes more widespread.

 

Ezra Kosviner

Ezra is going to be a third year biochemistry student. He is interested in how Zika Virus replicates in human cells. He is an avid surfer and
hiker.