Running DNA through Jello (no, really)

To nerds like me who find any part of the DNA barcoding process worthy of being labeled “cool,” I think it can go without saying that running gels is the coolest part. You probably have some questions - gel? Like for nail polish? And where are they running? I don’t blame you, it’s a little confusing. The scientific process is called Gel Electrophoresis, which, in simpler terms, means running an electric current through a gel made of agarose in order to move DNA molecules (which are pipetted into the wells at the start of the gel) through a small container. Why are we moving the DNA molecules? Well, the molecules will stop running through the gel at a certain time, once the content of the DNA has run out. The specific time the DNA of that specimen stops will also let us know how many base pairs of DNA were in the solution, through a “DNA ladder,” a control recording every 100 base pairs in the gel. We had just finished conducting PCR’s, or polymerase chain reactions, in order to amplify a specific gene, the COI gene, from the DNA extracted from our fish specimens. This gene is what is ultimately used to compare and contrast between species, and is traditionally ~650 base pairs long. In this way, Gel Electrophoresis acts as a method of double-checking the PCR and making sure 650 base pairs have been amplified. If the DNA stops at a point severely above or below it, we know something went wrong. I was particularly excited about this step because I realized last year at Brown, where I had first run a gel, that colorful dye is not only useful for making wacky shirts or weird colored slime, but turns out to be pretty useful for seeing DNA! Gel Electrophoresis is the only part of the process where this is possible, and I was sure that everything was going to run smoothly, as it did at Brown.

During the PCR, we amplified the COI gene in a couple specimens as a test run, and tried two different types of primers (molecules that bind to DNA). The gel would let us know which primer worked better, and after we pipetted the DNA of 8 specimens amplified with one primer and the DNA of 8 other specimens amplified with another primer into the gelatinous substance, I sat on my stool, turned on the thermocycler that would run the electric current (pictured above), and began to wait.