40 minutes on a Stool, praying to the DNA Gods

Turns out, research isn’t a streamlined process. There are setbacks, and those setbacks can be annoying, especially after you’ve sat for forty minutes on a stool waiting for DNA molecules to run through a gel and getting excited to see a visual product of months of hard laboratory work. As mentioned in the last post, we were testing two primers and seeing which one would work better for this DNA. As I sat there, listening to the low hum of the lab’s air conditioner, I prayed that the DNA molecules that had the primer that I had pipetted into the solution would reach the 650 base pair line of the gel, and not the other primer.

I was reminded of times when my brother and I would sit on the warm heater of our old apartment on cold January nights and watch cars line up to cross the 79th street intersection. We would each pick a car for ourselves, calling “yellow taxi!” or “black van!” As we waited for the light to turn green, we would cheer for our cars and reassure them of their high-speed potential as if the drivers could hear our tiny voices all the way up on the 10th floor. Finally, they would go and we would watch them race across the street, seeing which vehicle would reach the next light first. Whoever lost would always claim that they had chosen another car all along or that this game was stupid anyway, but the point was that one car would prove to be better than the other, just like one primer would make the DNA molecules reach and the other would not do so as well. I was thinking about this when my mentor’s timer went off and he instructed me to carefully bring the gel into another room, where we would be able to view the bands of DNA clearly under UV light. Slowly, I watched as he turned off all the lights in the room except for that one and finally an image of our gel was projected onto the screen. My stomach dropped. Not all the bands of DNA had appeared. There were light bands for a few species of fish DNA that had made it through the gel but an entire species, Aphyosemion elegans, had missing bands. 

My confidence had left and I looked at my mentor, waiting for him to give some explanation as to why this happened, but all he did was shake his head and express the same confusion that I was. I started to bombard him with questions, asking if there were other primers that could be used or if the company had sent over faulty solutions, even if the UV light wasn’t working. What he helped me realize was that the mistake might have been on our part, something we might not have considered when doing PCR or running the gel. I was immediately disheartened and began to pack my things when my mentor stopped me and had us sit down and discuss a few possible new modifications and parameters we could add in order to help this fish to work better the next time.

We considered changing the temperature for the PCR, adding more DNA, and allowing the gel to run for longer. After all, each fish was different and needed different adjustments. With these changes in mind, I left the lab disappointed yet motivated to return on Tuesday and try again. Isn’t that what research is all about?