Updated: Jul 11
I placed the square gel into the UV machine and closed the door to take an image of the bands of DNA inside. I was hoping there would be a band about an inch from the edge, which would mean cloned DNA of the approximately 7000 bp long: success. Instead, a long orange smear appeared: no success. My lab researches the origins of brain tumors, and this cloned DNA would allow us to control one protein involved in neurons’ mysterious path to cancer. Much like this unknown process, research was an elusive creature to me. I entered with lessons from biology at the forefront of my mind: clear-cut recipes for success. This limited perspective was my primary tool as I started my project: combining three separate segments of our targeted gene into one continuous strand. The entire gene was too difficult to clone in a single step, so my strategy was to “glue” them together one by one. Gluing the first two strands together was successful. But attaching that third segment failed. So I returned to the drawing board. I created a longer version of the third segment by redesigning the primers in hopes of increasing the probability of contact. In another sample, I played with the enzyme responsible for connecting the third piece. I used a slower but more resilient “normal” polymerase and added magnesium chloride to buffer the solution and facilitate polymerase’s function. After half a day cooking in the PCR machine, two more orange smears in the UV machine. I then tried altering the heating-cooling program of the PCR machine to accommodate both longer cooling times and a wider range of temperatures at which the DNA solution would be heated to increase the chances of connection at one of the temperatures. This didn’t work —orange smear. Research is often inexact and almost never by the book, a wild adventure. Chasing a solution is not unlike seeking to understand a rare species of the jungles. This wilderness thrives at the cellular level. Hunting for answers requires versatility and a willingness to play with options as the science plays with the mind. I shut the UV machine’s door and prepared to take another picture of the DNA in a new gel. Challenge accepted.