The start of a new experiment can be an exciting and nerve racking time. When working with RNA molecules, there is a substantial amount of prep work that comes into play before an experiment can even be run. You begin by studying certain shapes that RNA molecules can fold into. Currently I am studying a right angle motif of RNA. Based on the construct of study you can analyze the folding capabilities and assembly of the molecule by looking at the effects different point mutations have on the specific construct. There are sometimes hundreds of point mutations that you could make, however you have to deduce which ones would cause the biggest change in the molecules assembly into a 3D structure. Next you can design the different mutant forms of the wild-type right angle molecule of interest and design complementary DNA primers. Then the DNA can be synthesized via polymerase chain reaction and the RNA synthesized by transcription of the DNA. Hence, a good deal of work precedes the experimental testing of the designed RNA particles. Which is generally why I am kept on the edge of my seat when I am awaiting the results of my first experiments.
I ran my first polyacrylamide gel electrophoresis experiments today in order to analyzed the assembly patterns of my newly synthesized RNA molecules. I radioactively label the RNA molecules with radioactive phosphate in order to visualize where the RNA molecules migrate to on the gel. After running the gel it is dried and exposed to a storage phosphor screen which can be scanned in order to give an image of where the RNA bands occurred on the gel. We expose the gels to the storage screens over night, so I won’t know what the results of my experiment will be until Monday, which is even worse for my impatience since I will have to wait until the weekend is over to view my results. The best thing about the entire process is that you can either get the results you were expecting and prove the concept you came up with originally or you could see something completely unlike what you expected which is equally or more exciting because you are discovering something new that did not go along with preconceived ideas. Or maybe my experimental technique was a little off, but it will be fun to figure out the reasons behind whatever results are obtained.