Although my attempts at making a self-programmable RNA cubic structure did not work out as planned despite running several polyaccrylimide gel electrophoresis experiments, I have moved on to working on a project that stems from the same motifs I was using when constructing my cube. My new RNA molecules that I recently finished synthesizing are all mutants of the corner piece of the cube I was initially working on. There are three different point mutations that cause the corner piece to fold so that each strand is perpendicular to the other two. I have synthesized six mutants from the corner piece accounting for all of the possible combinations of one or two point mutations in order to see the effects the three mutations have on the folding of the corner piece. This should help me to grasp a better understanding of what role each of the mutations plays in the tertiary structure of the corner piece.
Last week I ran my first experiments using polyaccrylimide gel electrophoresis to analyze the assembly of my mutant molecules. We radioactively label or RNA molecules with phosphorus 32 in and expose the dried gels to a phosphor screen overnight before visualizing them on a scanner the next day. Hence there is always a tinge of suspense as to how the experiment turned out since I can never tell how the experiment went immediately after. The most anticipation is generally felt the first time I run an experiment with new molecules because you never know how they will behave. Sometimes I predict what the results will look like and sometimes it goes my way and other times it goes the completely opposite way; but this time I hadn’t really known what to expect which made the process very exciting when I was able to visualize my first experiment and see that my results could be explained in a reasonable fashion, something that does not always happen.