In my last post I spoke about the new mutant RNA corner pieces that I was sequencing.  The results I was able to get from the gel electrophoresis experiments were interesting and some of the molecules assembled into a tertiary structure we were expecting while others seemed to behave slightly mysteriously.  One of the mutations at the crux of the corner piece seems to play the largest role in interacting with adjacent bases in order to allow the RNA to fold into a corner piece where all three strands are perpendicular.  This point mutation is a guanine base that has been changed to a uracil.  Another point mutation that it interacts with is an adenine base that buldges out of the helical base pairing structure on the adjacent strand.  These mutations allow the uracil and the adenine to interact with each other to stabilize the corner motif’s tertiary structure.  According to the interactions between these two mutations it should seem that they would be the most critical sequence changes in making the corner piece rigid.  There is also a third mutation that separates the fiber motif from the corner motif, which is a guanine buldge, however it does not seem play as large of a role in causing the molecule to fold into a corner piece.  With the previous thoughts in mind I looked at the first couple of gel electrophoresis experiments I had run and found that the two mutations which seemed to form the most rigid strong species bands on the gel were caused by the A buldge and the G buldge.  My P.I. wondered if I had possibly mixed the tubes, and at the time I was fairly certain that I did not mix up two molecules because I had run the experiment several times and I didn’t think that I would make the same mistake that many times but who knows sometimes.  Later that day however I was talking with my graduate mentor and we remembered that when we were first transcribing our molecules a somewhat shady incident occurred.  When we were precipitating the ethanol washes from our newly synthesized mutant RNA molecules some ethanol spilled onto the caps and smeared some of the labels that had been written on the test tubes.  We thought that we had correctly re-labeled the molecules according to the remains of the smeared sharpie labels, however our weird experimental results made us rethink whether or not we actually did relabel the molecules correctly.