Computational investigation of thermocycling as a means of improving folding success rates of single-stranded RNA

In vitro selection has proven itself as a great tool for isolating functional single stranded RNA sequences from large random pools. However, the multitude of available folding pathways leave many potentially functional sequences in misfolded states. This research aimed to use kinetic folding simulations of single-stranded RNA to test thermocycling as a means of overcoming energy barriers that prevent sequences from reaching a functional secondary structure. In this pursuit, I tested the negative effects of adding a number of random bases to each end of a known sequence, and showed that additional bases can drastically diminish the folding success of sequences that otherwise fold correctly at a very high rate. I then simulated thermocycling of a typically unsuccessful sequence and demonstrated that high temperatures break most or all base-pairs within a sequence, allowing refolding to occur.