Project Design
Our goal is to create a viable short term cure for Huntington’s Disease by developing an RNA strand displacement technology that consists of a chaperone strand, a correct HTT mRNA strand, and a fluorescent reporter. The computational aspect of our project uses the program Vienna to fold and create various models of diseased Huntington’s mRNA strands with varying numbers of CAG repeats. All the models will be compared to find a common hairpin loop to target. The structure of the toehold of our chaperone strand will be based upon the universal hairpin loop, and the entire strand itself will be mostly complementary to a synthetic-mRNA strand that codes for the HTT gene followed by a fluorophore. RNA strand displacement will be able to readily occur as the toehold of the chaperone has a small RNAi like sequence that is specific to the hairpin loop of the diseased mRNA.
Once these complexes have been developed, the wet-lab team will come into play. Several types of diseased HTT DNA sequences, along with a sequence coding for another fluorophore, will be cloned into plasmids and then into E.coli. Afterwards, our complexes will be transfected into the E.coli. Over time, we should be able to observe the increasing presence of the fluorescent protein on the synthetic-mRNA strand of the HTT gene than the fluorophore of the diseased mRNA, which will prove that the RNA strand displacement has occurred. We will also further legitimize our findings by establishing negative and positive controls to show that the only reason for the changes in presence of the two fluorophores is due to the RNA strand displacement.
