Team:New York City/Model

Model

Our goal is to create a cure for Huntington’s Disease (HD) by developing a RNA strand displacement technology that can target and block mutated huntingtin (HTT) mRNA strands and replace them with corrected strands for proper protein synthesis. Since an increased number of CAG repeats in the HTT gene coding for the polyglutamine tail characteristic of HD contributes to neurotoxicity in this disease, we decided to find a cure for HD in the RNA level. Last year, we designed a modified plasmid consisting of a chaperone strand and a corrected HTT mRNA strand using the software programs Vienna and mFold. The chaperone strand contains a small RNAi like toehold sequence designed to bind to the hairpin loop sequence of mutated HTT mRNA strands. Upon binding of the chaperone strand to the mutated mRNA strand, the corrected HTT mRNA strand would be released into the cytoplasm for proper protein synthesis.

To design our modified plasmid, we first looked into various huntingtin (HTT) mutants and the percentage of their occurrence in genetic databases, including NCBI. The goal was to identify hairpin loop sequences in HTT mutants so that they could be targeted by the chaperone to achieve toehold strand displacement of mutated HTT with a corrected strand. Then, we used the software programs mFold and Vienna to model RNA sequence folds and to find a tractable hairpin within the 5’ UTR of HTT mutants. In addition, we used the programs Genstrip and RNAI designer to review more sequences for us to target. Lastly, UGENE was used to view and align all the sequences we reviewed, allowing us to target the most optimal hairpin loop in HTT mutants with the toehold sequence within the chaperone strand in our modified plasmid.