In the 2020 iGEM competition, Team SUNY_Oneonta aimed to create a genotyping system that would detect the A1 and A2 allele with on-site testing. For this competition year, we aimed to accomplish this goal whilst simultaneously expanding on it. Our new goal was to expand our testing system to not only detect the A1 and A2 allele but to detect other single nucleotide polymorphisms as well. With this goal in mind, we took several steps to refine and build upon our genotyping system project. In particular, we improved our heat block design by going through several cycles of data collection and device redesign and we employed information derived from our molecular model in the design criteria of our synthetic DNAs.
Refinement of the heat block design
- Utilizing information collected the previous competition year (2020), part refinements were made on the original heat block prototype.
- Each part of the prototype was exchanged with different models of the same part and tested for its ability to maintain a stable temperature.
- Parts that produced optimal results were chosen for our final design.
Bioinformatics research and development
- Due to the expansion of our project, new targets were identified for our genotyping system to detect. These targets were chosen because they are associated with cattle diseases that can be detrimental when breeding.
- Positive and negative control DNAs were designed and synthesized for each of the new targets.
- Detection oligos were designed for the wild and mutant type genomic sequences of two additional targets.
- Information from the molecular model initially developed in 2020 and refined this year was used in the development of design criteria for the synthetic DNAs used to detect the new targets.