While we were conducting our usual experiments, we noticed we had a lot of errors concerning gel extraction using the gels we had made with ethidium bromide. At the UK iGEM team meetup, we got to talking with Glasgow's team to discover they could have a novel method of working around our problem; specifically they had made their own fluorescent tag that could be used for gel electrophoresis. Glasgow was kind enough to send us some of their fluorescent dye for us to use in our next gel extraction.
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After we came up with a model of DNA Origami arms and the sequences for them and how they would bond we wanted to model the probability of the E.coli arms forming fully and how this probability would change as length of the arms increased. We came up with a basic model but thought it would be beneficial if we sought outside help with the mathematics.
We got in contact with NTNU to ask for assistance and they came back with a stochastic method for calculating said probabilities. After discussing the problem further we came up with various equations such as S_i= Σ_j (K_i,j / Σ_j K_i,j ) log K_i,j / E_j[K_i,j], where S is how well a zinc finger binds to an arm and P_i = S_i / W (S_i) where P is the probability of formation for that zinc finger arm.
One part of our project was create a DNA origami glue using a biobrick part from the distributed kit, specifically part BBa_K314110. Once we had designed it, we decided to collaborate with Oxford's iGEM team to help get it made.
Oxford's team sped up he production of our DNA origami by conducting a PCR using primers we had designed and sent to them to create seven PCR products, six of which would be directly used to create the DNA origami.
Once we received the PCR products, we combined and annealed them to form DNA origami structures, which could then be viewed under an electron micrograph.