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.
We had one particular experiment which repeatedly caused an issue for us at the gel extraction stage. We found it tricky to cut out the DNA from the gel under a blue light, and felt poor cutting technique could be the root of our problem. At the iGEM 2015 London Meet up we met the team from Glasgow University. They had just presented an ethidium bromide free method of producing gels, which then did not need to be visualised using a blue light. Instead these gels could be seen by eye, which we saw as extremely helpful to solve our issue. Glasgow kindly packaged off and sent us some AzureA, with which we set out producing the gel. This blue AzureA gel proved very useful, and it was easier to visualise clear bands just by eye. The collaboration helped us to solve our wet lab issues and supported the characterisation of Glasgow's gel staining method.
A key element of iGEM is outreach into schools in order to get the next generation of scientists thinking about synthetic biology and what they can do. As one of our team was born and bred Mancunion, we decided to set out on a collaborative outreach with the Manchester-Graz team. This involved iGEM members from the competing teams pairing up via the web to prepare lessons and presentations; ultimately leading to a full day of teaching where we presented to over 450 students. Our aim was to get the students thinking about going to university, studying a scientific degree, and for the older students; what they could achieve with synthetic biology. This collaboration brought together two teams to work alongside each other to plan and execute outreach within a school, this enabled a variety of experiences to be shared with students. We see this collaboration as a success; the Manchester-Graz team were fantastic to work with, and feedback from teachers has been hugely positive!