Our mentors from the Department of Biotechnology of the National Institute of Chemistry (NIC) were approached by the teachers from the Faculty of computer and information sciences if they could participate in this years's project. After some thought it become apparent that the simplest way to attempt to join those two fields might be using DNA binding proteins in order to achieve information processing in cells. Therefore at the meeting of student candidates interested in participating at iGEM in March 2010, we were given the task to explore the possibilities that DNA binding proteins might provide to achieve information processing and to prepare individual project proposals within a month. Initially we considered several different directions, since students of biotechnology saw the great potentials for applications in the biosynthesis. Among the suggesstions of the selected candidates there were also ideas to attempt to improve the bioynthesis of violacein and carotenoids based on DNA as a scaffold, particularly since the invividual genes for those two pathways were already deposited in the Registry of parts and were also experimentally verified. This in fact later become the main topic of our project. During the brainstorming sessions in summer, students of computer sciences proposed to investigate if we could extend the basic idea to genetic oscillators, since it had been proposed earlier that a cooperativity of DNA binding repressors (lac dimer, Tet tetramer) is a prerequisite for generating the oscillations.
The laboratory that hosted our iGEM team did not have any previous experiences with zinc fingers, engineering biosynthetic pathways or modelling oscillators, so the project was completely new for mentors as well. However mentors from the NIC seeked support of additional external advisors from NIC and from the University of Ljubljana, who are specialists in certain experimental techniques that could be useful for our project. They helped us learn and use techniques, such as surface plasmon resonance (SPR) and HPLC and TLC analysis of reaction products. All gene constructs were obtained from the Registry or ordered as synthetic genes exclusively for this project.
All the experiments connected to cloning, protein isolation, characterisation (SDS, WB) and purification, FRET experiments, EMSA, repression assays... as well as data analysis were performed exclusively by the undergraduate student team members. The only exception was that the advisors helped students with operating the instruments for SPR and HPLC ad MS analysis, which was done by the MS operator. Student team members were also assisted for the use of confocal microscope at the beginning.
In this way we were encouraged to try and learn as much as we could every day and to take benefit from all the various techniques and protocols we got in touch with. Apart from the fact that the project was quite intensive and laborious, we were given so many beneficial knowledge it is really hard to imagine. Not only the final goal or destination, the path we have taken makes all the difference.
During the summer we also helped other teams participating in iGEM with filling their surveys (check the results here: http://2010.igem.org/Team:METU_Turkey_Software) and with characterization of several parts previosly existing in the Registry (BBa_I0500, BBa_K165007, BBa_K165006, BBa_K274002).