Project:Public Biobrick
Overview
UCL's igem team got in touch with us in May about a collaboration with their project to make a biobrick that could help to clean up plastic floating in the ocean. From August the biohackers have been working with them to develop a 'public biobrick' (ie. one developed outside of the traditional university or research lab). This biobrick contains antifreeze and mercuric reductase genes from the marine bacteria Oceanibulbus Indolifex.
Designing primers to amplify the antifreeze and mercuric reductase genes from O. Indolifex
Generating competent cells (Hackspace)
The competent cells are what the biobrick is to be 'put into' at the end of the process. The procedure we followed is here. We built an [incubator with shaker] to achieve this. After 24 hours we did not see the expected colonies on the plates, we think this is because the streaks were cut too deeply into the growth medium. As an alternative we proceeded with some already prepared plates from UCL that did contain colonies.
Amplification of plasmid backbone (Hackspace)
The plasmid backbone is the vehicle for the biobrick, and is the means by which it will get into the competent cells. The procedure is in the same link as for competent cells. We did two versions of this reaction, one with the mastermix supplied by UCL, and one with the taq readymix that we use at the hackspace. We saw a band for the readymix one, but not for the mastermix one, so proceeded with the readymix one.
DNA extraction from O. Indolifex and PCR of two genes (UCL)
In this step we attempted to isolate the two genes to be used in the biobrick. The protocol is [TBA here]. Our PCRs failed, and it turned out that no DNA had been extracted by the Generation Column Capture Kit we used. So we proceeded with a previous extraction that had been done with ethanol.