Team:HokkaidoU Japan/Test


Dr. E.coli : The smallest protein injector in the world

There are several transfection methods to introduce nucleic acid into cells, however methods to introduce proteins directly into cells are complicated.

Unlike introducing DNA, which changes cell genetic makeup permenantly, proteins can act at pinpoint accuracy and afterwards be degraded leaving no permanent information in the target cell.

We tried to find an easy way to introduce desired proteins in the cell. Speficaly into eucaryotic cell. In order to do this we chose Type 3 Secreation System. Found in Salmonella and EPEc. These bacteria are pathogenic and working with them is problematic. To make things easier and safer we ordered DNA fragment which contains T3SS`s syringe part. As BAC vector came already inside a E.coli we were spared the enormous task of purifying and transforming it to the E.coli by ourselves.

We also designed a protein to secrete. For secretion the chimeric protein has to have secretion signal used in T3SS, we chose SrlP. To visualize the process and to make sure it did secrete we added GFP as a reporter. Arabinos promoter to switch it on on demand. And to make it even more interesting, a nuclear localization signal.

We tested this on rabbit colon cancer cells.

We think this technology will applicable by introducing proteins to the nucleus to fight cancer or induce normal cell to be stem cell.

HokkaidoU ToolBox

This is the first year that HokkaidoU team is joining iGEM. It was a journey full of errors and new experieneces. And most of the protocols we used we were unfamiliar with.

At the begining we decided to amplify most of the parts by PCR and not miniprep. This introduced it's own chalenges. So we would like to share some of the tools we thought useful in the procces.

Restriction Enzyme Digestion Visualization primers

When using standard assembly protocol after restriction enzyme digestion to acquire insert of the plasmid you can clearly see two bands in the electrophoresed gel. Not so with the parts PCRed with prefix and suffix primers. They very effective because they are the only truly universal primers. But we wanted to see if restriction was a success. To distinguish cut offs they must be big enought. So we ventured into vector to find some universal primer sites.Things got complicated because there are more than 40 vectors in registry. We couldn't tailor one set of primers for all but we did it for curent asembly standart and few other vectors.

This primers could also be used for checking how various primers effect restriction enzymes. And for purification small parts like RBS.

Easy 3 piece ligation program

This is program which calculates the neccesary reagants for restriction and ligation. You only have to choose well address, vector, PRC primers, concentration after PCR and part to plasmid ratio. It contributes greatly to the speed and precision of biobrick assembly.