Collaborations
Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
Genspace Collaboration
A huge part of igem is working with other teams to further the research of both parties. This is exactly what we did when we collaborated with the 2015 genspace igem team. One of the major obstacles in research today is the high price of new lab equipment. Often times, an expensive device is needed to carry out a one time procedure. Buying the device makes no sense, but you still need to use it. We circumvented this by sharing equipment between our two teams. The Genspace igem team came to Cooper Union in early August. They had several samples of DNA whose concentrations they needed to determine. To help them achieve this, we showed them how to use our Nanodrop 2000 spectrophotometer. This device measures the absorbance of a small volume of liquid and then calculates the concentration of nucleic acid present in the sample. After a brief tutorial, they were quickly able to measure the concentrations of all of their samples. To repay this favor, the Genspace igem team helped us by lending us their vacuum oven. This device was necessary in the protocol for the silanization of glass slides. In order for our DNA synthesizer to work, the DNA must bond to a glass slide so that it is not lost in the wash steps. This was done previously by forming a disulfide bond between the DNA oligonucleotide and the glass. To test this ourselves, we ordered sulfonated oligonucleotides and made silanized glass slides. Genspace’s vacuum oven was useful because the glass slides need to be kept in an anhydrous environment for part of the procedure. With the vacuum oven, we completed this protocol and were able to yield results on the effectiveness of bonding DNA to glass slides.
Heidelberg Collaboration
To further our project and potentially help out another igem team, we decided to use the software developed by the 2014 Heidelberg igem team. This software was designed to make heat stable variants of ordinary proteins. Since our project involves thermal cycling that could potentially denature our terminal deoxytransferase (TdT) protein, this software became a useful addition to our project. It also provided the added benefit of helping another team by testing their software to see if it could be improved. Specifically, Heidelberg’s code was intended to design an optimized sequence of amino acids to link the N-terminus of a protein to its C-terminus. The result is a circularized protein that, in theory, should maintain its function while also resisting denaturation by heat, salts, and other agents. After a bit of troubleshooting and a brief exchange of emails, we got the program to run using a variant of TdT. This yielded an amino acid sequence that would circularize the TdT protein. Using this sequence and Heidelberg’s intein system, we designed g-block DNA sequences that would allow for the synthesis and purification of various forms of heat stable TdT.