Team:Stuttgart/Parts

Parts

PhyCoVi Parts

In total, we used ten parts (nine basic parts and one composite part) and submitted them to the registry. Among them, five parts are tRNA genes from Vibrio natriegens which should be used to increase the levels of rare tRNAs in Vibrio natriegens. These tRNA genes should be cloned individually into a self-designed plasmid backbone. To increase the tRNA levels of all tRNAs simultaneously, a combined tRNA fragment was made.


Since the measurement of single tRNA species is complicated and not established, a qPCR method was developed. Using an adapter, specific tRNA levels could be measured. This adapter is available below.


Additionally, the Biobricks GFP (http://parts.igem.org/Part:BBa_E0040) and sfGFP (http://parts.igem.org/Part:BBa_I746916) have been improved by optimizing them for Vibrio natriegens. The sequences were analyzed for rare codons and then exchanged with more frequently used ones. This means that no classical codon optimization was performed, but rare codons, which could have a strong influence on the expression strength, were exchanged. By doing so, we wanted to increase the expression of GFP and sfGFP in Vibrio natriegens and thus provide a better measurement tool.



All biobricks were synthesized by Integrated DNA Technologies.
Original Table
Pos Name Type Description Designer Length
Pos Name Type Description Designer Length
1 BBa_K3014000 Coding Vibrio natriegens tRNA AGA Benedikt Schober, Jan Müller, Kai Schülke 135
2 BBa_K3014001 Coding Vibrio natriegens tRNA AGG Benedikt Schober, Jan Müller, Kai Schülke 135
3 BBa_K3014002 Coding Vibrio natriegens tRNA CGG Benedikt Schober, Jan Müller, Kai Schülke 160
4 BBa_K3014003 Coding Vibrio natriegens tRNA TGC Benedikt Schober, Jan Müller, Kai Schülke 161
5 BBa_K3014004 Coding Vibrio natriegens tRNA TCC Benedikt Schober, Jan Müller, Kai Schülke 151
6 BBa_K3014006 Plasmid_Backbone ptRNA_backbone Benedikt Schober, Jan Müller, Kai Schülke 2161
7 BBa_K3014007 Coding Codon optimized GFP for Vibrio natriegens Benedikt Schober 718
8 BBa_K3014008 Coding Codon optimized sfGFP for Vibrio natriegens Benedikt Schober 718
9 BBa_K3014009 Measurement DNA-RNA-Hybrid-Adapter for tRNA quantification Katharina Hofer, Sini Münßinger, Jan Seeger, Gabriele Kepp 130
10 BBa_K3014010 Terminator Terminator of rrnA operon V. natriegens Jan Müller, Kai Schülke 54
11 K3014011 Regulatory V. natriegens rrnA P1 Promoter Jan Müller, Kai Schülke 71
12 BBa_K3014012 Coding Vibrio natriegens tRNA construct Benedikt Schober, Jan Müller, Kai Schülke 915