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Parts Submitted to the Registry

An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the Registry, not on your team wiki.
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.

Primers and PCR

When we realised that it would be quicker to try to extract genes via PCR rather than via a DNA library, we BLAST searched for genes present in the Tod operon, and found the whole operon was remarkably conserved, with only a couple of the genes needing any kind of degeneracy in their primers. We concentrated on genes within the operon that didn't have any restriction sites incompatible with the basic Biobrick standard:

TodX: (544bp)
>TODXF
5'-atgcccgccagtctgacgcttg-3'
>TODXR
5'-accagccagcaccatgcggc-3'
TodX gene in all putida the same regardless of strain

TodF: (460bp)
>TODFF
5'-atgggtgccgttggcgtgag-3'
>TODFR
5'-gtttttgcgatcagtcctccgcg-3'
All putida appear to have the above sequences,though other species may react better to:
>TODFR
5'-gtttttgMgatcagtcctccgYg-3'

TodC1: (1353bp)
>TODC1F
5'-atgaatcagaccgacacatcacctatc-3'
>TODC1R
5'-tcagcgtgtcgccttcagcg-3'
one strain has a C rather than a G base
>TODC1R
5'-tcaScgtgtcgccttcagcg-3'

TobB: (324bp)
>TOBBF
5'-atgacttggacatacatattgcggcag-3'
>TOBBR
5'-tcacttcaactccccgttgtcgag-3'
^ all blast search results for this gene yielded 100% similarity

TobG:(807bp)
>TOBGF
5'-atgagcgaactagataccgcgcg-3'
>TOBGR
5'-ttatgcctttgcaaaagcggcggtc-3'
^ all putida results had the same gene sequence

Unfortunately, with the 2 strains of P. putida, none of the primers amplified the target genes, meaning that the strains do not encode any of the Tod operon genes. Because of this, it meant we couldn't make a biobrick.

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