IGEM Notebook

Wednesday, June 3, 2009

Romina and I are trying to find suitable reporter proteins to use. Yesterday, Leland and Alyndria were working on ways to insert the gene sequences into the plasmid. Upon seeing how they wanted to manipulated the reporter gene to include the logical clauses, we came up with a few criteria for the reporter genes we would use. The following criteria for genes are listed in order of the broadest aspect to look at to the narrowest aspect:

   a) Doesn't contain restriction sites for the 4 restriction enzymes (EcoR1, Xbal, Spel, Pst1) used to cleave the Biobrick part out of the plasmid.
   b)  Contains 6 cutter restriction sites.
   c) These restriction enzymes aren't blunt (cleave straight down at one spot).
   d) These restriction sites are close to thge 5' (beginning) end of the sequence.
   e) These enzymes are easiest to work with and cheapest.

We are finding the part numbers of the reporter genes we want to use (antibiotic resistance, fluorescence, LacZ) through our own GCAT because we know these ones work. We are then locating these parts on the parts registry [1] website. We copied and pasted the gene sequences we obtained from the registry onto the ApE software [2]. From here, we were able to generate a genetic map of each gene that outlined each restriction site that fit our criteria. We put each genetic map, alongside the part number used, into a Word document.

http://gcat.davidson.edu/GcatWiki/images/0/0e/Restriction_Site_Mapping_on_Reporter_Genes.doc

Later on in the day, we decided that the best way to test for suppression would involve placing the 5mers at the beginning of the reporter gene instead of inserting them into the reporter gene. To do this, we decided that the gene along with its start codon need to be expressed after the 5mer. We will insert a BioBrick plasmid with a 5mer and start codon that will be incorporated before the gene:

                                                  RBS-6-8nt-ATG-5mer--ATG-gene

Leland assembled the oligos that we will need for the BioBrick pieces.

In order to test whether the reporter protein would be expressed regardless of the 5mer being suppressed or not, we would need to remove the suppressor tRNAs from the cell.

Meanwhile, I helped figure out the coding sequence that we will need for the suppressor tRNAs that will bind to the 5mers. We decided that we would be using the following suppressor tRNAs on the Davidson side: CUAGU, CCCUC, CGGUC, CCAUC, and CCACU. We searched through several papers, with little result and finally emailed Dr. Christopher Anderson of UC Berkeley to request the DNA sequence. He emailed us back with a generic DNA code that we could use to create the tRNA; however, for each suppressor tRNA we would use, we would need to change base pairs in the anticodon loop.

The length of the tRNA is 92 nt. The anticodon loop is comprised of 9 nt. Once we have BioBricked the DNA sequence with 4 restriction sites and supplemental nucleotides, the length of the entire gene is 144 nucleotides. This is made up of the 92 nt +22 nt on each side of the sequence (44) + 4 nt on each side of the restriction ends (8).

At the end of the day, we decided to use tetracycline resistance and RFP as our reporter proteins for this tester experiment.