IGEM 2009 Project

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Biology Based:

  1. Which reporters are we going to use?
  2. What naming system are we going to use for the suppressor tRNAs?
  3. How do you build the tRNA construct?
  4. How are we going to build the 5-mer BioBricks?

Using Stop Codons to Truncate Translation
Davidson ATG+5mer BioBrick Sequences
Frameshift Mutation Leader PCR primers
Align E. coli tRNA sequences
Compare 2 tRNA structures

Team Progress Table

Student Name 5mer Codon Anticodon Sequence Codon Short Name tRNA Status 5mer+XFP Status 5mer+Drug resistance Status
Olivia Ho-Shing CCAUC GUGAUCCAA-9 Pro4 2 clones being resequenced 2 5mer+RFPs sequencing 5 5mer+Tets sequencing
Olivia Ho-Shing CCAUC UUUGAUGGAG-10 Pro5 1 clone being resequenced 2 5mer+RFPs sequencing 5 5mer+Tets sequencing
Romina Clemente CUAGU UUACUAGAC-9 Leu4 1 clone 100% match, putting pBAD upstream 9 5mer+RFPs sequencing 5 5mer+Tets sequencing
Shamita Punjabi CCACU CUAGUGGAC-9 Pro3 2 clones being re-sequenced 6 5mer+RFPs sequencing 5 5mer+Tets sequencing
Leland Taylor CCCUC CUGAGGGUC-9 Pro6 1 clone 100% match, putting pBAD upstream 7 5mer+RFPs sequencing 7 5mer+Tets sequencing
Alyndria Thompson CGGUC UUGACCGAC-9 Arg2 5 clones being sequenced 4 5mer+RFPs sequencing 6 5mer+Tets sequencing
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name tRNA Status 5mer+RFP Status 5mer+Tet Resistance Status


Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."