Project

From FreeBio

Synthetic Biology 101a: Recoding whole genomes to engineer novel biological function

In the spirit of engineering new biological function, we will utilize the most recent advances in genomics and biotechnology to recode the genome of an entire organism. Specifically, we will create synthetic DNA constructs that will subsequently be introduced into E. coli cells with the goal of introducing a genome-wide codon (tri-nucleotide units each coding for a single amino acid of a protein) replacement, thereby recoding the genetic code of E. coli. Many codons are degenerate, or redundant, meaning that two or more codons may code for the same amino acid. Thus, we will be able to replace a codon with one of its degenerate pairs, or silently mutate, across the entire genome and still create proteins with the same set of amino acid sequence. A number of various benefits stem from synthetically creating this altered genetic code. For example, eliminating a codon from the entire genome will make space for a novel tRNA-synthetase which uses novel amino acids supplied in the growth medium or synthesized internally. These changes will lead to new modes of post-translational control and proteins containing new, synthetic amino acids. In addition, these recoded E. coli may become resistant to viruses.

Techniques that will be learned or applied during the course include basic PCR, PCR mutagenesis, cross-over PCR, oligonucleotide-based gene assembly, gel electrophoresis, DNA ligation, DNA purificaitn, DNA sequencing, bacterial transformation, lambda red recombination, cell culture techniques and various cell-based assays.