Using synthetic DNA to test genetic elements and improve gene expression


We’ve recently published two papers involving the use of synthetic DNA libraries from microarrays. The first paper, published in The Proceedings of the National Academy of Sciences, details our work to build and test large libraries of synthetic genetic elements in high throughput. We developed a method called Flow-Seq, which combines next-generation sequencing and FACS (fluorescence-activated cell sorting) to measure many thousands of combinations of genetic elements simultaneously.

Fig S1

In our second paper, published in Science, we generated a synthetic gene library that extensively varied codon usage for natural E. coli genes and showed that rare codon usage at the N-terminus tends to increase gene expression. This effect is due to not to the codons themselves, but rather their low GC content and consequent effect on RNA secondary structure. This finding gives scientists a new way to easily optimize heterologous gene expression in bacteria, sometimes by as much as 100-fold.

As DNA synthesis and sequencing becomes cheaper, faster, and more accurate, designing and building large synthetic libraries of genetic elements, genes, and even whole genomes will become widespread. The bottleneck is now shifting to better methods for designing and analyzing these megabase-scale libraries.

I spoke about some of this work recently at my Synthetic Biology 6.0 talk, and GetSynBio also wrote an article about our research and the implications for the future of design and testing in synthetic biology.

Causes and effects of N-Terminal codon bias in bacterial genes. Goodman et al. Science. 6157:475-479 2013

Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Kosuri, Goodman et al. PNAS. Aug 7, 2013.