Sunday, August 11, 2013
Pavilion (Sheraton San Diego)
One limit to progress in metabolic engineering is the length of the design-build-test cycle: The time required to design new DNA constructs in silico, assemble these construct from natural or synthetic DNA parts, and measure phenotypes from a cell that contains the DNA. Amyris has received support from DARPA for four projects aimed at accelerating this cycle. First, to facilitate the design of DNA modifications for novel organisms of interest, we are building software that uses distributed networks of desktop computers to process, annotate, and visualize genome sequences, focusing on the conserved and most commonly engineered genes and pathways. Second, to ease the current bottleneck of DNA assembly, we are developing a ligase cycling reaction, wherein bridging oligos and a thermostable ligase catalyze the assembly of multiple (up to 20) blunt-ended DNAs into large (up to 20Kb) constructs. Because the annealing conditions are stringent and the single enzyme has no side activities, this technology will have higher fidelity than currently used assembly technologies. Third, to reduce the cost, time, and effort required to verify that DNA assemblies match their in silico design, we are developing an automated next-generation DNA sequencing workflow. Fourth, we are facilitating targeted genomic integrations in novel organisms by using designer DNA nucleases which cut the target genome at specific loci, thereby directing homologous recombination and allowing recovery of integrants without the use of a marker. These technologies will reach proof of concept in 2013 and be integrated into a demonstration project in 2014.