Multiplex Gene Synthesis in Emulsions

The availability of cheap and scalable gene synthesis techniques will open up the exploration of sequence-function relationships at unprecedented scales. Attempts to reduce the costs of gene synthesis have focused on how to assemble microarray derived oligo (OLS) pools into longer length genes. Here we present a new approach capable of assembling hundreds of genes simultaneously from a complex oligo pool by localizing only the fragments required for each individual gene assembly to barcoded beads before isolating the assembly reaction inside an emulsion droplet. Multiplexed reactions of 384 genes, each assembled from five oligos, have costs approaching $1 per 500 bp gene. We apply this to assemble a thousand phylogenetically diverse orthologs of phosphopantetheine adenylyltransferase (PPAT) representing over 500 kbp of coding sequence and use a sequencing based barcode readout to carry out a complementation assay in E. coli, highlighting how this technique can be applied to determine functional relationships of long sequences in high-throughput at low-cost.