Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

Development of cheap, high-throughput and reliable gene synthesis methods will broadly stimulate progress in biology and biotechnology(1). Currently, the reliance on column-synthesized oligonucleotides as a source of DNA limits further cost reductions in gene synthesis(2). Oligonucleotides from DNA microchips can reduce costs by at least an order of magnitude(3-5), yet efforts to scale their use have been largely unsuccessful owing to the high error rates and complexity of the oligonucleotide mixtures. Here we use high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols and enzymatic error correction to develop a method for highly parallel gene synthesis. We tested our approach by assembling 47 genes, including 42 challenging therapeutic antibody sequences, encoding a total of similar to 35 kilobase pairs of DNA. These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding similar to 2.5 megabases of DNA, which is at least 50 times larger than in previously published attempts.