My most recent Technology Feature, on the technology of genome synthesis, describes advances in the field of large-scale genome hacking. Researchers are rewriting the genomes of organisms from E. coli to yeast, with millions of bases written from scratch. Now, through projects like Genome Project-write, they are turning their attention to even more complex organisms, with concomitantly larger genomes.
How, though, does one actually write a genome? As I note in the article, researchers don’t do that in one step. The molecules are assembled hierarchically, from synthetic oligonucleotides to ever larger pieces, first in a test tube and ultimately in living cells.
That said, it is possible to purchase “gene-sized” pieces of synthetic DNA. But, since DNA today is synthesized mostly using the same error-prone phosphoramidite chemistry researchers have used for decades, the question is: how are those molecules made?
According to Harvard University geneticist George Church, who cofounded long-DNA provider, Gen9 (now part of Gingko Bioworks), phosphoramidite chemistry averages 1 error every 300 bases. As each base is added to the growing chain, a small fraction of molecules don’t react. As chains get longer, those losses can add up, and even with a 99.5% coupling efficiency, only about a third of molecules in a 200-base synthesis will actually be full-length.
To build kilobase-sized synthetic DNAs, companies can employ any of a number of ancillary methods, including gel purification, column chromatography, cloning, and mismatch-repair enzymes to select desired molecules. These are then enzymatically stitched together to build the desired full-length sequences.
Today, several companies now offer synthetic “genes” measuring a kilobase or longer. Integrated DNA Technologies promises gBlock synthetic DNAs up to 3,000 bases; Twist Bioscience, which has miniaturized the process onto the surface of a silicon chip, can make as many as 6,000 genes at a time, each 1,800 bases long. SGI-DNA sells a personal DNA synthesizer researchers can install in their labs, the BioXp 3200, which is capable of synthesizing 1,800 bases. But planned improvements should increase that to 10,000 bases within a year, says Daniel Gibson, who is Vice President of DNA Technologies at Synthetic Genomics, SGI-DNA’s parent company.
Startup firm Molecular Assemblies hopes to circumvent the problem of phosphoramidite chemistry altogether by taking DNA synthesis back to its enzymatic roots. The company is leveraging the enzyme terminal deoxynucleotidyltransferase, a template-less polymerase that normally synthesizes homopolymers. By combining that enzyme with in-development reversible terminator molecules, akin to the process underlying Illumina sequencing, Molecular Assemblies could theoretically synthesize kilobase-sized sequences directly in a single reaction, without the need for shorter oligos.
Of course, there are occasions when it would be nice to synthesize not DNA, but the products those nucleic acids encode. That, too, may be coming. Synthetic Genomics recently described a prototype “digital-to-biological converter,” which is capable of converting a digital DNA sequence into protein, RNA, or even bacteriophage without intervention. Among its potential applications, says Gibson, the company is exploring rapid development and deployment of personalized biologics and therapies: sequence in, vaccine out. “It almost truly is biological teleportation,” he says.
Image credit: Power and Syred/Science Photo Library
Jeffrey Perkel is Nature‘s Technology Editor.
Correction [27 July 2017]: Twist Bioscience was originally misspelled as Twist Biosciences. Nature regrets the error.