Make Mine A Double Helix

Stories of scientists who engineer cells with novel artificial genomes or with added pathways to produce critical medicines have made synthetic biology a hot topic these days. Just recently, a group of do-it-yourselfers got noticed when they crowdfunded a project to insert a gene to make plants glow.

Behind the headlines, though, is a community of small companies that enable these feats of biological engineering by supplying the needed genetic parts.

Since the sequencing of the human genome more than a decade ago, gene synthesis has become an established business. Within days or weeks, custom DNA manufacturers can make gene constructs that scientists want for producing medicines, fuels, and chemicals. As demand increases, synthesis firms are pushing the limits of what they can do, competing with each other and helping accelerate the pace of synthetic biology for both research and commercial applications.

For all the attention it gets, synthetic biology is seen by some in the field as just an extension of traditional genetic engineering, which relies on recombinant DNA, mutagenesis, gene shuffling, and directed evolution. But rather than laborious experimentation and manipulations to improve a gene’s function, scientists now write a sequence and chemically synthesize it. Automation and other synthetic advances are cutting the time and cost of the process and allowing for better quality and longer DNA.

The founders of Menlo Park, Calif.-based DNA2.0 have experienced the shift from shuffling existing genes to designing new ones from scratch. They came out of the core technology group at now-defunct protein engineering firm Maxygen. “We looked at the problems and believed there was a better way to do it,” says Claes Gustafsson, DNA2.0’s chief commercial officer.

In 2003, in the field’s dawning days, DNA2.0 began applying mathematical and engineering tools to biotechnology. “We started out as a protein engineering company but quickly realized that we needed gene synthesis as well,” Gustafsson recalls. “We also needed to have a revenue stream to support growth of the company,” which could come from making gene products for others. Still private and self-funded, DNA2.0 is a leading provider of synthetic genes and protein and strain engineering.

But DNA2.0 is not alone. It competes with other U.S.-based companies such as Gen9, SGI-DNA, and Integrated DNA Technologies. GenScript and GeneWiz, which also have headquarters in the U.S., were founded by Chinese scientists. Two other long-standing competitors are Blue Heron Biotech, owned by OriGene Technologies, and Germany’s GeneArt, which is part of Life Technologies.

More recently, firms are emerging from initiatives such as the SynBio Startup Launchpad at Silicon Valley’s Singularity University. One of the first is Evolutionary Solutions. Two other Singularity-based firms—the computer-aided design firm Genome Compiler and Cambrian Genomics, a maker of DNA printing systems—are part of the glowing plant project.

Each company has its own approach that influences pricing, synthesis time, capacity, and the length and complexity of the genetic material it creates. One customer, the Boston-based engineered organism maker Ginkgo BioWorks, conducted an informal comparison of three suppliers last year and concluded that turnaround time was a major variable and thus a potential bottleneck in getting materials for R&D.

Companies try to differentiate themselves with claims about speed, pricing, gene length, and quality on their websites, through which customers can place orders. DNA2.0 offers its Gene Designer software free to users who, after completing a de novo sequence, can order the DNA directly from the company. All in all, though, suppliers tend to follow a similar path from customer sequence through synthesis and quality control to gene product.

The ability to quickly and repeatedly design, build, and test genes is changing biotechnology, claims Jeremy Minshull, DNA2.0’s chief executive officer. “Being able to make any DNA sequence you want turns biology from an observational science into an experimental one,” he says. “We have a ringside seat for watching this nascent discipline of synthetic biology begin to emerge.”

At present, Minshull notes, most researchers are using synthetic genes as probes to help them better understand biological design and engineering principles. Although most customers want one or two genes, some are becoming interested in larger constructs. “Maybe they’ll put two or three genes together in a pathway because they feel like they understand it well enough,” he says.

Commercial customers in pharmaceutical, industrial biotech, agricultural, and diagnostic industries are trying to make things, but they haven’t yet fully exploited synthetic biology, Minshull suggests. “Practical applications of synthetic biology are still simply incremental advances over what has been done previously through genetic engineering.” For example, about half of DNA2.0’s customers are pharma and biotech firms exploring synthetic genes for making protein therapeutics.

Although the target products may not differ much from those in the past, using synthetic genes can get to them more efficiently. Not only can genes be deployed quickly, but the sequence also can be easily edited for optimum expression in a host organism of choice. Recently, Novartis reported that it could quickly and safely generate materials for flu vaccines by using synthetic viral sequences in tissue culture (Sci. Transl. Med. 2013, DOI: 10.1126/scitranslmed.3006368).

Costs have also improved. Dramatic declines in gene-sequencing prices have put tremendous amounts of genetic information in the hands of researchers hoping to understand and design new genes. Along with this, the cost of preparing synthetic genes has dropped, making them more affordable.An average gene is a few thousand to several thousand base pairs, or kbp, long. Per-base-pair prices have dropped to about 40 cents or much lower, so customers may find that buying a gene is cheaper than cloning it themselves.

According to Kevin Munnelly, CEO of Cambridge, Mass.-based Gen9, the market for synthetic genes is about $200 million per year. “That translates to 200 to 250 Mbp of DNA,” he says. Market research firm BCC Research predicts the market for DNA, genes, and synthetic cells will grow more than 40% per year to reach nearly $700 million in 2016.

Gen9 was founded by prominent academic scientists in 2009 around semiconductor-based synthesis technology to improve cost, capacity, and accuracy, Munnelly explains. With its high-throughput BioFab system, Gen9 focuses on customers interested in bulk orders. “We are not making single genes for people,” he says. “Every time we design and run a chip, we want to run hundreds or thousands of genes because the price will come down significantly the more we put onto the chip.”

Gen9 spent two years developing its technology before launching its first products in 2012. “Most of our business is with large industrial biotech groups where we are providing genes that they designed and are using for their internal processes,” Munnelly says. The firm also supplies genes to academic collaborators.

“This year, we are really scaling up our commercial operations to hopefully supply a significant portion of the world’s synthetic genes to the research community,” he says. In April, instrumentation maker Agilent Technologies invested $21 million in Gen9 and contributed its oligonucleotide library synthesis technology.

Speed and cost are important, but quality is critical, especially as customers and suppliers move toward larger or more complex gene constructs. Software helps optimize construction, dividing sequences into manageable subsets that are then joined together. Oligonucleotides often are the building blocks, and the best of these typically have an error rate of about 1 base per every 200 to 400 bases. Errors also arise when the pieces are joined.

Error correction and quality control have improved gene synthesis. Suppliers use a variety of enzymatic methods to check for and repair errors during synthesis. Once synthesized, a gene can be cloned and sequenced to identify an error-free, or “base perfect,” sequence. Suppliers then deliver microgram quantities of the final gene product in a linear form or inserted into a plasmid or vector of the customer’s choice.

Companies say they hope eventually to produce not just synthetic genes but whole genomes on the order of a million base pairs. Last month, Gen9 launched GeneBytes—DNA constructs in the range of 1 to 3 kbp. By the end of the year, the company’s goal is to offer synthesized genes of up to 10 kbp. Likewise, DNA2.0 promises guaranteed turnaround times on sequences under 3 kbp and says it routinely produces genes larger than 50 kbp, with 230 kbp being the largest it has made.

This year, Integrated DNA Technologies and SGI-DNA launched synthetic DNA constructs up to 2 Mbp to enable gene, genetic pathway, and genome engineering. Production of these long sequences is possible with technology developed by Synthetic Genomics and the J. Craig Venter Institute, which created a synthetic bacterial cell in 2010.

Synthetic Genomics launched SGI-DNA in February as a gene synthesis subsidiary. “It became clear to us that there was a real business opportunity to provide services to some key players in industry and to generate revenues in the short term,” says Fernanda Gandara, the subsidiary’s general manager. Rather than offering its synthesis services broadly through a website, she says, SGI-DNA will work with strategic customers who make requests via a secure portal.

The number of potential academic and commercial customers conducting synthetic biology R&D is expanding rapidly. Between 2009 and 2013, “there’s been a tripling in the number of companies and a doubling in the number of universities doing work,” says David Rejeski, director of the science and technology innovation program at the Woodrow Wilson International Center for Scholars. The center’s Synthetic Biology Project 2013 survey found 192 companies and 204 universities in the field.

In contrast to capital-intensive fields such as nanotechnology, synthetic biology is growing rapidly, partially as a result of the ease and relative low cost of setting up operations. “The barriers to entry into some of the synthetic bio work are much smaller and are being reduced exponentially every year in terms of the cost of sequencing and synthesizing,” Rejeski says. Open-source repositories or registries, such as the nonprofit Registry of Standard Biological Parts, can also provide many of the enabling genetic pieces.

Along with the growing number of small companies and universities, do-it-yourself labs and others outside traditional academic or industrial settings are active in synthetic biology, Rejeski points out. To assist this emerging community, the Wilson Center and DIYbio.org launched an “Ask a Biosafety Expert” service earlier this year to provide professional biosafety advice.

Safety is both a concern of synthetic gene suppliers and a smart business practice. In principle, customers have unlimited flexibility in designing gene sequences, and suppliers have no control over the fate of the genes. In practice, however, gene synthesis companies won’t fill every order they get. The Registry of Standard Biological Parts, which is managed by the International Genetically Engineered Machine Foundation, requires requesters to be members of a current iGEM team or registered academic group.

Suppliers say they follow voluntary guidance that the Department of Health & Human Services has published for commercial providers of synthetic DNA. Under these guidelines, when an order is placed, they screen the sequences against those for known pathogens and toxins. “If we have been requested to make something risky, we do not pursue any synthesis,” SGI-DNA’s Gandara says.

Several firms, representing about 80% the world’s commercial gene synthesis capacity, have taken a further step to protect at least the front end of the emerging industry they serve. They formed the International Gene Synthesis Consortium to work on biosecurity policy and practices. The group also serves as a point of contact with government, health, and law enforcement agencies. Glow-in-the-dark plants aside, they want to prevent any headline-making misuse of synthetic genes.