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Synthetic DNA Startup Elegen Gains Traction With Customers, Funders


This story has been updated to include comment from Ginkgo Bioworks and to correct stats about IDT's length capabilities.

NEW YORK – Elegen, a Bay Area startup founded by Natera's former head of R&D, is making a splash in the synthetic DNA market by promising longer DNA than can currently be made by the highest-throughput manufacturers.

Offering synthetic DNA of 1 Kb to 7 Kb with high accuracy and fast turnaround time, the company has secured funding from private investors, grants from the National Human Genome Research Institute, and patronage from several companies — including Ginkgo Bioworks, a mainstay in the emerging synthetic biology industry, and Ensoma, a cell therapy firm.

Customers like Ginkgo are looking for longer, more complex DNA, with faster delivery, Elegen CEO and Founder Matt Hill said. "All these different features or aspects of the DNA are interwoven, so you really need to solve all of them," he said. "And there's no way to decouple any specific feature from the rest."

"We've found Elegen’s product to perform to the expectations they set with us," a Ginkgo spokesperson said in an email. 

"It is encouraging to see companies like Elegen push the boundaries of DNA synthesis," Adam Fisher, principal scientist at Ensoma, said in a statement. "We are very excited about their innovative approach to solving the supply challenge of high-quality long DNA."

Though Elegen has not yet fully revealed its manufacturing process, the fact that Ginkgo — which possesses its own capabilities for making long DNA through its acquisition of Gen9 in 2017 — has signed up with Elegen should serve as a vote of confidence. 

Elegen's progress has convinced Hill to build out a commercial team, now nearly a third of its 40 total employees, and ramp up for full commercialization. The firm is "on a path" to have hundreds of customers by the end of the year, Hill said.

San Carlos, California-based Elegen emerged from stealth a year ago at the Built With Biology meeting, formerly known as SynBioBeta. It was one of several startups that showcased technology to make longer synthetic DNA molecules. Large-scale providers of synthetic DNA such as IDT and Twist Bioscience are limited to about 5 Kb.

Though it was only recently announced, the firm has been working on its technology since 2017 when Hill founded the firm after serving as Natera's VP of R&D. "I started thinking about all the things you can do with synthetic biology, only then to realize that the actual fabrication of the DNA, the programmatic code for the cell itself, was a key bottleneck in this process," he said. "No revolution in synthetic biology was ever going to happen until you actually solved the DNA problem."

Rather than one high-impact change, Elegen's improvements to the DNA-making process are distributed throughout it, Hill said. "I wish I could tell you this one simple, elegant, key innovation. But there are multiple innovations and multiple steps that work in a complimentary way to achieve faster, more accurate, longer, more complex DNA," he said.

Hill was reluctant to detail all of Elegen's process improvements but said that developing a cell-free cloning method was a "key aspect."

"[Cloning] constitutes the majority of the time cost and operational complexity of manufacturing today," he said. Elegen's cell-free method, which the firm has applied for at least one patent on, simplifies and streamlines the process.

The firm also has applied for patents on DNA assembly using microfluidic devices. Hill noted that Elegen has hired former Fluidigm R&D exec Marc Unger as chief scientific officer. In total, Elegen owns more than 20 active patents and applications worldwide, the firm said.

The firm's technology and ambitions helped it raise a Series A financing round in late 2021 led by KdT Ventures, joined by A16Z, 8VC, Digitalis, Alix, and ACVC. The firm declined to provide the size of the round. It has also received a $2 million Small Business Innovation Research grant from NHGRI.

Like other synthetic DNA makers, Elegen has an online portal where customers can submit sequences to be made. Elegen boasts seven-day turnaround, including overnight shipping, for sequences between 1 Kb and 7 Kb long. Most customers order sequences between 2 Kb and 5 Kb, the firm said.

Customers pay $.25 per base for Elegen's Enfinia DNA, a premium rate for the length, speed, and an error rate as low as 1 in 70,000. For comparison, Twist advertises gene synthesis as low as $.09 per bp but tops out around 5 Kb. On its website, Genscript suggests it can deliver complex DNA sequences up to 8 Kb in eight business days; a 5.1 Kb complex sequence would cost approximately $.43 per bp.

"Pharma customers are using [Elegen's DNA] directly in their workflows without additional cloning, both streamlining and accelerating the development of new therapies," said Elegen VP of Marketing Randy Dyer. "For customers in agriculture and biomanufacturing, Enfinia DNA dramatically simplifies the process of building long and complex constructs, enabling a faster transition from design to experimentation and better allocation of their internal resources."

Hill said the company will be looking to raise another financing round by the end of the year. "The current macroeconomic conditions are challenging," he said. "But we're well situated as a company to succeed, nonetheless, having a product in the market that's gaining traction and having a strong R&D pipeline to deliver improvements and extensions that customers will appreciate."

Even further ahead, Elegen may one day offer benchtop devices, like those currently available from Codex DNA and DNA Script. The firm's NHGRI grants specify that it will use the funding to develop a prototype instrument.

"It's a capability that we are creating," Hill said. "A key part of our vision is to shrink that factory down to the bench scale."