Elegen’s Cell-Free DNA Synthesis Speeds the Discovery and Development of Genetic Medicines

Company to Watch – Elegen

In the third of four features on Elegen, Marc Unger, Chief Scientific Officer, talks about Elegen’s cell-free DNA synthesis technology ENFINIA DNA, how it changes the paradigm of discovery and development for genetic medicines, and the company’s recent collaboration with GSK. In the final feature, Elegen will present a case study illustrating the benefits  ENFINIA DNA has brought to its customers.

By Marie Daghlian

Marc Unger, Ph.D., Chief Scientific Officer​, Elegen

Synthetic DNA is the backbone of genetic medicine development. However, DNA manufacturing hasn’t changed in the past 50 years.

Elegen is changing that paradigm by rapidly producing high-quality synthetic DNA without using bacterial cells. With its proprietary technology, Elegen delivers complex DNA sequences of up to 7 kilobases in half the time of conventional manufacturers, NGS-verified to ensure high accuracy and purity.

A Novel Approach to DNA Manufacturing

Elegen Chief Scientific Officer Marc Unger leads the team behind Elegen’s innovative technology. They intend to disrupt the status quo for DNA manufacturing by employing innovative technologies to bypass the age-old process of cell-based molecular cloning. Unger explains, “The conventional method is to start with oligonucleotides, on the order of 60 to 90 bases of DNA, and then assemble them into pieces several hundred bases long. And then if you want DNA thousands of bases long, further assembly is required. Today everyone does this by molecular cloning DNA in bacteria, and that’s how it’s basically been done since the early 1970s.”

It’s a long and tedious process that includes sequencing DNA isolated from many clones to identify a clone containing sequence-perfect DNA.

Molecular cloning involves assembling the synthetic DNA into a vector that is then transfected in bacteria. The bacteria grow and spread as colonies across the surface of an agar plate. Each colony comes from a single bacterium and therefore a single clone acts as a representative of the DNA sequence replicated within its colony. Clones from each colony are sequenced to determine which colony contains DNA with a perfectly correct sequence. The selected colony is grown further before DNA is isolated from it, purified, and sequenced again prior to shipping to a customer.

“That’s the way everybody has done it until now, but there are a lot of problems and steps associated with this way of manufacturing DNA,” says Unger. “Elegen has innovated the DNA production process to selectively amplify a single, sequence-perfect molecular species, but without the bacteria. This allows us to avoid several steps and the problems associated with them.”

Those problems include extraneous DNA that, if expressed, could be toxic to cells. Also for certain complex sequences, it’s difficult for the bacteria to actually propagate the DNA or do so without making mistakes or errors.

“Elegen’s speed advantage comes from eliminating the operational complexity of working with bacteria — thus reducing the number of steps to manufacture the DNA of interest,” says Unger. “Another benefit of eliminating bacteria from the workflow is that there’s no need to purify the DNA before using it.”

The DNA assembly and purification process can take several months for long multi-kilobase sequences of DNA. Unger says Elegen’s process cuts that time drastically. “The product we have on the market right now, ENFINIA DNA, is up to 7 kilobases in length. We ship that in 6 to 8 business days, and it’s NGS verified with a 99.999% per base accuracy.”

Accelerating Genetic Medicine Development

Following the launch of ENFINIA DNA in 2023, Elegen has seen a large interest in its products and technology coming from the biopharma space. “It’s our contention that the production of DNA for a genetic medicine is often the rate-limiting step,” Unger says. “If I want to produce enough of an mRNA vaccine to treat millions of people, I may need a gram or tens of grams of DNA.”  The same can be said for screening through hundreds or thousands of mRNA vaccine designs  ̶  the supply of DNA quickly becomes a bottleneck.

Elegen is disrupting the status quo for DNA manufacturing with their innovative technologies that bypass the decades-old processes like cell-based molecular cloning.

The development of gene therapies often involves the use of viral vectors, long DNA constructs—sometimes up to 15 kilobases. If they assemble this DNA construct hierarchically from smaller pieces of low-quality DNA, it could take several weeks to months to perform multiple rounds of assembly and cloning.

“Part of why researchers approach Elegen is because they can get longer DNA faster at very high quality,” Unger says. “And then if they are making even longer constructs, say 15 kilobases, they can buy three 5 kilobase pieces of really high-quality DNA from us and assemble them in one step. That’s a lot faster than building from many small pieces that require cloning.”

Fewer steps means the customer can explore many more constructs in the same amount of time, saving costs as they go from in vitro screening into mice until the final drug candidate is identified.

Even when Elegen’s customers clone their DNA, they rarely have to pick more than a few colonies because the error rate of ENFINIA DNA is very low. “You pay a significant time and cost to build DNA the conventional way,” says Unger. “For larger constructs especially, you’re going to pay that multiple times over in the course of making a single construct. With ENFINIA DNA, researchers can do this faster and with fewer steps.”

Opportunities Ahead: From IVT-Ready DNA to Bypassing Master Cell Banks

For companies developing mRNA vaccines and mRNA therapeutics, Elegen is already developing a new capability to streamline their workflows. mRNA is conventionally produced by in vitro transcription (IVT), which requires the addition of a poly-A tail of 30 to 160 bases to the 3’ end. “Right now, ENFINIA DNA is not available with the poly-A tail, but that’s coming,” says Unger. “With this enhancement, our customers will be able to use ENFINIA DNA directly in their IVT reactions to more quickly produce mRNA.”

Elegen is also developing a technology to accelerate the process of scaling up the production of DNA required to produce milligram or gram-scale quantities of mRNA for clinical testing. The current way to do this is to build a “master cell bank” and prove that the DNA construct doesn’t change over time as the bacteria amplify. Larger quantities of the bacteria can then be grown from cells from the master cell bank.  But it often takes three months or more to establish a master cell bank. It can take six to nine months to produce a single gram of DNA under GMP conditions, and that’s after you reach the top of the queue of a contract manufacturer.

“Part of what makes this approach hard is the work required to purify the DNA from the bacteria,” Unger says. “And then there’s a lot of quality control (QC) testing required to prove you did it right.”

By synthesizing DNA in larger quantities without using cell-based cloning, Elegen anticipates enabling customers to bypass the bottleneck associated with master cell banks to save production costs and time. “We can get to a GMP product a lot faster with a lot less QC required because we’re doing it with a purely cell-free, molecular-based method as opposed to using bacteria,” Unger explains.

At the end of January, Elegen entered a multi-year collaboration and licensing agreement with GSK that allows the pharmaceutical giant to leverage Elegen’s cell-free synthetic DNA production technology in the development of GSK’s vaccines and medicines. The deal includes up to $35 million in upfront fees and purchase commitments of ENFINIA DNA, plus potential near-term milestone payments relating to the development of new product features and a potential equity investment in Elegen.

The deal is a marker of Elegen’s strategy to partner with leading biopharma companies. “Given what we’re doing and the value of it, we’re talking to folks at the top, because they are the ones for whom we’re making the most difference,” Unger said. “We have the full stack of innovative technology here, and I’m going to say we have more copies of the innovation gene in our genome than some of the other companies that are making DNA—we replaced a technology that everyone has been using that was the standard and only way to do it for the last 50 years. That makes me sleep pretty well.”


This is part 3 of the Big4Bio Company to Watch program for April 2024: Elegen
For more information on the series, click here.