Moving Synthetic Biology Into the 21st Century

In the second of four features on Molecular Assemblies, based on a conversation with CEO and President Mike Kamdar and Co-founder and Chief Scientific Officer Bill Efcavitch, Big4Bio takes a deeper look at the company’s enzymatic DNA synthesis technology, why it is needed, and the markets it serves.

Companies to Watch – Molecular Assemblies

by Marie Daghlian

Synthetic biology and concurrent advances in writing DNA hold promise for transforming a wide range of industries, from life sciences and materials sciences to industrial applications, data storage, and DNA electronics.

As the demand for synthetic DNA intensifies, Molecular Assemblies is moving to transform the process of synthesizing DNA from a decades’ old phosphoramidite chemical method with limits on the length of a synthesized sequence to an enzymatic process that holds the promise of making the business of writing DNA cost-effective, faster, sustainable, and more accurate.

Molecular Assemblies’ offices in San Diego

The company is fine-tuning an enzymatic process for DNA synthesis that holds vast opportunities for a range of industries requiring long, high-quality, sequence specific DNA, and expects the first enzymatically synthesized DNA products to enter the market in the next year.

Molecular Assemblies’ enzymatic, platform-independent synthesis technology can produce long, high-quality, sequence specific DNA reliably and affordably in just three steps that are simple, seamless, and sustainable.

DNA synthesis is a step-by-step procedure of attaching one nucleotide at a time to build the DNA strand. With any stepwise synthesis, the yield decreases exponentially at each step. If a yield of 99.5 percent is assumed, which is the chemical industry standard today, by the time 70 nucleotides are attached, yield drops to about 50 percent of the full-length product, with the other 50 percent a mixture of smaller, contaminating shorter sequences. Consequently, to make genes with the current phosphoramidite chemistry, short stretches of DNA must be stitched together, compounding error rates, and increasing costs.

The current phosphoramidite chemical method has many limitations that consign its use primarily to the probe and primer market, including the synthesized sequence limited to 100 mers at best, lower yields at higher mers, and the need for post synthesis processing that render it cost prohibitive.

Molecular Assemblies’ enzymatic DNA synthesis process can produce long, high-quality, sequence specific DNA of more than 150 bases in length. The process is aqueous, uses no hazardous chemicals, requires less post processing steps, and is scalable.

“It means that even though we’ll be faced with diminishing yield of the full-length product, we will be able to enrich it and produce a pure fraction of a longer molecule,” says Bill Efcavitch, chief scientific officer and co-founder of Molecular Assemblies. “All of that’s only possible through an enzymatic method as opposed to the chemical method, and that’s why we focus on this approach.”

The ability to build longer DNA sequences can be a game changer for applications requiring longer sequences such as gene editing, DNA therapeutics, DNA nanotechnology, and other synthetic biology applications.

What will the world make using synthetic DNA and how will the technology be applied? Molecular Assemblies CEO Mike Kamdar says the company will operate under a service model. “Ultimately customers would come to us in whatever quantities that they’re looking for and say, ‘Hey, we would like this sequence or this series of sequences,’ whether it be an oligonucleotide or gene, and we would be able to provide that for them.”

The applications are numerous: in life sciences longer read DNA sequences are needed for CRISPR/Cas gene editing, CAR T cell therapies, DNA and RNA vaccines, and personalized diagnostics to name a few. Industrial applications include development of bio-based fuels and chemicals and improving agricultural crops.

Perhaps one of the most interesting uses could be for DNA storage. As the world produces more and more data, it must be stored somewhere. “When you think about DNA data storage, the amount of DNA that you would need to synthesize to write and to read is vastly larger than is going to be required for the life sciences industry, so you need a very high throughput, low-cost method of synthesizing DNA,” says Efcavitch.

Molecular Assemblies has conceived a unique method of writing DNA using enzymes that dovetails nicely into both the write and the read aspects, Efcavitch says. The company has an issued patent on the process, which is slightly different than what they use for life sciences.

“It has the advantage of being scalable to really, really, large simultaneous writing of many sequences, and, importantly, it would make nonbiologically useful DNA. So, it couldn’t be repurposed for bioterrorism purposes,” says Efcavitch. “So, this methodology that we’ve invented—it’s key factor is it’s not biological DNA so that synthesis hardware can’t be repurposed.”

DNA electronics is still in the realm of science fiction. But that could change if long DNAs can be made cheaply and on demand, says Efcavitch. “It’s one of those they will come if you build it aspects—again, the longer the DNA you can make, the less expensive you can make them—that would be enabling.”

Scalability of the enzymatic DNA synthesis process also makes it applicable to material sciences because the reactants used can be recycled, lowering the cost of synthesizing the large quantities that will be needed, grams or even kilogram amounts of synthetic DNAs. The ability to recycle the reactants, which you can’t do with the chemical method, could drive down the cost of making large quantities of synthetic DNA that could be used for industrial purposes and material science applications.

As far as a nanotechnology application: “The one that I think is perhaps the most interesting is making DNA origami, which is two-dimensional DNA that can be then used as a mask for breaking through the 10-nanometer line width problem in integrated circuit production,” says Efcavitch. “There are people who are publishing papers, where they are using the DNA, not in a biological sense, but purely as a method of semiconductor fabrication—definitely on the cutting edge and would require a very low-cost method of synthesizing lots of DNA.”

In life sciences, Molecular Assemblies is working with a multidisciplinary team led by GE Research to enable on-demand production of DNA/RNA-based vaccines, anywhere in the world in just days. The project is under a DARPA NOW (Nucleic Acids On-Demand Worldwide) program to build a rapidly scalable and deployable mobile platform to deliver new medical countermeasures, such as vaccines, in response to a pandemic.

“It sounds a little at first like science fiction, but the idea is to generate a six-by-six-by-six-foot box that essentially would have our enzymatic approach to making DNA, coupled with GE technology, which is a vectorized technology for delivering vaccine,” says Kamdar. “This box could be dropped into a hot zone and could deliver several thousand-unit doses of vaccines overnight.”

The company was picked for the project in part because its enzymatic approach does not require harsh chemicals, beneficial in this type of situation.

“I think that it’s an example of the sort of doors that enzymatic DNA can open. That’s what excites us about it,” says Kamdar.


NEXT: Podcast feature – more on the technology and opportunities

This is part of the Big4Bio Company to Watch program for September 2021: Molecular Assemblies.
For more information on the series, click here.