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"Technology Dance" Looks Set To Transform the Field of DNA Synthesis

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The applications of DNA synthesis are firmly recognized in several scientific fields including synthetic biology, biopharmaceutical development and modern agriculture. Over recent years, it has become increasingly clear that there are boundless opportunities that stem from the ability to synthesize DNA in a laboratory setting.

Take DNA-based storage, for example. Digital data can now be encoded into a DNA sequence for long-term storage, offering a possible solution to the data storage crisis of the twenty-first century. In drug discovery, scientists are working to create biological systems that can produce drugs which – for years – have been synthesized chemically. Such innovations in modern biology are reliant on DNA synthesis, for which a bottleneck currently exists – the traditional chemical process that has been adopted since the 1980s.

Codexis, a leading protein engineering company, and Molecular Assemblies, a pioneer in the field of enzymatic DNA synthesis, recently announced a partnership through which the companies aim to engineer enzymes that will optimize the process of enzymatic DNA synthesis – an alternative approach to chemical DNA synthesis.

Codexis and
Molecular Assemblies expect to be at the forefront of a "transformation in DNA synthesis". Technology Networks spoke with John Nicols, president and CEO, Rob Wilson, PhD, senior vice president and general manager (performance enzymes) and Aaron Hammons, senior director (life science enzymes business development) at Codexis to find out how.

Molly Campbell (MC): Please can you discuss the importance of DNA synthesis and its applications?

Rob Wilson (RW):
The importance of DNA synthesis to modern life increases by the year, and that shows no sign of changing. Synthetic DNA is used in applications as wide ranging as biologic drug discovery and manufacturing, improvement of crop properties and yields in agriculture, synthetic biology for the sustainable production of new chemicals and materials and – increasingly – data storage. The ability to make increasingly long sequences far more efficiently and accurately, to enable the continuing reduction in cost and expansion in applicability of synthetic DNA, has long been a critical goal of the genomics community.

MC: What is enzymatic DNA synthesis, and how is it different to chemical synthesis?

Firstly, it is important to say that the purified products of both enzymatic and chemical synthesis are the same: to all intents and purposes sequences of normal DNA, just as nature would produce, just made synthetically and potentially with the sequence (or code) modified to fit the desired function. In both processes, the sequence is built up iteratively, one nucleotide at a time.

The difference comes in the manufacturing process: chemical synthesis utilizes harsh reagents, solvents and processes that would be familiar in almost any chemical factory in the world, whereas enzymatic synthesis relies on variants of the natural enzymes which have been evolving since the very start of life on this planet, and which operate efficiently in water, under benign conditions.

MC: What are the benefits of enzymatic DNA synthesis?  

Aside from the environmental benefits described above, enzymatic synthesis is fundamentally simpler than the chemical alternative and – critically – has the potential to be much more precise than the chemical approach, thereby introducing fewer errors into the code. This makes producing much longer sequences possible, without the need for cumbersome, inefficient and costly purifications or workarounds.

MC: Can you discuss the decision to partner with Molecular Assemblies?

John Nicols (JN):
Our whole company is focused on seeing the needs and delivering on the promise of improved enzymes to make for a better life for humans and the planet we inhabit. We study many different novel enzyme opportunities accordingly. We elevated enzymes for DNA synthesis as part of that focus in early 2019 and have increasingly validated that substantial benefits could be enabled by Codexis engineered enzymes for improving the manufacture of high-quality DNA. 

With that driving force to get involved in DNA synthesis, we performed careful diligence on a range of companies that are currently invested in enzymatic approaches for synthesizing DNA. Molecular Assemblies stood out in our analysis, given their intellectual property and patent estate, their excellent in-house scientific team lead by DNA synthesis veteran Bill Efcavitch and their synergistic, collaborative Board and investor base. Those capabilities made Molecular Assemblies our top choice to be our strategic DNA synthesis partner, and so we embarked to see if we could make a deal.

From there, working out the details of the technology development collaboration and equity purchase agreements proceeded smoothly, and validated a strong cultural fit at all levels between our two companies. That synergy is evident today, as we’ve kicked off the enzyme engineering work in support of the partnership at Codexis’ R&D center in Redwood City, California.

MC: How do you anticipate harnessing the power of Codexis’ protein engineering capabilities with Molecular Assemblies’ scalable enzymatic DNA synthesis technology will accelerate the enzymatic DNA synthesis revolution?

Our platform protein engineering technology, CodeEvolver®, will bombard the target nucleotide assembly chemistry with tens of thousands of different enzyme variants over the life of this project.  The parallel optimization between rapidly improving engineered enzymes and the downstream chemistry that uses them will be continuously challenged and evolving in tandem.

The enzymes we finalize in this project will not look much at all like those we are starting with today, and similarly, the nucleotide chemistry will have to rapidly move through a series of shifting bottlenecks that little resemble today’s constraints. The result of the companies "technology dance" will liberate a patented enzymatic DNA synthesis methodology that will be orders of magnitude more efficient than today’s enzyme-based processes. That eclipsing of today’s state-of-the-art is what is required to effectively outperform traditional phosphoramidite synthetic approaches, and to open up the DNA synthesis differentiators that the partnership has set as its primary goals – DNA synthesizable with unparalleled oligonucleotide quality and length.

MC: What are the greatest challenges in DNA synthesis?

DNA-synthesizing enzymes have evolved over hundreds of millions of years to perform their function inside cells in living organisms, exquisitely. As such, they operate under complex conditions where many regulatory processes stop errors from happening and enable natural, unprotected nucleotides to be efficiently added to the end of the new DNA chains being produced. In a manufacturing environment, these cellular regulatory processes are absent and the challenges of reducing errors and introducing new nucleotides to the sequence require a different solution.

Therein lies the greatest challenge of enzymatic DNA synthesis: getting the enzymes to work with modified starting materials which are protected (modified with additional chemical functionality) to prevent errors occurring. An enzyme which is highly active and selective for an unprotected nucleotide is likely almost wholly inactive against a modified nucleotide which is required to perform the step-wise, one-at-a-time additions to extend the DNA chain, before the protecting group is removed to once more expose the natural nucleotide.

This is where protein engineering is transformative – by engineering the natural enzymes to work equally well with modified nucleotides as they once did with the natural nucleotides, they can be enabled to perform, with commercially relevant efficiency, in a DNA synthesizer instead of a living cell.

MC: What do you envision the field of DNA synthesis will look like in five to ten years' time?

Aaron Hammons (AH)
: In five to ten years the synthesis of DNA will be a common utility found in biology, agriculture, pharmaceutical, textile and even in many computer and engineering labs.  Researchers will be able to print a custom gene or even a genome at their benchtop or have one ordered and delivered the next day. 

Scientists will be able to print custom genes for gene therapy and personalized medicines, archivists will be able to store data in a format that can remain stable and readable for millennia, engineers will design and create custom bacteria and viruses to manufacture, build, or deliver sustainable biomaterials. The barriers-to-entry for DNA-dependent research will be reduced through improved cost, speed, accuracy, and availability of DNA allowing for rapid adoption of a currently-niche technology. This prolific adoption will cause a Cambrian-like explosion of research areas and industrial applications that will enable the shift to a more sustainable, biology-driven future.

John Nicols, Rob Wilson and Aaron Hammons were speaking to Molly Campbell, Science Writer for Technology Networks.