DNA Synthesis Goes Green

DNA (or deoxyribonucleic acid as your high school teacher might say) are molecules made up of nucleotides, which are linked by covalent and hydrogen bonds in a repeating sequence. Like Lego® blocks or letters, nucleotides can be joined together in a million ways to form the instructions that build nature from the ground up.

DNA synthesis, i.e. the creation of DNA, occurs naturally as cells divide and replicate, with each daughter cell containing the same basic genetic information as its parent. DNA synthesis which occurs in a living organism is often categorized as in vivo, whereas DNA synthesis which occurs outside of the cell (i.e., in a laboratory) is often referred to as in vitro (Latin for “in glass”).

Biologists first began synthesizing DNA in laboratory settings almost 40 years ago. This process, called “phosphoramidite synthesis,” was developed by Marvin Caruthers and his team at the University of Colorado beginning in 1981. Their work was based on the chemical manipulation of nucleotides and proved highly successful in identifying and replicating short DNA sequences. We use these short (30-120 nucleotide) chains today in critical scientific and diagnostic applications such as PCR primers. Phosphoramidite synthesis has become a mainstay of the industry and is a widely applied commercial DNA synthesis used by companies like Twist Bioscience, Ginkgo Bioworks, and Genscript.

Over the past 7-8 years, an increasing amount of focus has been placed on “enzymatic” DNA synthesis, which eschews the use of outside chemical agents and leverages natural enzymes, i.e., the same molecular machines used by a living cell to catalyze DNA synthesis reactions. Currently, most enzymatic DNA synthesis relies on the use of terminal deoxynucleotidyl transferase (TdT), an enzyme responsible for introducing “extra” nucleotides into the gene splicing process2. The purported benefits of enzymatic synthesis include the ability to avoid the use of harsh chemical substances (which often results in toxic waste) and an ever-increasing ability to produce longer and longer DNA strands… which in turn, result in not only a more “green” form of DNA synthesis but also some incredibly powerful new uses for the longer DNA chains (e.g., vaccines, therapeutics, and data storage).

Five companies lead the market in DNA enzymatic synthesis: Molecular Assemblies, DNA Script, Evonetix, Touchlight Genetics, and Ansa Biotechnologies. Each of these companies provides their own brand of enzymatic DNA synthesis tools, which tend to fall under two broad categories of business solutions: desktop DNA synthesis (that which is accomplished via free-standing replication machines) or DNA synthesis as a service (that which is accomplished by the company on behalf of its clients).

Of particular interest is Molecular Assemblies, founded in 2014 by industry experts Mike Kamdar and Bill Efcavitch, PhD. In 2020, Molecular Assemblies partnered with Codexis, led by DNA veteran John Nicols, as a means to increase their speed to market and raise new funding. With those combined resources, Efcavitch believes, “Our proprietary in-process product enrichment, which is a feature only accessible through enzymatic synthesis, means that we can eliminate post-synthetic purification and decrease turn-around-time to our customers.”

Molecular Assemblies recently announced a new $26MM investment round (anchored by leading DNA-focused companies like Agilent). According to Molecular Assemblies CEO Michael Kamdar, use of funds will entail commercializing the Company’s “Fully Enzymatic Synthesis” (FES) platform, one which uses aqueous, non-toxic reagents and requires minimal post-synthesis purification and processing. As stated by Kamdar, “The ability to generate long, pure, accurate DNA with our FES technology can accelerate many applications, such as CRISPR, next generation sequencing, and the assembly of genes for numerous synthetic biology applications.”

Investors and companies aside, we in the general public stand to benefit greatly from these advances in enzymatic DNA synthesis. The “holy grail” of longer, more cost-effective DNA strands (up to 1000-1500 nucleotides) can be used to produce better vaccines in a shorter amount of time. Advances in CRISPR technology provide highly precise gene editing tools which can be used to alter genes in plant, bacteria, and animal models. This capability can prove highly effective in identifying and implementing treatment for diseases like cancer, Alzheimer’s, etc. Lastly, DNA (as a data-rich molecule) can potentially be used to encode tremendous amounts of information as dense arrays of oligonucleotides… in mind-staggering (exabyte level) amounts. Both the US government (e.g., DARPA or “Defense Advanced Research Projects Agency) and consumer companies (e.g. Netflix or Google) have partnered with molecular biologists as a means to investigate how DNA strands could be used as a durable, cost-effective storage medium.

In conclusion, DNA enzymatic synthesis represents an enormously valuable next step in harnessing the power of DNA replication and our ability to use it for developing cutting-edge, biotechnology solutions. To learn more about DNA synthesis and the companies using such to make the planet a better place, please visit us at Built With Biology.

Thank you to Larry Upton for additional research and reporting in this article. I’m the founder of SynBioBeta and some of the companies that I write about are sponsors of the SynBioBeta Conference and our weekly digest.

Citations

1 Sandahl, A.F., Nguyen, T.J.D., Hansen, R.A. et al. On-demand synthesis of phosphoramidites. Nat Commun 12, 2760 (2021).

NatureOn-demand synthesis of phosphoramidites – Nature Communications

2 Eisenstein, M. Enzymatic DNA synthesis enters new phase. Nat Biotechnol 38, 1113–1115 (2020).

NatureEnzymatic DNA synthesis enters new phase – Nature Biotechnology

3 Writing in the book of life: Applications in biology and biomedicine. SynBioBeta (2018)

BuiltwithbiologyMolecular Assemblies: Rewriting synthetic biology with enzymatic DNA synthesis – Built WIth Biology

Reference-www.forbes.com

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