Blog Post
Enzymatic DNA synthesis:
Turning a lab concept into an industrial solution Part 1 - The challenge
For over 50 years, DNA has been synthesized using organic chemistry. Although current approaches have reached a high level of performance, there are still strong limitations, especially for new applications in genomics, cell and gene therapy and synthetic biology. With enzymatic synthesis, DNA Script hopes to overcome these limitations.
The ability to write DNA efficiently is a key necessity for almost all applications in the life science industry. DNA synthesis enables the engineering of biological systems (enzymes, antibodies, bacteria, yeast, plants, cells, etc.) to create new applications, most notably in biotherapeutics, the production of chemicals and materials, agriculture or nanotechnology.

DNA Script is developing a novel enzymatic technology to synthesize DNA that will increase performance in strand length, purity, turnaround time and cost. This blog series reports key technological milestones — initially revealed at the GP-write Conference in May 2018 — which demonstrate the potential of enzymatic synthesis, even at this early phase in the development of our technology.

Chemical DNA synthesis reaches a plateau

Since the discovery of the structure of DNA in 1953, there has consistently been a strong demand from the scientific community to synthesize — or manufacture — this molecule: first for a better understanding of its mechanisms, then for bioengineering. Since the 1960s, chemical DNA synthesis has enabled tremendous progress in synthetic biology. While various DNA synthesis methods have been developed, early approaches were based on organic chemistry, as biochemical methods were not initially available.
In 1983, a major step forward for the chemical synthesis of DNA was achieved, with the introduction of phosphoramidite reagents. This technology allowed synthetic DNA to enter its industrial age; it is still in use today in every DNA provider's factory. Along with PCR (polymerase chain reaction, the method for "photocopying" DNA), the introduction of phosphoramidites in the 1980s completely reshaped the field of molecular biology.
Fig. 1 - Milestones in DNA synthesis history
Nonetheless, this chemical technology has now hit a performance plateau: it is extremely difficult to reach an efficiency superior to 99.5% for each nucleotide addition. This translates to an overall purity of 35% when synthesizing a 200-nucleotide strand, which puts a limit on the length of synthetic DNA. Nearly all commercial DNA providers limit synthesis to 150 nucleotides in length. Longer fragments need to be stitched together in a tedious process called DNA assembly.

For applications that require DNA, this translates into very practical limitations: DNA is expensive, turnaround time is prohibitively long and some sequences are very difficult to make. In life science, R&D relies on repeating a Design / Build / Test / Learn R&D cycle. Due to the limitations of DNA synthesis (the Build step), these cycles are too slow, preventing many groups from conducting their research efficiently.

Overcoming these limitations with the next generation of DNA synthesis: enzymatic DNA synthesis

DNA Script pioneers a completely new approach to solve these challenges: enzymatic DNA synthesis. Our goal is to unlock the power of DNA to write the future of life science.

The basic idea comes from a simple observation: Nature is extremely efficient at synthesizing DNA. When bacteria replicate their genomes, they couple millions of nucleotides together in less than 20 minutes (the average time of cell division) and make very few mistakes. They do so by using a very efficient catalyst to synthesize DNA: polymerases. Polymerases are enzymes, or small "robot-like" molecules, that are present in every living cell, dedicated to one task: synthesizing DNA. They have been optimized through billions of years of evolution to be extremely efficient in catalyzing the addition of a nucleotide to a strand of DNA. This process can be very fast, at speeds such as one nucleotide addition every millisecond.
Fig. 2 - Proprietary couples enzyme/nucleotide are used to synthesize DNA
DNA Script's technology captures this level of performance by taking advantage of these enzymes to synthesize any DNA sequence needed. Our core technology relies on deep polymerase engineering and on the use of specific nucleotides (DNA monomers). It has the major advantage of using only aqueous reagents compatible with life, whereas the harsh organic solvents used in phosphoramidite chemistry are an environmental issue and can damage the DNA. The use of aqueous reagents preserves DNA integrity and opens the possibility to synthesize nucleic acid products with modifications that are complex to get today (with controlled epigenetic patterns for instance). Finally, synthesized DNA can be readily used in downstream processes without a tedious post-processing including a change of medium.

DNA Script's patented process can be automated in various devices, including those currently used for phosphoramidite chemistry.

Next episode on June, 12th : Enzymatic synthesis' first major milestone
JUNE, 7th 2018