DNA is the backbone of synthetic biology — from producing high-value proteins de novo through fermentation to solutions for reading and writing data in DNA — and everything in between — you need DNA.
For years, chemical synthesis methods have been used to synthesize DNA molecules, and novel enzyme-based methods are arriving to solve the toxicity and other issues associated with chemical synthesis. But neither method is great for amplifying large DNA molecules, and as the field grows, plasmid development, microbial genome modification, synthesis of artificial genomes, and even DNA data storage all stand to benefit from the ability to quickly and accurately produce large-scale DNA.
Today we leverage cells (usually E. coli cells), which are equipped with everything necessary to amplify DNA molecules. But cells aren’t perfect. Some DNA sequences yield proteins toxic to the chassis organism, and E. coli also doesn’t do well with GC-rich DNA sequences.
Recently, we spoke with Seiji Hirasaki, CEO of OriCiro Genomics, a Tokyo-based company with a novel cell-free approach to large DNA amplification. He discussed some of the challenges facing large DNA amplification, how OriCiro is addressing those challenges, and his plans to make OriCiro a global supplier of large DNA. The following conversation has been edited for clarity.
Why is large DNA a critical tool for synthetic biology?
Current research and development focuses on relatively short regions of DNA. But looking into the future, we will need to handle large DNA as research and development makes progress. For example, by designing and synthesizing an entire microbial genome rather than modifying partly existing genomes, we could obtain artificial microbes with far better characteristics and performance. Future genetic diagnoses could include reading long sequences of human DNA and future gene therapy could use a much bigger size of DNA that contains a group of genes, not just a single gene.
How is OriCiro seeking to disrupt large DNA amplification?
As a de facto standard tool for large DNA amplification, E. coli cloning is widely used today — we are still dependent on it even though it was invented more than forty-five years ago. OriCiro started with the idea that we need to accelerate the innovation in this technology space.
Current cell-based cloning methodologies are only applicable up to approximately 300 kb DNA due to the difficulties transforming cells [with larger DNA]. OriCiro was founded based on the cell-free DNA amplification technology invented by Dr. Masayuki Su’etsugu, Associate Professor of Rikkyo University in Tokyo, who is also the CSO of the company. He has always seen a great potential of his invention for industrial applications, in particular for synthetic biology. Discussions with UTEC, a Tokyo-based VC firm, led to the formation of the company in December 2018.[Since then] we have successfully demonstrated the amplification of 1Mb DNA with our cell-free technology. We have not yet tested our technology with larger DNA, but because it mimics the replication mechanism for the E. coli genome (4.6 Mb), we believe that the technology is applicable to larger DNA. The biggest challenge will be to handle large DNA in a stable manner because DNA of this size is prone to physical breakage.
Our technology is not only about the size of DNA, but also the sequences of interest. It is applicable for sequences that are difficult to amplify with current methods, such as GC-rich and repeat sequences in PCR and cell-toxic sequences in E. coli cloning. [Addressing these limitations] are more important than the size of the DNA [we can produce] in the short term. Synthesizing large DNA on a cell-free basis can unlock the power of synthetic biology.
OriCiro is based in Japan, but you have sights on being a global provider of large-scale DNA. Where are you on that journey?
Since we started operations in April this year, we have attended several international conferences including BIO, SEED (Synthetic Biology: Engineering, Evolution & Design) and BIO World Congress on Industrial Biotechnology and AgTech, where we met many potential customers. We will also participate in SynBioBeta in October. We have already started providing sample products overseas, and we have a plan to establish US operations in the near future.
What kind of feedback have you gotten from the users of your product?
We have received very positive feedback from users of our sample products. Many of the companies and research institutions who we met at partnering conferences showed interest in testing our technology, which is very encouraging to us as a start-up company.
Some potential customers seek to use our technology on a large-scale basis in terms of the quantity of amplified DNA, but our current scale is not yet large enough to meet their requests. We have a plan to scale up both our reagent manufacturing capabilities and the amplified DNA quantities.
What are some of the biggest milestones OriCiro has achieved, and what’s next?
We closed Series A successfully in March this year raising $3.6M to kick-start the company’s activities. We have recently commenced providing our sample products to early adopters, and we plan to launch our product officially by the end of the year. We expect our next round of financing in 2020, which will move us forward further in our projects bringing us to a growth stage.
What are you looking forward to at SynBioBeta 2019?
We look forward to meeting potential customers, collaborators and investors at SynBioBeta. We would like the audience to understand the true innovativeness of our technology and to become interested in trying it. Because ours is a platform technology, we think it has the potential to be used in many different ways for different purposes, including those that we haven’t even thought of yet — we would like to audience to help us learn how to use our technology to its full potential.
Meet OriCiro Genomics at SynBioBeta 2019 in San Francisco, CA, where Masayuki Su’etsugu, Co-founder and Chief Science Officer (CSO) of OriCiro Genomics will be taking the stage on Wednesday, October 2 at 9:00am.0