DNA is the backbone of synthetic biology. Whether you’re making high-value proteins de novo through fermentation or working on solutions for reading and writing data in DNA — or anything in between — you need DNA.
Cells are equipped with everything necessary to amplify DNA molecules, making copies of their genetic material every time they split. For years, scientists have leveraged the fast growing E. coli bacterial cells for amplifying DNA — whether that DNA is the gene for producing insulin for human health care or an antibody required for basic research. The chassis organism has been the gold standard for years to amplify large DNA molecules — impractical (not to mention toxic to the environment) using chemical DNA synthesis and still inefficient using brand-new enzyme-based DNA synthesis methods.
Yet for all their power, cells have certain limitations. Scientists have struggled for years with DNA sequences that yield proteins that are toxic to E. coli (or other chassis organisms), and amplification of GC-rich DNA is notoriously difficult in the bacteria. What if you could preserve all of the best features of E. coli while eliminating the cellular characteristics that inhibit amplification of certain DNA sequences?
That’s exactly what one synthetic biology company in Japan has done.
Leveraging E. coli machinery outside of the cell
It may not come as a surprise that a new cell-free technology for DNA amplification is coming out of the Asian island nation — the PURE system, one of the first cell-free protein expression systems, was invented by Japanese scientist Takuya Ueda, former professor at Tokyo University — and is now sold commercially worldwide. But Seiji Hirasaki, CEO and co-founder of Tokyo-based company OriCiro Genomics, is ready to take cell-free DNA amplification up a notch.
“Cell-free technology is one of the most important enabling technologies in synthetic biology because it can not only enhance the efficiency but also widen the scope of R&D. Our core technology is about cell-free assembly and amplification of genome-scale, large [<1 Mbp] DNA,” he says, adding, “we want to eliminate the need for E. coli and cell-based cloning for producing large DNA.”
So, how exactly do they do it?
Founded last December, the company’s technology is based on genome propagation in E. coli — but the process is ten times faster. Dr. Masayuki Su’etsugu, OriCiro’s CSO and other co-founder, identified 25 proteins essential for genome replication in E. coli, and then figured out a way to reconstruct the entire process in vitro, outside of the cell. All that is needed to get the process of DNA amplification going is a single molecule of circular DNA with an oriC sequence (the sequence of DNA that signals DNA replication in E. coli). With this system the company has achieved 1010-fold amplification from a single DNA molecule within 3 hours — and the system works for DNA molecules as large as 1 Mbp.
OriCiro has streamlined the DNA assembly process, too, achieving one-step assembly of up to 50 DNA fragments, completely enzymatically, in less than an hour. Combining such rapid DNA assembly with amplification has a synergistic effect, as circular DNA can be selectively amplified, leading to highly efficient DNA synthesis. And, because the entire process is cell-free, there is no need for downstream purification steps, either.
Image source: OriCiro Genomics
The potential uses for the technology are numerous — essentially any life sciences application requiring long DNA can benefit from OriCiro’s system: plasmid development, microbial genome modification, synthesis of artificial genomes, DNA data storage. As Hirasaki says, his company’s technology has the power to unlock the possibilities of synthetic biology.
Investors seem to agree with Hirasaki on this point — the company already closed a $3.6 million funding round this past March (a mere three months after the company was founded) from the Japanese VC University of Tokyo Edge Capital (UTEC).
“This is relatively a large amount when it comes to early-stage financing by a life sciences start-up in Japan,” says Hirasaki, which he says reflects an increasing interest in synthetic biology among Japanese investors. OriCiro has joined a burgeoning synthetic biology startup landscape in the country that includes the likes of Synplogen, BioPalette, and Spiber.
Yet, due in large part to a risk-averse employment culture in Japan, much of the synthetic biology research there is centered in academic institutions. Hirasaki says that increasing the visibility of synthetic biology by introducing new products and services to the market is necessary to increase the value of synthetic biology in industry and society as a whole.
In the case of OriCiro, the technology is likely to be well received by Japanese industries where fermentation technology has played a significant role traditionally. But Hirasaki has his sights set globally.
“OriCiro is a Japan-based company but looks at the global market. We strive to become a worldwide player as a leader in cell-free DNA technologies for synthetic biology,” he says. This strategy is well in line with his belief that, at least in the near-term, Japan will be increasingly recognized as a source of new synthetic biology technologies rather than a local market for those technologies.
Yet the winds are changing. More and more researchers in Japan are willing to take on the risk of starting a new company, and investors are increasingly excited to back such efforts. OriCiro may be one of the current few, but I’d bet that in the near future they’ll be seen as a charter member of a burgeoning Japanese synthetic biology landscape. I can’t wait to see what the great scientific minds of Japan bring to our industry.
Meet OriCiro and other companies working on cell-free technologies at SynBioBeta 2019 October 1-3 in San Francisco, CA.3