At Ansa, we’re fortunate to have not one but three scientific founders, all of whom are still with the company and helping to improve our DNA synthesis technology with new innovations on a regular basis. We sat down with them to learn more about some of the key insights and motivations that have driven the development of the tech and our DNA synthesis company.
The importance of addressing complex DNA
Jared Ellefson, PhD, Ansa Head of DNA Assembly
Complex DNA is found everywhere in nature. We call DNA “complex” only because it’s difficult to manufacture using current technology – for nature, this is just “normal DNA.” Biologists have become accustomed to contorting DNA sequences to be easier to manufacture, and then make the assumption that manipulating the sequences has little consequence. However, it’s clear that a lot of hard-to-manufacture DNA is interesting to scientists and engineers — look at tissue-specific promoters, repetitive proteins, or structural RNA. Take CRISPR arrays, for example: repeated DNA segments are found throughout because nature invented an elegantly modular solution for sticking guide RNAs to Cas enzymes. While elegant, it also makes it very hard to synthesize from scratch because it’s a heavily repeated piece of DNA. The current status quo is sad; only synthesizing easy sequences eliminates huge swaths of interesting biology and limits the pace of discovery. We’re in our infancy in terms of discovering how complex DNA will reshape biology. There’s not a lot of literature on it because the techniques required don’t exist yet. That’s what we’re here to change.
Shifting from a chemical to enzymatic approach for DNA synthesis
Sebastian Palluk, PhD, Ansa Chief Technology Officer
The importance of DNA synthesis has been historically underestimated. It’s almost impossible to predict what faster and better access to DNA constructs will enable, but one thing is clear: history has shown that improvements in DNA availability led to breakthroughs no one could have expected.
When we set out to replace what was the most efficient and best-established chemical process that humankind has evolved, that has been proven for four decades, we were told it wasn’t possible to get something more efficient. Because of the laws of nature, people said, we just won’t be able to go above 99.9% stepwise yield. It just can’t be done.
The key to the rapid improvement of our synthesis has been using enzymes for all parts of the process. We initially used a chemical deprotection reaction and kept running into issues when we pushed synthesis beyond 50 nucleotides. Only when we switched from chemical to enzymatic deblock were we essentially able to synthesize DNA as long as we wanted, with no decay in synthesis quality over time. We went from 50 nucleotides that were barely working to over 400 nucleotides in a week.
The people are the key to our rapid progress
Dan Lin-Arlow, PhD, Ansa Chief Scientific Officer
This is a highly multidisciplinary problem that we’re trying to solve. From the inception of the company, I’ve always tried to build a culture where people don’t feel constrained by swim lanes, that they can speak up about things outside of their area. A lot of the best technological leaps that we’ve made have come from “diagonal moves on the chess board.” One example of this is the “dipping” principle employed by our synthesizers.
Most of the traditional DNA synthesizers operate by dispensing reagents onto a solid support, typically resin-packed columns. In this approach, it takes some time for the dispense head to travel over the length of the column bank, contributing to the synthesis cycle time, and resulting in a different duration of exposure to reagents to the columns in different positions in the bank. Another disadvantage of this approach is that any problem with a dispense operation, such as a bubble of air getting trapped between the reagent solution and the solid support, is unrecoverable, resulting in a useless oligo. Our head of chemistry — far outside of his swim lane — proposed that we could dip rods functioning as our solid support into our reagent solutions instead of dispensing reagents onto the solid support. This alternative approach provided many advantages: first, the exposure time between the rods and the reagent solutions is the same for every rod because they are all dipped for the same duration. Second, the plate of reagents for the next step can be filled concurrently with the dipping of the current step, eliminating the contribution of dispense time to the reaction cycle and resulting in shorter synthesis run duration. Finally, the rods can be dipped repeatedly to shake off any bubbles that might become attached to the surfaces, making the synthesis process much more robust.
These were all hypothetical advantages when he proposed the dipping concept, but the engineering team thought that it could actually work, so we developed a prototype and were very pleased to see that it worked as well as we hoped. Two generations of dipping-based synthesizers later, the production instruments that power our DNA synthesis service are still based on the dipping concept. There are many other examples of these kinds of cross-disciplinary insights that have made Ansa into the technological powerhouse that it is today.
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