Life science research has been limited for decades — not because of scientists’ ambitions but because of outdated technology. Phosphoramidite chemistry, the “gold standard” for DNA synthesis, has undoubtedly pushed biology forward in amazing ways. But here’s the catch: it’s reached its peak. The chemistry can only go so far; we’ve been butting up against those limits for years. Take long oligos, for example. When you finish synthesizing them, you’re left with a minuscule fraction of your desired sequence in a sea of truncated and error-filled synthesis products. It’s inefficient, and the yield is painfully low.
When it comes to manufacturing gene fragments, most DNA synthesis companies max out at around 5,000 base pairs (5 kb). This isn’t because scientists don’t want larger constructs but because the DNA synthesis technology can’t handle it. To synthesize larger genes, companies stitch together smaller oligos — usually 100 to 150 base pairs — using polymerase cycling assembly (PCA), followed by Golden Gate cloning, or Gibson assembly. These techniques work by enzymatically joining short oligos into longer sequences. However, as the sequences grow, so does the complexity of the assembly reactions.
Assembling oligos into gene fragments isn’t as straightforward as it sounds. Take PCA, for example. This method involves synthesizing overlapping oligos and then joining them using a PCR-like reaction. The problem is that each round of assembly can introduce errors, and with longer sequences, the likelihood of mistakes and misassemblies grows exponentially. Golden Gate assembly uses Type IIS restriction enzymes to cut and paste DNA adjacent to specific recognition sites, but that requires the user to remove certain commonly occurring short sequences from their desired sequences.
The assembly process breaks down once you hit that 5 kb ceiling. It becomes too complex, too inefficient, and too costly to scale. At this point, scientists often have to cobble together multiple “sub-assemblies,” which are smaller stitched segments that eventually form the final, larger gene. Each additional sub-assembly step compounds the risk of failure and increases the hands-on time, making it almost impossible to achieve the desired outcome without significant investment in resources. As a result of this 5 kb limit, scientists are left with a system that restricts their ambitions, forcing them to make do with smaller, more manageable sequences, or to spend more money and time on complicated workarounds.
Lately, some vendors have attempted to innovate by synthesizing millions of oligos at a time using semiconductor-based or miniaturized platforms. Sounds great, right? Not quite. This approach introduces new problems, like minuscule amounts of DNA that require amplification just to be usable. Ultimately, it’s the same: more people in the lab, higher costs, and frustration for scientists.
At Ansa, we’re throwing out the rulebook and rewriting what’s possible in DNA synthesis. Instead of struggling with inefficient short oligos, Ansa is building something far more powerful. Enter Ansamer™ oligos, our long oligos that significantly reduce downstream problems. Unlike the traditional 150 bp oligos, we’re starting at 600 bp and scaling fast. Later this year, we’ll hit 1,000 bp, and we have 1,500 bp on the roadmap for next year. Imagine what that means for assembling complex, multi-kilobase constructs: we’ll be able to assemble a 5 kb sequence faster and more efficiently than anyone else. With Ansamer™ oligos, we’re improving assembly, speeding up processes, and slashing the need for laborious cloning.
By Jason T. Gammack, Ansa CEO