Synthorx reaches another artificial life milestone
The San Diego Union-Tribune
By Bradley J. Fikes
The world’s first functioning organism with an expanded DNA alphabet has now met another milestone in artificial life: making proteins that don’t exist in nature.
The organism, a bacterium created by scientists at The Scripps Research Institute, incorporates two synthetic DNA letters, called X and Y, along with the four natural ones, A, T, C and G. A team led by Floyd Romesberg published a study last year demonstrating that the organism, an engineered strain of E. coli, can function and replicate with the synthetic DNA.
Synthorx, a biotech startup that licensed the technology from Scripps, has now used the bacterium to produce proteins incorporating artificial amino acids, the building blocks of proteins. These are placed at precisely specified intervals along the protein sequence, obeying the code of the expanded DNA alphabet.
The La Jolla startup plans to make drugs out of these artificial proteins with properties that can be adjusted, such as the length of action inside the body, and how tightly they bind to their target. By using the bacterium as living factories, Synthorx plans to make these drugs far more efficiently and cheaply than by traditional chemistry.
Synthorx announced the feat on Aug. 18. The addition of X and Y allows generation of new codons, the genetic labels that specify each amino acid.
“We’ve run this experiment hundreds of times since the first time, with different Synthorx codons, and so now we’re poised to move forward and apply it to drug discovery applications,” said Court Turner, president of Synthorx.
Further down the road, the company is looking for partners to produce DNA-scale microelectronics, or to use the DNA to protect against counterfeiting. Since the synthetic DNA molecules are made with proprietary Synthorx technology, they could be used as a guarantee of authenticity for drugs or even currency.
(As a safety measure, the artificial DNA letters must be fed to the bacterium. It can’t make them on its own, and they don’t exist in nature. So if the bacterium were to escape the lab, it would quickly lose the expanded DNA alphabet and the functions it bestows.)
The unnatural amino acids can serve as linkers to other molecules of interest, such as hooking up a drug to a precisely specified location on the protein. They can even link to metals, enabling the design of DNA nanocircuitry.
Like others in the expanding field of synthetic biology, Synthorx is striving to expand the capabilities of life beyond its naturally occurring limits. Nearby in La Jolla, Synthetic Genomics is helping Virginia’s Revivicor genetically engineer pigs that can provide organs for human transplant.
Synthetic Genomics is working with natural DNA, produced in artificially created sequences. Synthorx works with DNA that itself doesn’t exist in nature. That means the artificial DNA letters must work in harmony with naturally occurring genetic machinery that has existed for billions of years.
Showing that adding X and Y to the genetic alphabet doesn’t disturb the bacterium’s cellular machinery was important, because it showed that life isn’t confined to using the natural letters, Turner said. Up until Romesberg’s team succeeded, there was considerable doubt artificial DNA letters could exist in a viable life form.
But that was just the door-opener. Now Synthorx, funded by La Jolla’s Avalon Ventures and Correlation Ventures, in the UTC area, is commercializing the research.
“A year ago, the conversation was, you’ve expanded the genetic alphabet, expanded the hard drive of data,” Turner said. “The question was, could you pull that amount of additional information out and use it to produce things that are actually useful, and those are the proteins.”
All the complicated machinery inside a cell — far more intricate than anything humans have created — has to work with the unnatural “base pair” of X and Y. (X always pairs with Y in the synthetic DNA, just as A pairs with T and C with G). The machinery must read the expanded genetic code, generate the messenger molecules of RNA, and interpret it correctly inside the ribosome, the organelle where protein is actually made, Turner said.
At any step along the way, the machinery could have jammed, and the scientists would have had to figure out what went wrong and try to fix it. But that didn’t happen.
“The translation machinery treats it as natural,” Turner said. “It’s pretty amazing.”
Determining what the additional letters actually do in protein synthesis was a matter of trial-and-error, Turner said.
Proteins are made by stringing together amino acids, of which 20 are generally used in nature. The process starts when DNA is transcribed into messenger RNA, that carries the protein code out into the cell for assembly.
Combinations of three letters of messenger RNA, called triplets, code for the individual amino acids. Some codons signal the machinery to cease making the protein; these are called “stop codons.”
Since there are four possible choices for each of the letters in the triplet — A, T, C and G — a maximum of 64 possible amino acids can be coded for with natural DNA. But since there are stop codons, and some of the triplets code for the same amino acid, in practice just 20 amino acids are possible.
By adding two new letters to the original four in DNA, Synthorx says the maximum number of amino acids that can be coded for rises from 20 to as many as 172. This expanded triplet set is what makes it possible to incorporate unnatural amino acids into the proteins.
“It was a pretty special day,” Turner said. “Not only were we able to produce proteins using our system, but we were able to identify handfuls of semi-synthetic or unnatural codons, made with our unnatural base pair, that the ribosome treats as if they were natural.”
The functionality of the unnatural X-Y base pair is a tribute to the 15 years that Romesberg spent on identifying the best one, Turner said.