In May 2014 a team at the Scripps Research Institute in La Jolla, California, announced the first living organism to carry an expanded genetic alphabet. Their E. coli bacteria held two man-made DNA “letters” alongside the natural four (A, T, C and G), copied them and passed them on as they divided. The work, led by chemical biologist Floyd Romesberg and published in Nature, did not create a new species or an “alien” life form. It showed that the chemistry of heredity is less fixed than biology textbooks once implied.
Here is what the scientists did, why it took about fifteen years, what followed in 2017, and why the research matters for medicine.
Life’s four-letter alphabet
All known organisms store their genetic instructions in DNA, a long double-stranded molecule shaped like a twisted ladder. The sides of the ladder are made of sugar and phosphate; the rungs are pairs of chemical units called bases. There are four: adenine (A), thymine (T), cytosine (C) and guanine (G). A pairs with T and C pairs with G, which is why each strand can serve as a template for copying the other.
Cells read the bases three at a time. Each three-letter “word,” or codon, stands for one of the 20 standard amino acids that link up into proteins, or for a stop signal. With four letters there are 64 possible codons, many of them redundant. Adding even two new letters multiplies the number of possible words, which is what makes an expanded alphabet so attractive to chemists.
A long road from the test tube
Scientists wondered as early as the 1960s whether life could store information with other chemicals. The first practical step came in 1989, when Steven Benner’s group at the Swiss Federal Institute of Technology (ETH) in Zurich built DNA containing modified versions of cytosine and guanine and showed that these extra bases could be copied in a test tube.
Romesberg’s team took a different route. Instead of tweaking natural bases, they designed molecules that look quite unlike them and pair through shape and water-repelling forces rather than the hydrogen bonds that hold A to T and C to G. In work published from 2008 onward, they screened thousands of possible combinations made from dozens of candidate molecules. The pair that performed best, called d5SICS and dNaM, could be copied by DNA polymerases and transcribed into RNA in laboratory reactions. Getting enzymes that evolved over billions of years to accept such strangers was a surprise even to the researchers.
Getting new letters into a living cell
A cell cannot use a base it cannot obtain. Bacteria do not make d5SICS or dNaM, and the building blocks cannot easily cross the cell membrane. The Scripps team solved this by giving E. coli a gene from a microscopic alga (a diatom) that produces a nucleotide transporter, a protein pump that brought the synthetic building blocks inside.
The researchers then built a small circular piece of DNA called a plasmid carrying a single unnatural base pair and placed it in the bacteria. As long as the cells were fed the synthetic ingredients, they kept copying the plasmid with the new pair intact. When the supply ran out, the cells gradually swapped the foreign letters for natural ones. Romesberg summed up the result for Nature’s news team: “What we have now is a living cell that literally stores increased genetic information.”
The first author of the 2014 paper was Denis Malyshev, then a graduate student in Romesberg’s lab. Outside experts, including Benner, called the result a genuine leap, because many had assumed that DNA copying in a living cell was too precise to tolerate such unusual chemistry.
What happened in 2017
The 2014 bacteria had two problems: the transporter made them sickly, and the extra letters tended to drop out over time. In January 2017, in Proceedings of the National Academy of Sciences, the team reported fixes. They modified the transporter so the cells grew more normally, redesigned one of the bases, and used the gene-editing system CRISPR-Cas9 as a kind of spell-checker that destroyed DNA copies which had lost the new letters. The bacteria, now carrying bases the team called X and Y, kept them through 60 cell divisions.
In November 2017 the group went further. In a Nature paper led by Yorke Zhang, the bacteria not only stored X and Y but used them: genes containing the new letters were transcribed into RNA, and the cell’s protein-making machinery built a version of green fluorescent protein that carried unnatural amino acids at a chosen position, with purity above 98 percent. “I would not call this a new lifeform—but it’s the closest thing anyone has ever made,” Romesberg said.
Is this “alien” or dangerous life?
Headlines in 2014 spoke of alien DNA and artificial life. Both phrases overstate what happened. The organisms are ordinary E. coli with a tiny addition: a single unnatural pair among millions of natural ones in the original work. Every other part of the cell is natural.
The design also has a built-in safety feature. Because no living thing can make X and Y on its own, the bacteria depend on scientists to feed them. If they escaped the lab, they would lose the extra letters and become normal bacteria, or fail to use them at all. Researchers see this dependence as a useful form of biological containment, although some groups have since explored cells that could make unnatural bases themselves, which would raise new questions.
Could scientists one day build an organism that uses only synthetic letters? Romesberg himself thought that was unlikely, because so many cellular systems recognise natural DNA. Benner was more open to the idea in principle, suggesting that evolution, if rerun, might have produced a different genetic system.
Why it matters for medicine
The main practical goal is new proteins. With extra letters, cells can be instructed to insert amino acids that nature does not use, at precise places in a protein. The Scripps team estimated that X and Y could in principle code for up to 152 new amino acids. Such building blocks could make protein drugs last longer in the body, attach them to other molecules, or tag them with fluorescent labels so researchers can track biological processes under the microscope.
Romesberg co-founded a company, Synthorx, in San Diego to turn the platform into medicines. Its researchers co-wrote the 2017 Nature paper, and its early work focused on modified versions of signalling proteins for cancer and autoimmune disease. The French drug maker Sanofi later acquired the company, a sign of how seriously industry took the idea.
Other groups have expanded the code in different ways. In 2019 Benner’s team reported “hachimoji” DNA, an eight-letter system that worked in test-tube reactions, though not in a living cell.
The bigger picture
Expanding the genetic alphabet is part of synthetic biology, the effort to redesign living systems for useful purposes. The 2014 experiment was a modest step in practical terms, a single extra base pair in a bacterium, but a large one conceptually. It showed that A, T, C and G are not the only chemistry a cell can use, and it opened a route to proteins that biology has never made. Questions about safety, regulation and how far such changes should go remain open, and they deserve public debate as the technology matures.
Sources: Malyshev et al., Nature (2014); Scripps Research, 23 January 2017; Scripps Research, 30 November 2017; Wikipedia: Unnatural base pair; Benner et al., JACS (1989); Romesberg group, JACS (2008). Original news report: Nature News via Huffington Post.
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