Engineered bacterium is first living organism to use artificial DNA "letters"

US researchers have engineered a bacterium whose genetic material includes DNA or bases not found in nature (Image: Shutterstock)

Scientists at the Scripps Research Institute (TSRI) in California have produced a living bacterium that has a strand of artificial DNA made with chemical “letters” not found in nature or any other organism.

Deoxyribonucleic acid (DNA) is the famous double helix discovered by Watson and Crick in the 1950s and commonly known as the carrier of the “genetic code” of life. It’s found in all living things on Earth, from the smallest cells to the largest redwood trees, and in each and every one of these organisms the basic DNA structure is exactly the same.

Though the models of DNA that are on display in museums seem impossibly complex, it is actually a very simple molecule. It’s twisty double backbone of phosphates and sugars carries branches that link the two spirals together like steps in a ladder. These steps consist of a surprisingly simple pairing of four nucleic acid bases: guanine (G), adenine (A), thymine (T), and cytosine (C). These bases pair up to one another like lock and key with guanine pairing with cytosine and adenine pairing with thymine.

This simple, predictable pairing allows life to happen. It provides a way to encode the genetic instructions needed to build and maintain cells. Under the influence of various enzymes, the DNA molecules unfasten and come apart like zippers, which provide the pattern for creating new strands of DNA.

This sort of base pairing is universal in all known life. If it has DNA, then it uses G-C and A-T pairs. The question is, is this pairing universal because of all life on Earth having a common ancestor, is it because of some fundamental law of chemistry, or both?

The result of years of research going back to the late 1990s, the TSRI team’s project aimed to find molecules that would pair like those in DNA and would form stably on the helix backbone of the DNA molecule. They would also need to unzip like the known bases and transcribe onto the RNA molecules to create new DNA strands. In addition, they had to be able to survive the DNA repair mechanisms in the cell that might see the new bases as faulty strands and remove them.

In 2008, the team was able to create semi-artificial strands of DNA that would replicate in a test tube in the presence of the right enzymes and would transcribe onto RNA, but, according to the team, the big leap was to get the strands to work in a living cell. They did this by creating a plasmid, which is a circular strand of DNA, that was a mixture of natural and artificial DNA elements made of molecules known as d5SICS and dNaM, and then inserting it into escherichia coli bacteria.

Obviously, the result isn't artificial life, but it is, by any definition, a novelty. The bacteria carried in their nuclei DNA with bases not found in any other living organism. The pairs are able to duplicate so long as the chemical materials are available, and the duplication occurs with reasonable speed and accuracy, the repair mechanism didn't interfere, and the growth of the cells was not impaired.

However, the new bacteria are also no Frankenstein’s micro-monsters waiting to break out of the lab on an unsuspecting world. Since 5SICS and dNaM are not found in nature, the scientists have to supply them for the DNA strands to form and they need what are called triphosphate transporter molecules produced by a species of microalgae to move the molecules into the cells. What all that adds up to is that the artificial DNA won’t work outside of the laboratory.

"When we stopped the flow of the unnatural triphosphate building blocks into the cells, the replacement of d5SICS–dNaM with natural base pairs was very nicely correlated with the cell replication itself – there didn’t seem to be other factors excising the unnatural base pairs from the DNA,” says team member Denis A. Malyshev. "An important thing to note is that these two breakthroughs also provide control over the system. Our new bases can only get into the cell if we turn on the ‘base transporter’ protein. Without this transporter or when new bases are not provided, the cell will revert back to A, T, G, C, and the d5SICS and dNaM will disappear from the genome."

According to team leader Floyd E. Romesberg, the next goal will be see if the new bases can be used to create proteins. “In principle, we could encode new proteins made from new, unnatural amino acids — which would give us greater power than ever to tailor protein therapeutics and diagnostics and laboratory reagents to have desired functions. Other applications, such as nanomaterials, are also possible.”