In a truly incredible breakthrough, scientists have engineered a bacterium with three pairs of DNA bases, rather than two.

The extra letters make the organism different to every other known form of life.

Not only has the unique bacterium been created, but it appears to be able to can replicate the unnatural DNA bases as normal, as long as molecular building blocks are supplied.

“Life on Earth in all its diversity is encoded by only two pairs of DNA bases, A-T and C-G, and what we’ve made is an organism that stably contains those two plus a third, unnatural pair of bases,” said The Scripps Research Institute (TSRI) Associate Professor Floyd E Romesberg, who led the research team.

“This shows that other solutions to storing information are possible and, of course, takes us closer to an expanded-DNA biology that will have many exciting applications - from new medicines to new kinds of nanotechnology.”

The expanded genetic alphabet could allow researchers to code proteins and organisms that have never existed before.

“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,” Romesberg said.

“Other applications, such as nanomaterials, are also possible.”

The Scripps team spent years finding pairs of molecules that could serve as new, functional DNA bases.

This was not easy, but a breakthrough came when the team identified sets of nucleoside molecules that can hook up across a double-strand of DNA almost as snugly as natural base pairs.

A report in 2008 showed that DNA containing these unnatural base pairs could replicate in the presence of the right enzymes.

The following year, researchers were able to find enzymes that transcribe this semi-synthetic DNA into RNA.

“These unnatural base pairs have worked beautifully in vitro, but the big challenge has been to get them working in the much more complex environment of a living cell,” said Denis Malyshev, a co-author on the latest report.

In their most recent study, the team synthesised a stretch of circular DNA known as a plasmid and inserted it into cells of the common bacterium E. coli.

The plasmid DNA contained natural T-A and C-G base pairs along with the best-performing unnatural base pair the laboratory had discovered, two molecules known as d5SICS and dNaM.

The goal was to get the E. coli cells to replicate this semi-synthetic DNA as normally as possible.

This proved difficult too, as there are no natural mechanisms for carrying the unnatural DNA.

Researchers eventually came upon a working triphosphate transporter, made by a species of microalgae, which took on the task of importing the unnatural triphosphates.

Before anyone panics, Malyshev says the replication of unnatural DNA still needs lots of help, and can not occur accidentally.

“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,” Malyshev said.

“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.”

The next step will be to look for in-cell transcription of the expanded-alphabet DNA into RNA, which feeds the protein-making machinery of cells.

The latest report is accessible here.