Scientists add two new letters to DNA's 'alphabet'

Using bacterial cells, scientists have managed to create a 'semi-synthetic organism' whose DNA has six 'letters,' instead of the usual four.

Researchers say that they have successfully incorporated synthetic DNA bases within the genetic material of E. coli cells, and had the cells copy the artificial base pair in their DNA.

Floyd Romesberg, Associate Professor of Chemistry at the Scripps Research Institute in California and an author of the study published in the journal Nature says that he and his team have managed to create a "semi-synthetic organism" by integrating the artificially synthesized base pair "into the machinery of life" where the semi-synthetic component functions alongside the natural components..

First, the team had to engineer base pairs that could be recognized by DNA polymerase, a natural enzyme that replicates DNA. After examining some 300 different analogues, in 2009, researchers zeroed in on two molecules known as d5SICS and dNaM after they observed that in a test tube, these molecules worked very well with DNA polymerase.

After figuring out which molecules would be compatible with the enzyme, the team then attempted to introduce these into a living cell.

What they needed was a "transporter" that could effectively deliver the components – one at a time – into the cell. "We borrowed the triphosphate transporter from a species of microalgae," says Romesberg.

“That was a big breakthrough for us — an enabling breakthrough,” said Denis A. Malyshev, a member of the Romesberg laboratory who was lead author of the paper, in a press release.

After the tools were in place, the team got down to the actual process of introducing the components into the bacterium.

E. coli cells were chosen for the experiment because, along with their large main chromosome, they contain plasmid that can be easily manipulated. The plasmid is a circular stretch of DNA and is slightly smaller than the main bacterial chromosome.

Researchers introduced two different stretches of DNA within the bacterial cell – a synthetic plasmid containing the base pair and a plasmid containing the gene capable of encoding the transporter.

The transporter could then help bring the artificial base pair into the cell so that DNA polymerase could replicate the genome with it.

The team observed that the E. coli cells could successfully integrate the synthetic base pair within their genome along with the natural base pairs of adenine–thymine and cytosine–guanine. What's more, the synthetic base pairs persisted in successive E. coli cultures.

By introducing new base pairs, organisms could be made to code for proteins that could be used for specific purposes, such as nanotechnology, medicine, or manufacturing.

This experiment is the first successful attempt made by scientists to integrate a completely foreign base pair within a cell, but the idea of engineering a synthetic life is not new.

According to the Scientific American, Steven Benner, "then at the Swiss Federal Institute of Technology in Zurich, and his team coaxed modified forms of cytosine and guanine into DNA molecules. In test-tube reactions, strands made of these 'funny letters', as Benner calls them, copied themselves and encoded RNA and proteins."

Very recently, researchers managed to create the very first synthetic eukaryotic chromosome by rebuilding yeast chromosome III. Dubbed synIII, this new chromosome is much smaller, with 43,000 or so fewer base pairs in its chromosome III than nature gave it.  

Those critical of synthetic life are asking how safe it is to tamper with nature. Romesberg says that an E.coli cell cannot manufacture the DNA containing the unnatural base pairs on its own. But there are indeed huge risks associated with synthetic biology, especially what the Presidential Commission for the Study of Bioethical Issues calls an "inadvertent release of a laboratory-created organism into nature and the potential adverse effects of such a release on ecosystems," according to the Presidential Commission for the Study of Bioethical issues.