Organism with Artificial DNA Bases Marks Milestone in Synthetic Biology

By Bio-IT World Staff

May 8, 2014 | A paper by a team of researchers from the Scripps Institute, published yesterday in Nature, describes the first stable, self-replicating organism whose DNA contains bases other than the well-known A, G, C and T. The research group, led by Floyd Romesberg, has long been a leader in the field of synthetic DNA, creating new bases that are capable of pairing, replicating and being transcribed into RNA in vitro; however, it was not previously clear whether any artificial base pairs are stable enough to replicate on their own in a living organism.

The new base pairs introduced into the Scripps lab's partially synthetic organism, called d5SICS and dNaM, were selected after randomly screening combinations of 60 different artificial bases to find two with the most promising properties as a pair. To avoid cross-talk between the new bases and the naturally occurring ones, d5SICS and dNaM do not form hydrogen bonds with each other, like adenine and thymine or guanine and cytosine. Instead, the synthetic bases are both strongly hydrophobic, and join without forming atomic bonds.

A great deal of engineering went into the creation of an organism that could adopt these bases into its native DNA. Neither d5SICS nor dNaM can yet be synthesized in vivo, so a strain of E. coli had to be engineered to express a transport protein found in diatomic algae, which allows the bacterium to import the new bases through its membrane. Fed on a steady diet of d5SICS and dNaM, the organism is able to maintain, reproduce, and even transcribe into RNA a stretch of genetic material containing the artificial bases.

The limitations of this first experiment with in vivo synthetic DNA bases are severe. Each bacterium contains just a single base pair of d5SICS and dNaM, which is contained not inside the E. coli chromosome, but in a small, separate plasmid. Without a constant outside supply of the new bases, they will quickly disappear, and while they can be transcribed into RNA, they do not code for any protein or have any function. Still, Romesberg and his group are optimistic that organisms such as this could one day have a wide variety of uses. They imagine making bacteria that use synthetic bases to code for new amino acids, allowing them to express proteins that no naturally occurring organism could produce. Such bacteria might be used to mass produce drugs or other useful compounds, unlimited by the library of 20 amino acids that all life on Earth currently works with. Romesberg and his colleagues have formed a new company, Synthorx, to move toward these commercial applications.

It should be stressed that serious challenges would need to be overcome for this model to be viable. No one has yet moved all the way from synthetic DNA bases to proteins, even in vitro, and it remains to be seen whether an organism could successfully incorporate a larger number of synthetic bases into its DNA. Nevertheless, an exciting milestone has been passed in synthetic biology, which for the first time opens the possibility of organisms that do not use the same essential code of four bases and 20 amino acids shared by all known life.