Synthetic Genetic Evolution

Scientists show that manmade nucleic acids can replicate and evolve, ushering in a new era in synthetic biology.

Apr 19, 2012
Ruth Williams

WIKIMEDIA COMMONS, CHRISTOPH BOCK (MAX PLANCK INSTITUTE FOR INFORMATICS)

Synthetic genetic polymers, broadly referred to as XNAs, can replicate and evolve just like their naturally occurring counterparts, DNA and RNA, according to a new study published today (April 19) in Science. The results of the research have implications not only for the fields of biotechnology and drug design, but also for research into the origins of life—on this planet and beyond.

“It’s a breakthrough,” said Gerald Joyce of The Scripps Research Institute in La Jolla, California, who was not involved in the study—“a beautiful paper in the realm of synthetic biology.”

“It shows that you don’t have to stick with the ribose and deoxyribose backbones of RNA and DNA in order to have transmittable, heritable, and evolvable information,” added Eric Kool of Stanford University, California, who also did not participate in the research.

Over the years, scientists have created a range of XNAs, in which the ribose or deoxyribose portions of RNA and DNA are replaced with alternative molecules. For example, threose is used to make TNA, and anhydrohexitol is used to make HNA. These polymers, which do not exist naturally, are generally studied with various biotechnological and therapeutic aims in mind.  But some researchers, like Philipp Holliger of the MRC Laboratory of Molecular Biology in Cambridge, UK, think XNAs might also provide insights into the origins of life. They might help to answer questions such as, “why is life based on DNA and RNA, and, if we ever find life beyond earth, is it likely to be based on the same molecule or could there be other possibilities?” Holliger said.

To get at some of these questions, Holliger and his colleagues had to first create enzymes that could replicate XNAs, a necessary first step to evolution. They did this both by randomly mutating and screening existing DNA polymerases for their ability to read XNA, and by an iterative process of selecting polymerase variants with capacities for XNA synthesis. In the end, they had several polymerases that could synthesize six different types of XNA.

To see whether XNAs could evolve, they generated random HNA sequences, then selected for those that could bind to two target molecules. After selection, the HNAs were amplified by the newly designed polymerases and again selected for their ability to bind the targets. Eight rounds of selection later, the HNA sequences were no longer random, as those with a particular target-binding motif became more abundant. Through selection and replication, the HNAs had evolved.

The finding in itself is not surprising, said Kool. “Chemists have been working for 20 years to find new backbones for DNA and the feeling always was that it would be interesting and quite possible that some of them might be replicated one day.” It was, nevertheless, impressive, he added. “The hard part was finding the enzymes that could do it. So the big leap ahead for this paper was finding those enzymes.”

The new polymerases synthesized XNA through rounds of DNA-to-XNA and XNA-to-DNA synthesis. Generating polymerases that can make XNA direct from XNA will be the next step, Holliger said, but it will be a lot harder “because both strands would be foreign to the polymerase.”

Holliger also explained that there was actually a benefit to having a DNA intermediate. “It allowed us to access the whole gamut of technologies that are available for analyzing DNA sequences.” Working with XNAs uniquely, he said, “is like being thrown back to the way molecular biology was in the early 1970s, in that we have to develop all our tools afresh.”

Holliger’s polymerases maybe the first addition to the XNA toolbox but, as more tools are created the potential for XNA biology will grow, said Jack Szostak of Harvard Medical School, who was not involved in the study. “In the longer run, it may be possible to design and build new forms of life that are based on one or more of these non-natural genetic polymers,” he said. That said, “I think it’s too early to say whether such novel life-forms would have any practical applications,” he added.

Regardless of what the future holds, the new polymerases could have applications right away. “We hope to be able to evolve XNA aptamers”—molecules that bind specific targets—“against medically interesting targets,” Holliger said. Scientists are already creating DNA and RNA aptamers, but their use in the body is severely hampered by their susceptibility to naturally occurring nucleases that degrade DNA and RNA. “XNAs are not natural and so are not susceptible to nucleases,” explained Joyce. “These things are bullet-proof.”

Beyond the medical applications of the work, Holliger is finally getting some answers about the basis of life. “The exciting finding of our work is that there really seems to be many possibilities,” he said. “There isn’t anything Goldilocks about DNA or RNA.” Does this mean that life elsewhere in the cosmos is more likely than previously thought? “I would say a cautious yes,” said Holliger.

V.B. Pinheiro et al., “Synthetic Genetic Polymers Capable of Heredity and Evolution,” Science, 336: 341-44, 2012.