New research has brought us closer than ever to synthesizing entirely new forms of life. An international team of researchers has shown that artificial nucleic acids – called “XNAs” – can replicate and evolve, just like DNA and RNA.
We spoke to one of the researchers who made this breakthrough, to find out how it can affect everything from genetic research to the search for alien life.
The researchers, led by Philipp Holliger and Vitor Pinheiro, synthetic biologists at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, say their findings have major implications in everything from biotherapeutics, to exobiology, to research into the origins of genetic information itself. This represents a huge breakthrough in the field of synthetic biology.
The “X” Stands for “Xeno”
Every organism on Earth relies on the same genetic building blocks: the the information carried in DNA. But there is another class of genetic building block called “XNA” — a synthetic polymer that can carry the same information as DNA, but with a different assemblage of molecules.
The “X” in XNA stands for “xeno.” Scientists use the xeno prefix to indicate that one of the ingredients typically found in the building blocks that make up RNA and DNA has been replaced by something different from what we find in nature — something “alien,” if you will.
Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of three chemical components: a phosphate (labeled here in red), a five-carbon sugar group (labeled here in yellow, this can be either a deoxyribose sugar — which gives us the “D” in DNA — or a ribose sugar — hence the “R” in RNA), and one of five standard bases (adenine, guanine, cytosine, thymine or uracil, labeled in blue).
The molecules that piece together to form the six XNAs investigated by Pinheiro and his colleagues (pictured here) are almost identical to those of DNA and RNA, with one exception: in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA (corresponding to the middle nucleotide component, labeled yellow in the diagram above) have been replaced. Some of these replacement molecules contain four carbons atoms instead of the standard five. Others cram in as many as seven carbons. FANA (pictured top right) even contains a fluorine atom. These substitutions make XNAs functionally and structurally analogous to DNA and RNA, but they also make them alien, unnatural, artificial.
Information Storage vs Evolution
But scientists have been synthesizing XNA molecules for well over a decade. What makes the findings of Pinheiro and his colleagues so compelling isn’t the XNA molecules themselves, it’s what they’ve shown these alien molecules are capable of, namely: replication and evolution.
“Any polymer can store information,” Pinheiro tells io9. What makes DNA and RNA unique, he says, “is that the information encoded in them [in the form of genes, for example] can be accessed and copied.” Information that can be copied from one genetic polymer to another can be propagated; and genetic information that can be propagated is the basis for heredity — the passage of traits from parent to offspring.
In DNA and RNA, replication is facilitated by molecules called polymerases. Using a crafty genetic engineering technique called compartmentalized self-tagging (or “CST”), Pinheiro’s team designed special polymerases that could not only synthesize XNA from a DNA template, but actually copy XNA back into DNA. The result was a genetic system that allowed for the replication and propagation of genetic information.
A simplified analogy reveals the strengths and weaknesses of this novel genetic system: You can think of a DNA strand like a classmate’s lecture notes. DNA polymerase is the pen that lets you copy these notes directly to a new sheet of paper. But let’s say your friend’s notes are written in the “language” of XNA. Ideally, your XNA-based genetic system would have a pen that could copy these notes directly to a new sheet of paper. What Pinheiro’s team did was create two distinct classes of writing utensil — one pen that copies your friend’s XNA-notes into DNA-notes, and a second pen that converts those DNA notes back into XNA-notes.
Is it the most efficient method of replication? No. But it gets the job done. What’s more, it does all this copying to and from DNA with a high degree of accuracy (after all, what good is replication if the copy looks nothing like the original?). The researchers achieved a replication fidelity ranging from 95% in LNA to as high as 99.6% in CeNA — the kind of accuracy Pinheiro says is essential for evolution:
“The potential for evolution is closely tied with how much information is being replicated and the error in that process,” he explains. “The more error-prone… a genetic system is, the less information can be feasibly evolved.” A genetic system as accurate as theirs, on the other hand, should be capable of evolution.
The researchers put this claim to the test by showing that XNA strands made up of the HNA xeno-nucleotides like the one pictured here could evolve into specific sequences capable of binding target molecules (like an RNA molecule, or a protein) tightly and specifically. Researchers call this guided evolution, and they’ve been doing it with natural DNA for some time. The fact that it can also be accomplished in the lab with synthetic DNA indicates that such a system could, in theory, work in a living organism.
“The HNA system we’ve developed,” explains Pinheiro, is “robust enough for meaningful information to be stored, replicated and evolved.”
A Step Toward Novel Lifeforms
The implications of the team’s findings are numerous and far-reaching. For one thing, the study sheds significant light on the origins of life itself. In the past, investigations into XNA have been largely driven by the question of whether simpler genetic systems may have existed before the emergence of RNA and DNA; the fact that these XNAs appear to be capable of evolution adds to an ever-growing body of evidence of a genetic system predating DNA and RNA both.
Practical and therapeutic applications abound, as well. “The methodologies [we’ve developed] are a major step forward in enabling the development of nucleic acid treatments,” says Pinheiro. Natural nucleic acids [i.e. DNA and RNA] can be forced to evolve so that they bind tightly and specifically to specific molecular targets. The problem is that these nucleic acids are unsuitable for therapeutic use because they are rapidly broken down by enzymes called nucleases. As a result, these evolved nucleic acid treatments have a short lifespan and have a difficult time reaching their therapeutic targets.
To get around this, Pinheiro says medicinal chemistry is used to modify evolved DNA sequences in an attempt to create a functional molecule that can still bind to a therapeutic target but resist nuclease degradation. But doing this is tough:
“Overall, this leads to high cost and a high failure rate for potential therapies – there is still only a single licenced [nucleic acid-based] drug on the market (Macugen).”
But all six of the XNAs studied by Pinheiro and his team are stronger than regular DNA or RNA, in that they’re more resistant to degradation by biological nucleases.
As a result, these molecules would need little or no adaptation for therapeutic (or diagnostic) use. “Since these molecules can now be selected directly on XNA, medicinal chemistry should no longer be limiting,” says Pinheiro. You could select a suitable XNA for its biocompatibility and therapeutic potential, and not worry about having it rapidly degrade inside the body.
Pinheiro also says the outcome of the research could even have a strong impact on exobiology:
In my view, exobiology looks for life in regions it cannot physically visit. In that context, it searches for tell tale signs of life that can be remotely monitored but it has only life on Earth as examples to identify such suitable markers. Based on extant biology, DNA and RNA are good candidates for such a search. However, by showing that other nucleic acids can also store information, replicate and evolve, our research may force a rethink as to whether DNA and RNA are the most suitable tell tale signs of life.
Of course, nothing would call the indispensability of DNA- or RNA-based life into question more than the generation of an entirely synthetic, alternative life form, built from the ground up entirely by XNA. Such an organism would require XNA capable of driving its own replication, without the aid of any biological molecules. Pinheiro says that’s still a ways off. “Even in its simplest setup… it would be very challenging to develop an XNA system within a cell.” Such a system would require XNA capable of self-replication, and capable of undergoing evolution in a self-sustained manner.
That said, his team’s work represents a major step in the right direction. As the molecular machinery designed to manipulate XNAs grows, so, too, will the capacity for synthetic genetic systems to stand and operate on their own.