John Chaput and his research team are developing new exotic molecules called XNA, that are alternatives to natural DNA and RNA. The team is simultaneously working with these molecules in two very different directions.

In one effort, they are determining whether XNA contributed to the rise of life on Earth. At the same time, the team also is evolving XNA molecules with functions that could be used to diagnose and treat human diseases.

It is multi-tasking at an extreme level.

Chaput’s group, at the Biodesign Institute at Arizona State University, is intent on finding the building blocks of life by fabricating what might have been the very first genetic system on the planet. The XNA molecules they make could have preceded RNA in the evolution of life on Earth.

In addition, because these molecules are so exotic, Chaput also believes they could be used to identify and treat several of today’s more perplexing maladies, including cancer.

Made to order molecules

Everything they do in the lab is novel, Chaput says, and stems from his background in nucleic acid chemistry, molecular biology and genetics.

“We are working on molecules that you can’t buy,” he explains. “You have to make them, which is a challenge. Once we have the molecules in hand, then we need to find enzymes that will recognize them as substrates and polymerize them into long chains of sequence-defined polymers.”

“Nature does this very well with DNA and RNA, but the enzymes to make XNA don’t exist, so we have to discover those too,” he adds. “In the end, this is a huge project.”

The Chaput team recently reported some very encouraging results with a specific type of XNA, called TNA, which substitutes threose for ribose.

Like RNA, TNA is single stranded and carries a genetic code of four letters (A, T, C, and G). But because TNA incorporates threose rather than ribose, it leads to a different backbone structure than RNA.

“As an early genetic polymer, TNA is interesting because it’s chemically much simpler than RNA, which would have made it easier to synthesize on the early Earth,” Chaput says. “TNA also is able to exchange genetic information with RNA, which would have allowed information to pass from one type of genetic polymer to another, for example from TNA to RNA. Carrying it further, maybe that RNA information was passed on to DNA, and that is the world as we know it today.”

Chaput’s group has made TNA substrates and discovered enzymes that recognize the substrates to make TNA polymers. They then took the next step and made TNA libraries, and, most recently, showed that they could evolve TNA in the laboratory.

Chaput says that the team is now taking all of the tools they have developed over the past 10 years and fusing them together to see if they can evolve and manipulate their XNA molecules to do specific tasks, like ligand binding or catalysis.

“Now that we can evolve XNA in the lab, can we create XNA molecules with functions that would make them useful for biotechnology or medicine,” he asks.

“For example, can we create XNA molecules that can bind to small molecules or protein markers,” he asks. “Early work in our lab has shown that this is possible, but we still have a long ways to go to understand the full spectrum of ligand binding.”

The outcomes of these experiments could lead to new ways to detect disease.

“We are interested in developing XNA catalysts that can cut RNA messages and silence gene expression,” Chaput says. “If successful, this could lead to new antisense therapies to treat a wide range of diseases from cancer to inflammatory diseases like asthma and arthritis, or possibly even viral infections like HIV.”

Chaput adds that the XNA molecules are robust.

“Because XNA has an unnatural nucleic acid backbone, these molecules are not recognized by the enzymes inside our cells, which naturally degrade DNA and RNA. This property makes them ideal candidates for these applications,” Chaput adds.