Scientists develop a self-destruct button for DNA

Christopher Voigt dreams of programming living cells the same way engineers program robots. Over the last few years, the MIT bioengineer and a small army of researchers have created a programming language for life, allowing scientists to coerce cells to do all sorts of things nature never intended them to do. So far, they’ve gotten yeast to produce painkillers and bacteria to make biofuels. But their ambitions are much grander than that. They want to be able to program our bodies to delete diseases like Alzheimer’s disease and cancer.

Part of that quest involves gene-editing, a process in which scientists replace parts of an organism’s natural DNA with bits that change what the cells do. The most promising gene-editing technique in use now is called CRISPR, short for clustered regularly interspaced short palindromic repeats. Multiple labs around the world are testing out the technology in various organisms. Most recently, a group in China used it to reprogram human embryos and remove genes that would cause a blood disease. But the cool thing about CRISPR is that even though it’s a tool for synthetic biology, it’s actually a completely natural process bacteria use as a defense mechanism against viruses.

The fact that CRISPR evolved to pinpoint specific viral gene sequences gives it a leg up over other gene-editing techniques out there. Scientists can design CRISPR systems to target just about any gene.  For that reason, it’s been hailed as one of the most powerful tools in modern molecular biology by many high-profile scientists, Voigt included. In theory, it lets you insert any gene into any organism’s cells much more easily than ever before.

Most CRISPR applications have focused on adding new gene sequences and fixing malfunctioning ones. But, drawing on previous research, Voigt saw an opportunity to harness the technique to delete specific DNA sequences, in particular novel DNA sequences that had been artificially inserted into bacterial genomes, leaving the rest of the genome intact. In theory, when the synthetic DNA that makes a particular GMO resistant to certain pathogens is chewed away by CRISPR, that organism should go back to “normal.”

While it’ll be years before this technique can be used in humans , for instance, to un-modify immune system cells that have been engineered to fight cancer more effectively, Voigt’s latest work is very exciting for the titans of the GMO industry. Published in a new study today in the journal Nature Communications, it shows how CRISPR could be used to protect genetic intellectual property—by self-destructing synthetic sequences—and to allay GMO fears by keeping genetically modified organisms from spreading in the wild.

Rodolphe Barrangou, a CRISPR expert at North Carolina State University, who used the gene-editing technique to defend the good bacteria in your yogurt, says that controlling the dissemination of bioengineered strains is a huge concern for all companies in the food, agricultural and biotech industries. While activists worry about genetic modifications getting into the wild, these companies have a parallel concern: that their valuable genetic modifications will be stolen by competitors. “Just killing the strain is not good enough, especially when people have access to quick, powerful and cheap ways to sequence DNA,” said Barrangou, who wasn’t involved in the study.

For biotech companies, that’s important because their intellectual property is written into the genes of their genetically modified organisms, like the pathogen-resistant bacteria Barrangou worked on while he was at Dupont. In many cases, says Voigt, companies won’t even seek patents because doing so would require that they disclose the sequences they want to keep secret. The trouble comes when they dispose of their prized microbes. For instance, Novo Nordisk A/S, a pharmaceutical company, gets rid of old bioengineered microbes by putting them into NovoGro, a common agricultural fertilizer used in Denmark. It’s a move to leverage its biotrash to fertilize plants, but that means the plant food has the carcasses of the company’s proprietary genetic work. Before disposing them, the company kills them off using heat and other methods so they won’t run amok, but much of the bugs’ DNA, according to research, is still intact, meaning that enterprising sleuths could use that genetic slush to fish out the DNA Novo Nordisk has spent years creating, reverse engineer the company’s microbes, and possibly uncover some of its trade secrets. That could amount to millions of dollars in losses.

Potential applications of Voigt’s technology, though, says Barrangou go beyond safeguarding industry interests. It could be used as a general containment and environmental protection method. There’s a lot of debate about how GMOs might affect naturally occurring plants and animals. If the genetically modified part of an organism could be systematically “erased,” that could help assuage public concern. After all, the GMO part would be gone. And when scientists need to work with potentially dangerous pathogens, such as deadly strains of avian flu, the bugs could theoretically be bioengineered with Voigt’s killer CRISPRs, so they would self-destruct and minimize the risk for an accidental outbreak.

“There’s a lot of interest in trying to create organisms that you can safely put out in a natural environment to perform a specific function,” Voigt told me. “A lot of efforts have been made around creating [biological] kill switches. We’re building on that, so that [a bacterium] wouldn’t just kill itself, but delete its synthetic DNA before doing that.” It’s like the biological version of hitting CTRL-Z.

Voigt’s study in genetic self-destruction was conducted on E. coli, a bacterium commonly used for research, known in non-scientist circles for being left on unwashed lettuce and causing severe food poisoning. Voigt and Brian Caliando, a postdoctoral researcher in his lab, did experiments introducing a plasmid—a chunk of DNA—into E. coli’s genome, along with a CRISPR-based DNA-deleting system that could be turned on and off. The researchers used a sugar called arabinose as the molecular on-off switch. When the team’s E. coli detected the sugar, it set off a chain reaction that ultimately led to the degradation of the synthetic DNA plasmid. To make sure their self-destruct button was working as it should, they had to make sure the CRISPR system was only activated by this particular sugar compound. If the deletion sequence could be set off too easily, the bioengineered microbe would be defective, like a spaceship that tries to keep self-destructing instead of taking you around the solar system.

One big step forward here is that Voigt and Caliando’s CRISPR system is responsive to environmental cues. But for this to work in the real world, it would have to be responsive to more types of stimuli. His lab has already engineered biosensors that can be activated at specific temperatures or by the presence of oxygen, certain metals or wavelengths of light. For instance, let’s take those painkiller-producing yeast that made headlines this week. If they could be engineered to only grow in the presence of a metal, then as soon as someone tried to grow yeast without that metal, they’d stop producing drugs. The plan is to use these biosensors as switches in new CRISPR systems. If they succeed, that could make the technology useful outside the lab.

For now, the research, which is being funded by DARPA—the Defense Department’s research arm—is most readily applicable to simple organisms like bacteria and yeast. Scientists hope to harness the technology in more complex organisms, like plants and mammals, but that could take years because scientists just don’t have as deep an understanding of their more complex genomes. For bacteria, researchers have pretty well-defined DNA libraries, repositories of known DNA sequences with known functions they can mix and match like legos to produce a specific function. That’s just not possible in most other systems.

“As an engineer you want to go to a book and have all these DNA sequences and know what they code for in a way that’s been characterized so you can tinker with them to get the system that you want,” Voigt told me. If you can’t predict with certainty how a synthetic system is going to behave, it could lead to trouble, so scientists want to be careful.

As new applications develop, another thing to keep in mind, says Barrangou — the North Carolina State University CRISPR expert — is who actually owns the patents for the CRISPR techniques that Voigt and Caliando leveraged for this study. The research dates back to 1987, and Barrangou says, it’s unclear at this point who owns the patents. The researchers don’t go into it much in the paper, which Barrangou finds surprising, especially given the patent wars we’ve seen unfold for other CRISPR technologies as investors and institutions pour millions of dollars into this space. Voigt’s research is impressive and important, he said, but if the community doesn’t figure out who owns the intellectual property, the availability of these methods might not be as widespread as some would have predicted.

“CRISPR intellectual property is challenging, difficult, volatile and unpredictable,” he said. In other words, the next patent battle might be over who owns the rights to the tools that enforce genetic property rights.

Daniela Hernandez is a senior writer at Fusion. She likes science, robots, pugs, and coffee.