If you ask Kevin Weeks, he’s sitting on a technological gold mine. Although he predicts it’ll take two years before RNA researchers can get their hands on the fruits of his research, “we think this will become the PCR of RNA secondary structure analysis,” he says.
Weeks’ enthusiasm is understandable. The PI of an NSF-funded grant for high-throughput RNA analysis designed to study the structure of these molecules and how that affects function in a cell, he and his team at the University of North Carolina, Chapel Hill, have been working on this technology for several years. The methods available today for studying RNA structure are essentially the same as they were 20 years ago, he says, and are characterized by being “extremely laborious and time-consuming.” He adds, “RNA structure analysis is the kind of experiment that currently is not done as often as it should be because it’s so hard.”
Weeks’ lab members, who explore RNA and RNA-protein interactions, found that their studies were hamstrung by the status quo technology used to evaluate RNA structure. Several years ago, he and his crew began delving into the chemistries used to glean information on RNA structure and came across a new method that seemed much more effective and accurate than its predecessors. The uniqueness of each RNA base proved to be a major challenge, but one that Weeks believes he has overcome: “We’ve developed chemistry that reacts at the ribose component of RNA,” he explains. “Since every nucleotide has a ribose group, every nucleotide is potentially reactive.”
In practice, the technology works this way: using purified or in vitro synthesized RNA, researchers coax the molecule to fold, and then use Weeks’ chemistry. That work is analyzed by a cDNA synthesis step using a fluorescently labeled detection technology, and “the final output is a nucleotide reactivity profile for your entire RNA,” he says. The reactivity highlights positions that are flexible or unconstrained, and can allow scientists to “rapidly design optimal sites as targets for antisense technologies or siRNA approaches,” Weeks says. Comparisons of reactivity between wild type and mutant RNA could be used to determine a structural basis for pathogenic mutations or other changes involved in RNA regulation, he adds.
In the not-too-distant future, Weeks envisions the technology being used at a core facility where researchers could send in a sample and get their structure back in a couple of days. Ultimately, he hopes that it will help solve long-standing biological problems such as whether RNA folding is hierarchical.
In the meantime, though, Weeks has plenty of hard work ahead of him to get the technology in shape for the labs of other scientists. “The basic idea of the project is to make it possible — almost trivially possible — to analyze the structure of RNA,” he says. No doubt other RNA scientists wish it would be so easy to translate his concept into a robust research tool.
— Meredith Salisbury