Rice team makes CRISPR enzyme 100-fold more sensitive, in lab

Scientists have long used CRISPR, the gene-editing tool, to make precise changes to DNA. Its cousin Cas13a works on something else: RNA, the genetic material carried by viruses such as HIV. At Rice University, a team has now made Cas13a 100 times more sensitive, in lab tests, at spotting that RNA. The work was led by associate professor Yang Gao and graduate student Seye Oladeji, who is the first author of the study published in Cell Chemical Biology.

The problem they set out to solve was a familiar one in diagnostics. A detection test uses an enzyme that binds to a target strand of RNA and then produces a signal, such as a colour change, that a person or a machine can read. Most such assays need harsh conditions to produce that signal. The team's starting version of Cas13a could handle those conditions, but it missed very small amounts of the target. Oladeji's stated ideal is a test that detects as little as one strand of RNA per microliter, around a drop of blood. The starting enzyme was far from that.

The fix began with the protein's shape. Cas13a moves a great deal when it binds its target, which makes its structure hard to capture in fine detail. Oladeji designed a way to hold the enzyme and its RNA target still long enough to resolve it. With the structure in hand, the team picked two candidate regions and tested them in the lab. Altering both made the enzyme too sensitive, so it signalled even without the target. Altering just one raised sensitivity 100-fold, with no loss of stability. The engineered enzyme was then tested against a synthetic, noninfectious HIV sample, where it worked with the same 100-fold improvement.

What changes for diagnostics is that the detection target can be swapped. The enzyme is paired with a guide sequence, and the guide is easy to reprogram. The team says the same enzyme could be redirected to SARS-CoV-2, influenza, Ebola, Zika, respiratory syncytial virus or hepatitis C virus. Gao argues that the enzyme itself is the critical part, and his team's version is "optimized for sensitive and stable RNA detection assays" that could potentially be used in commercial tests like RT-qPCR and lateral flow. Those are conditional words, and the study does not test any of these uses. The researchers give no timeline, and the results so far come from lab samples, not from patients or field sites. For a clinic or a water-testing lab, the practical gain would come only once the enzyme is built into a commercial kit and checked against real samples.