How a CRISPR Protein Could Lead to New Virus Tests

 Jan 04, 2023

According to photos taken using a cryo-electron microscope, a Cas12a2 protein unzips a DNA double helix in order to break DNA single strands (blue and green). Jack Bravo credited with the University of Texas at Austin

Austin, Texas A recently discovered protein has been found to function as a sort of multipurpose self-destruct system for bacteria, capable of breaking down single-stranded RNA, single-stranded DNA, and double-stranded DNA. This is a first for the genetic toolkit known as CRISPR. According to the authors of a recent research published in the journal Nature, the discovery has potential for the creation of new low-cost and extremely sensitive at-home diagnostic tests for a variety of infectious illnesses, including COVID-19, influenza, Ebola, and Zika.

When this protein, Cas12a2, connects to a particular sequence of genetic material from a potentially hazardous virus, termed a target RNA, the scientists observed that a side section of Cas12a2 swings out to disclose an active site, resembling a spring-loaded switchblade knife. Then, any genetic material that comes into touch with the active site is chopped without regard for context. The discovery that the Cas12a2 protein's active site exclusively breaks down single-stranded DNA with a single mutation is particularly helpful for the development of novel diagnostics that are specifically suited for any of a vast variety of viruses.

Theoretically, a test based on this technique might combine the greatest qualities of quick at-home diagnostic tests with the best qualities of PCR-based tests that identify genetic material from a virus (high sensitivity, high accuracy, and the capacity to detect a current infection) (inexpensive to produce without requiring specialised lab equipment). It would also be simple to modify for any new RNA virus.

As co-corresponding author of the new study and an associate professor of molecular biosciences at The University of Texas at Austin, David Taylor said, "If some new virus comes out tomorrow, all you'd have to do is figure out its genome and then change the guide RNA in your test, and you'd have a test against it."

The team's modified Cas12a2 protein, the piece of guide RNA that serves as a mugshot to identify a particular virus, and a fluorescent probe designed to light up when its single-stranded DNA gets cut would need to be combined with saliva or a nasal sample from the patient for this diagnostic, which would still require separate work.

The term "CRISPR" refers to a collection of tools that are found naturally in bacteria and have been modified by researchers for use in gene editing. This CRISPR protein is the first to be discovered to be able to destroy such a variety of genetic material.

The DNA double helix is essentially grabbed by cas12a2 and bent extremely tightly, according to Jack Bravo, a postdoctoral fellow at UT Austin and a co-first author on the study. The middle helix splits apart as a result, allowing the active site to cut up the single-stranded DNA into smaller pieces. Cas12a2 differs from all other DNA-targeting mechanisms due to this.

Thomson Hallmark and Ryan Jackson, both of Utah State University, are co-first authors on the article and co-corresponding authors. Chase Beisel of the Helmholtz Centre for Infection Research and the University of Würzburg in Germany and Bronson Naegle of Utah State are the other co-authors.

The University of Texas at Austin's Sauer Structural Biology Laboratory's cryo-EM capabilities were used to gather structural data.

The Cas12a2 protein has been modified in a patent application by Taylor, Bravo, Hallmark, and Jackson to allow it to solely cut single-stranded DNA and for diagnostic purposes. The intellectual property is being managed by the UT Austin Office of Technology Commercialization, which is also looking for business partners to assist the technology reach its full potential.

The German Federal Agency for Disruptive Innovation, the Welch Foundation, the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation, the National Institute of General Medical Sciences of the National Institutes of Health, and other organisations contributed to the funding of this research. David Taylor is a Cancer Prevention and Research Institute of Texas (CPRIT) scholar.

The biological roles of Cas12a2 are detailed in a companion publication in the same issue of Nature, whereas the processes by which the protein fulfils these roles are discussed in the paper referenced in this press release.