Cas13a

The Cas13a gene editing system, a groundbreaking advancement in CRISPR technology, enables precise RNA targeting and manipulation without altering DNA. Unlike DNA-editing Cas9, Cas13a uses a single RNA-guided endonuclease to bind and cleave specific RNA sequences, leveraging two distinct ribonuclease activities: one for processing its own CRISPR RNA (crRNA) and another for degrading target RNA.^[1][2][3] This system’s RNA-directed specificity allows it to correct disease-causing mutations at the transcript level—such as repairing KRAS-G12D mRNA in pancreatic cancer with >90% efficiency while sparing healthy cells^[1] and has been adapted into tools like the REPAIR platform, which edits RNA bases to treat genetic disorders like Usher syndrome in animal models. Beyond therapeutics, Cas13a's collateral RNA-cleavage activity underpins diagnostic innovations like SHERLOCK, achieving attomolar sensitivity for detecting pathogens, tumor DNA, and viral variants.^[3] Its PAM-independent targeting and minimal off-target effects further position it as a versatile tool for RNA imaging, phage genome engineering, and transient gene regulation, offering safer alternatives to traditional DNA-editing approaches.^[2]

History

In 2016, the nuclease Cas13a (formerly known as C2c2) from the bacterium Leptotrichia shahii was characterized by researchers in Feng Zhang's group at MIT and the Broad Institute. Cas13 is an RNA-guided RNA endonuclease, which means that it does not cleave DNA, but only single-stranded RNA. Cas13 is guided by its crRNA to a ssRNA target and binds and cleaves the target. Similar to Cas12a, the Cas13 remains bound to the target and then cleaves other ssRNA molecules non-discriminately.^[4] This collateral cleavage property has been exploited for the development of various diagnostic technologies.^[5][6][7]

In 2018, a team led by Silvana Konermann and Patrick Hsu at the Salk Institute reported the discovery of Cas13d, a new subclass of compact RNA-targeting CRISPR effectors. An engineered variant of Ruminococcus flavefaciens Cas13d, termed CasRx, exhibited robust activity in human cells, with high efficiency and specificity relative to RNA interference, and could be packaged into adeno-associated virus (AAV) for applications in transcriptome engineering and gene therapy.^[8]

In 2021, researchers in China characterized novel miniature Cas13 protein (mCas13) variants, Cas13X and Cas13Y. Using a small portion of N gene sequence from SARS-CoV-2 as a target in characterization of mCas13, revealed the sensitivity and specificity of mCas13 coupled with RT-LAMP for detection of SARS-CoV-2 in both synthetic and clinical samples over other available standard tests like RT-qPCR (1 copy/μL).^[9]

Applications

Scientists have discovered how to turn Cas13, a naturally occurring RNA-cutting protein, into a kind of RNA “editor” that can fix certain mutations without touching the DNA. This system, called REPAIR, starts with a modified version of Cas13 known as dCas13, which still finds and binds to target RNA but no longer slices it. Researchers then attach a part of an enzyme called ADAR2 to it—this enzyme has the special ability to change one letter in RNA, an “A,” into another molecule called “I,” which the cell reads as a “G.” By guiding this combined tool to a specific spot on the mRNA with a small mutation that causes disease, they can correct the error on the spot.^[10]

When combined with a high-accuracy ADAR2 variation REPAIR repairs about half of its targets in dish-based tests with very few unwanted modifications. Scientists have also encapsulated the dCas13–ADAR system in harmless viral carriers and administered them to Usher syndrome modeling mice's eyes. The treatment was successful and restored the missing usherin protein, rewrote the defective transcripts, and also enhanced the animals' vision. The results provide some proof that Cas13-mediated RNA editing can be a adjustable and safe method of treating genetic disorders.^[11]

In another part of the research, scientists fine-tuned this system even further. They made small changes to Cas13’s structure to create “dead” Cas13b, which can still find its target but won’t cut anything. Then they paired it with a guide RNA designed to match up perfectly with the target—except for one small A-to-C mismatch right where the edit needs to happen. This guide leads the ADAR2 enzyme to make a precise change to that single base. In early tests with human cells, the edits worked reliably within a 30-nucleotide range, hitting the right spot about 50% of the time and barely affecting anything else nearby.^[12]