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Cas13 (also written Cas 13) is a family of CRISPR-associated enzymes that find and cut RNA rather than DNA. A short guide RNA steers the enzyme to a matching RNA sequence, and the enzyme’s two HEPN domains then cleave RNA. Once active, Cas13 can also cut nearby RNAs it was not aimed at, a behaviour called collateral cleavage that is useful in diagnostics and a confound in cell experiments.
Short answer
Cas13 is a class 2, type VI CRISPR effector: a single protein that, guided by a CRISPR RNA (crRNA), binds complementary RNA and cleaves it. It is used to knock down RNA, to track or edit RNA when a catalytically dead version (dCas13) is used, and to detect nucleic acids in the SHERLOCK diagnostic method.
Definition and scope
Cas13 belongs to the class 2, type VI CRISPR systems. Class 2 means the whole effector is a single protein, in contrast with multi-protein class 1 complexes. The family now has 11 described subtypes (Cas13a through Cas13i, plus Cas13x and Cas13y). In mammalian cells, Cas13a, Cas13b and Cas13d are the subtypes most often used.
The key contrast with Cas9 is the target. Cas9 cuts DNA; Cas13 acts on RNA and leaves the genome unchanged. Another difference is that, in eukaryotic cells, Cas13 shows no strong protospacer flanking site (PFS) requirement, so almost any RNA sequence can in principle be targeted. This guide covers the concept and its place in lab work. It is not a protocol. For a DNA-targeting CRISPR approach that activates genes, see CRISPRa.
How Cas13 works
Cas13 carries two HEPN (higher eukaryotes and prokaryotes nucleotide-binding) RNase domains that come together to form one catalytic site. The crRNA directs the protein to a complementary RNA, and the HEPN site then cleaves it.
Two modes matter in practice:
- Cis cleavage. The enzyme cuts the RNA it was guided to.
- Collateral (trans) cleavage. Once activated, Cas13 can also cut other nearby RNAs. This does not depend on those RNAs matching the guide, so it differs from ordinary off-target effects, which come from partial guide complementarity.
When the HEPN domains are mutated, the result is dCas13, which still binds RNA but does not cut it. Researchers have fused dCas13 to other proteins for RNA imaging, splicing modulation, RNA editing (A-to-I and C-to-U), m6A methylation or demethylation, and translation control.
Types and related concepts
| Subtype | Use and collateral activity in mammalian cells |
|---|---|
| Cas13a | Among the three most used in mammalian cells; second-strongest collateral activity of the three in a comparison reported in the 2024 Shi and Wu review. The Cas13a collateral effect underlies SHERLOCK detection. |
| Cas13b | Among the three most used in mammalian cells; weakest collateral activity of the three in the same comparison. |
| Cas13d | Among the three most used in mammalian cells; strongest collateral activity of the three in the same comparison. |
Related ideas: RNA interference (siRNA and shRNA) is the other common route to knock down RNA; see the shRNA knockdown guide. CRISPR-Cas9 edits DNA, and the wider ethics of CRISPR use are covered in CRISPR ethics.
Where it matters for labs and clinics
Cell experiments: a checklist of caveats
Published work on Cas13 in mammalian cells points to several issues worth planning controls around:
- Collateral activity is debated. Early mammalian studies reported none, mostly with low-abundance targets; later studies found substantial collateral cleavage that tracks target abundance and varies by subtype and cell type.
- Mismatch tolerance. A single mismatch between guide and target is tolerated; guide positions 15 to 21 are more sensitive.
- Long spacers. A guide with a 31-nucleotide spacer degraded a viral RNA in mosquito cells without the Cas13 protein present, and spacers longer than 40 nucleotides can form a long duplex that recruits the ADAR1 editing enzyme. Both are Cas13-independent effects.
- Guide-independent effects. Cas13 and dCas13 recognise a short hairpin in the pre-crRNA, and similar hairpins in cellular RNAs may lead to cleavage of endogenous transcripts and toxicity. Cas13 proteins have been reported to cleave endogenous RNAs in vitro without a matching guide.
- Abundant targets. The size of the growth defect has been reported to track target RNA abundance, and one study found reduced cellular metabolic activity and DNA replication.
Diagnostics
SHERLOCK pairs Cas13a collateral cleavage with isothermal amplification. Its authors reported detection of DNA or RNA with attomolar sensitivity and single-base mismatch specificity, applied to Zika and Dengue strains, pathogenic bacteria, human DNA genotyping and cell-free tumor DNA mutations. The reagents could be lyophilized, which removes the need for a cold chain.
Biosafety and oversight
Work that delivers Cas13 constructs, for example with viral vectors, is reviewed like other recombinant nucleic acid work. See institutional biosafety committees and the NIH Guidelines for recombinant and synthetic nucleic acid molecules.
Common misunderstandings
- “Cas13 is just Cas9 for RNA.” The targeting logic is similar, but Cas13 is a different class 2 type (VI), uses HEPN nuclease domains, and has collateral cleavage that Cas9 does not.
- “It has no off-target effects.” Mismatch tolerance, long-spacer effects and collateral cleavage all mean controls are needed.
- “Cas13 edits DNA.” It does not. Even RNA editing with dCas13 changes RNA, not the genome.
- “Collateral cleavage is always a problem.” In SHERLOCK it is the signal; in cell experiments it is a confound.
FAQ
Is “Cas 13” the same as Cas13?
Yes. Both spellings refer to the same family of RNA-targeting CRISPR enzymes.
What does Cas13 target?
RNA. A crRNA guides it to a complementary RNA sequence, and its HEPN domains cleave that RNA.
What is dCas13?
A catalytically dead Cas13 with mutated HEPN domains. It binds RNA without cutting it and is used for imaging, editing and regulation of RNA.
Which Cas13 subtypes are used in mammalian cells?
Cas13a, Cas13b and Cas13d are the most widely used.
What is collateral cleavage?
After Cas13 recognises its target, it can also degrade nearby non-target RNAs. This needs no sequence match to the guide, unlike ordinary off-target effects. It is the signal in SHERLOCK diagnostics and a possible confound in cell experiments.
How is Cas13 different from Cas9?
Cas9 targets DNA, while Cas13 targets RNA and leaves the genome unchanged. Cas13 is a type VI effector with HEPN nuclease domains and shows no strong PFS requirement in eukaryotic cells.
Sources
Date checked: 2026-10-29.
- Shi P, Wu X. Programmable RNA targeting with CRISPR-Cas13. RNA Biology 2024;21(1):1-9. DOI 10.1080/15476286.2024.2351657. https://pmc.ncbi.nlm.nih.gov/articles/PMC11110701/
- Gootenberg JS et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017;356(6336):438-442. https://pubmed.ncbi.nlm.nih.gov/28408723/
