Quick Summary: Cas12 and Cas13 are the two most commonly used CRISPR enzymes for nucleic acid lateral flow detection. Cas12 targets double-stranded DNA, Cas13 targets single-stranded RNA. Both produce collateral cleavage of a labeled reporter that is read by a lateral flow strip. For most diagnostic developers, the choice is dictated by the target nucleic acid type rather than enzyme performance. TiosBio’s LF-detect Cas12/13 Dedicated Strips (JY0301) and Dual-system Dual-target CRISPR Strips (JY0308) support both enzymes in a single product family.
What Cas12 and Cas13 actually do
Both Cas12 and Cas13 are CRISPR effectors with a programmable guide RNA. When the guide RNA recognizes its target, the enzyme is activated and starts to cut nearby nucleic acid molecules indiscriminately — the so-called “collateral cleavage.” Diagnostic assays exploit this by adding a labeled reporter oligo (typically Biotin–FAM or Biotin–TAMRA). When the reporter is cut, the labels separate, and a lateral flow strip detects the resulting label pattern.
- Cas12a (also known as Cpf1) recognizes double-stranded DNA via a TTTV PAM and performs collateral ssDNA cleavage. Used for SHERLOCK-DETECTR-style DNA assays.
- Cas13a (also known as C2c2) recognizes single-stranded RNA and performs collateral ssRNA cleavage. Used for SHERLOCK-style RNA assays.
Direct technical comparison
| Parameter | Cas12 (Cas12a / Cpf1) | Cas13 (Cas13a / C2c2) |
|---|---|---|
| Target nucleic acid | Double-stranded DNA | Single-stranded RNA |
| Recognition motif | TTTV PAM | Protospacer flanking site (PFS) |
| Collateral cleavage substrate | ssDNA reporter | ssRNA reporter |
| Typical reporter labels | Biotin–FAM, Biotin–FITC | Biotin–FAM, Biotin–FITC |
| Reaction temperature | 37 °C (typical) | 37 °C (typical) |
| Reaction time | 5–30 min after amplification | 5–30 min after amplification |
| Pre-amplification needed | Recommended (RPA/RAA/LAMP/PCR) | Recommended (RT-RPA/RT-RAA/RT-LAMP) |
| RT step required | Only if target is RNA → cDNA first | Direct RNA detection |
| LFA strip | JY0301 Cas12/13 Dedicated | JY0301 Cas12/13 Dedicated |
| Common applications | HPV typing, bacterial pathogens, AMR genes | SARS-CoV-2, Influenza, RSV, Dengue, Zika |
Workflow: from sample to lateral flow line
The standard CRISPR-LFA workflow has four stages:
- Sample release: Lyse the sample with a reagent such as TiosBio’s 5× Lightning (BT0066, 10 min @ 95 °C) for blood/swab samples or Cool Flash (BT0068, <1 min RT) for animal/plant samples.
- Pre-amplification: RAA, RPA, LAMP, or PCR. RPApex Basic (JY0800) at 39–42 °C is the most common pairing for both Cas12 and Cas13 workflows.
- Cas detection: Add Cas12 or Cas13 with the guide RNA and labeled reporter. Incubate 5–30 min at 37 °C.
- Lateral flow readout: Apply the reaction to a Cas12/13 Dedicated Strip (JY0301). Read the result visually within 1–2 minutes.
When to choose Cas12
Cas12 is the right choice when:
- Target is genomic or plasmid DNA (e.g., HPV, MRSA, drug resistance genes).
- You can design a guide RNA against a TTTV PAM in the target.
- You want to skip the reverse-transcription step.
- You are pairing with isothermal DNA amplification such as RAA or LAMP.
When to choose Cas13
Cas13 is the right choice when:
- Target is RNA (most respiratory viruses, arboviruses, mRNA biomarkers).
- You want to detect RNA directly without DNA conversion at the detection step.
- You are pairing with RT-RPA, RT-RAA, or RT-LAMP for amplification.
- You want the option to multiplex with orthogonal Cas13 enzymes (Cas13a/Cas13b/Cas13c) for distinct color or label channels.
Multiplexing Cas12 and Cas13 in one strip
For two-target panels covering both DNA and RNA targets — for example, a respiratory-virus panel (RNA) plus an antimicrobial-resistance gene (DNA) — TiosBio’s Dual-system Dual-target CRISPR Strips (JY0308) support simultaneous Cas12 and Cas13 reporting in a single strip. This is uncommon outside specialized OEM workflows and significantly reduces hands-on steps for clinical decision-making in stewardship-driven settings.
Frequently Asked Questions
Can the same strip be used for Cas12 and Cas13 reactions?
Yes. TiosBio’s JY0301 Cas12/13 Dedicated Strip is designed for both Cas12 (ssDNA reporter) and Cas13 (ssRNA reporter) cleavage products, as long as the same Biotin/FAM-style label scheme is used.
Do I need pre-amplification before CRISPR detection?
For diagnostic-level sensitivity, pre-amplification with RAA, RPA, LAMP, or PCR is strongly recommended. Direct CRISPR detection without amplification is possible only at very high target concentrations.
What is collateral cleavage?
Once Cas12 or Cas13 binds its specific target, it becomes broadly active and starts cutting nearby ssDNA (Cas12) or ssRNA (Cas13) molecules indiscriminately. This is what cuts the labeled reporter and produces the lateral flow signal.
Can Cas12/13 detection deliver quantitative results?
Lateral flow readout is qualitative or semi-quantitative. For quantitative readout, fluorescence-based collateral cleavage detection on a basic plate reader is required.
Conclusion
The Cas12 vs Cas13 choice is dictated by your target nucleic acid: Cas12 for DNA, Cas13 for RNA. Both pair naturally with RAA isothermal amplification (RPApex JY0800/JY0808) and the same lateral flow strip family (JY0301). For mixed DNA + RNA panels, TiosBio’s Dual-system Dual-target CRISPR Strips (JY0308) support both enzymes in a single readout. Contact us for technical specifications and OEM design discussion.