Nomenclature
A glossary of key terms used throughout SPACER and the CRISPR diagnostics literature.
Guide RNA Terminology
| Term | Definition |
|---|---|
| crRNA | CRISPR RNA — the short RNA molecule that guides a Cas enzyme to its target. In diagnostic contexts, this is the molecule you design and synthesize. |
| Spacer | The variable portion of a crRNA that is complementary to the target sequence. In SPACER, this is the sequence being scored and ranked. |
| Protospacer | The target-side complement of the spacer — the region on the target nucleic acid that the crRNA binds to. |
| Guide RNA (gRNA) | General term for the RNA molecule that directs Cas enzyme activity. For Cas12/Cas13, this is synonymous with crRNA. |
| Direct repeat | The conserved structural hairpin flanking the spacer in a crRNA. Required for Cas enzyme binding but not part of the target-matching region. |
Target Recognition Terms
| Term | Definition |
|---|---|
| PAM | Protospacer Adjacent Motif — a short DNA sequence (typically 2–5 nt) adjacent to the protospacer that is required for Cas enzyme recognition. Cas12 enzymes require a PAM; Cas13 enzymes do not. |
| PFS | Protospacer Flanking Sequence — the nucleotide(s) immediately flanking the protospacer on the target RNA. Some Cas13 variants show a preference for certain PFS motifs (e.g., non-G at the 3′ end). |
| Seed region | The PAM-proximal portion of the spacer (~8–10 nt) that is critical for initial target recognition. Mismatches in the seed region are particularly disruptive to binding. |
| Target strand | The strand of dsDNA that is complementary to the crRNA spacer. For Cas13, the target is preferrably ssRNA. |
| Non-target strand | The strand of dsDNA that has the same sequence as the crRNA spacer (with T instead of U). Cas12 spacers are reported in the non-target strand orientation. |
Activity and Detection Terms
| Term | Definition |
|---|---|
| Collateral cleavage | Non-specific nuclease activity triggered after the Cas enzyme binds its target. Cas12 cleaves nearby ssDNA; Cas13 cleaves nearby ssRNA. This is the basis for signal amplification in diagnostics. |
| DETECTR | DNA Endonuclease-Targeted CRISPR Trans Reporter — a Cas12-based diagnostic platform that detects DNA targets via collateral ssDNA cleavage of a fluorescent reporter. (Chen et al., 2018) |
| SHERLOCK | Specific High-sensitivity Enzymatic Reporter UnLOCKing — a Cas13-based diagnostic platform that detects RNA (or DNA after amplification) via collateral ssRNA cleavage. (Gootenberg et al., 2017) |
| RPA/LAMP | Isothermal amplification methods (Recombinase Polymerase Amplification / Loop-mediated Amplification) often used upstream of CRISPR detection to increase target concentration. |
DETECTR SHERLOCK
SPACER-Specific Terms
| Term | Definition |
|---|---|
| Composite score | A weighted sum (0–100) of individual scoring components that quantifies overall guide quality. |
| Tier | A quality classification (Excellent, Good, Fair, Poor) assigned to each guide based on its assay score. |
| Quality flag | A binary indicator that a guide has a specific structural or sequence concern (e.g., high homopolymer content, extreme GC). |
| Scoring weight | A user-configurable multiplier that determines how much each scoring component contributes to the assay score. |
Tip
SPACER follows the convention of reporting Cas12 spacers on the non-target strand (5′→3′) and Cas13 spacers on the target RNA strand (5′→3′). All exported sequences use this orientation.