ArticleNature communications2022
A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Stepwise DNA-unwinding gates TnpB genome-editing activity.Molecular cell · 2026Article
- Operating CRISPR/Cas12a in a complex nucleic acid sequence background.Nucleic acids research · 2026Article
- Stepwise DNA unwinding gates TnpB genome-editing activity.bioRxiv : the preprint server for biology · 2026Article
- Prime editing in mammals: From promise to practicalities.Molecular therapy. Nucleic acids · 2025Review
- Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1.Nucleic acids research · 2025Article
- Single-molecule perspectives of CRISPR/Cas systems: target search, recognition, and cleavage.BMB reports · 2025Review
- Iterative crRNA design and a PAM-free strategy enabled an ultra-specific RPA-CRISPR/Cas12a detection platform.Communications biology · 2024Article
- Computationally guided high-throughput engineering of an anti-CRISPR protein for precise genome editing in human cells.Cell reports methods · 2024Article
- Advances in Virus Detection Techniques Based on Recombinant Polymerase Amplification.Molecules (Basel, Switzerland) · 2024Review
- Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex.Nucleic acids research · 2024Article
- Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing.Nucleic acids research · 2024Article
- The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex.Nature structural & molecular biology · 2023Article
- Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system.Nature communications · 2023Article
- Nucleic acid strand displacement - from DNA nanotechnology to translational regulation.RNA biology · 2023Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
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