ArticleNature communications2022
CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context.
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 52 papers.
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Who cites it
52 citing papers in PubMed, 94 citations in OpenAlex.
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- High-throughput evaluation of in vitro CRISPR activities enables optimized large-scale multiplex enrichment of rare variants.Nature biomedical engineering · 2026Article
- Deep learning-driven prediction of on-target activity, off-target risk, and repair outcomes in CRISPR/Cas9: current landscape and multi-scale perspectives.Journal of translational medicine · 2026Review
- Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming.bioRxiv : the preprint server for biology · 2026Article
- Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction.PeerJ · 2026Article
- Advancing CRISPR with deep learning: A comprehensive review of models and databases.Molecular therapy. Nucleic acids · 2025Review
- Integrating CRISPR/Cas technology with clinical trials: Principles, progress and challenges.Asian journal of pharmaceutical sciences · 2025Review
- Nick-and-Digest Strategy for Programmable Circular ssDNA Production and Scalable DNA Origami Assembly.JACS Au · 2025Article
- Precision T cell correction platform for inborn errors of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Protocol for permanent gene repression by CRISPR-adenine base editing of promoter CCAAT motifs.STAR protocols · 2025Article
- Off-target effects in CRISPR-Cas genome editing for human therapeutics: Progress and challenges.Molecular therapy. Nucleic acids · 2025Review
- Off-target interactions in the CRISPR-Cas9 Machinery: mechanisms and outcomes.Biochemistry and biophysics reports · 2025Review
- dCas12a-mediated CRISPR interference for multiplex gene repression in cyanobacteria for enhanced isobutanol and 3-methyl-1-butanol production.Microbial cell factories · 2025Article
- Nickase fidelity drives EvolvR-mediated diversification in mammalian cells.Nature communications · 2025Article
- Virus-free CRISPR knockin of a chimeric antigen receptor into KLRC1 generates potent GD2-specific natural killer cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- The Interface of Gene Editing with Regenerative Medicine.Engineering (Beijing, China) · 2025Article
- Breaking Barriers to an HIV-1 Cure: Innovations in Gene Editing, Immune Modulation, and Reservoir Eradication.Life (Basel, Switzerland) · 2025Review
- CRISPR-Cas9-based electrochemical biosensor for the detection ofADMET & DMPK · 2025Article
- Efficient CRISPR/Frontiers in plant science · 2025Article
- Prediction of CRISPR-Cas9 on-target activity based on a hybrid neural network.Computational and structural biotechnology journal · 2025Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs (gRNAs) cleave the DNA efficiently. Although the heterogeneity of gRNA activity is well recognized, the current understanding of how CRISPR/Cas9 activity is regulated remains incomplete. Here, we identify a sweet spot range of binding free energy change for optimal efficiency which largely explains why gRNAs display changes in efficiency at on- and off-target sites, including why gRNAs can cleave an off-target with higher efficiency than the on-target. Using an energy-based model, we show that local gRNA-DNA interactions resulting from Cas9 "sliding" on overlapping protospacer adjacent motifs (PAMs) profoundly impact gRNA activities. Combining the effects of local sliding for a given PAM context with global off-targets allows us to better identify highly specific, and thus efficient, gRNAs. We validate the effects of local sliding on gRNA efficiency using both public data and in-house data generated by measuring SpCas9 cleavage efficiency at 1024 sites designed to cover all possible combinations of 4-nt PAM and context sequences of 4 gRNAs. Our results provide insights into the mechanisms of Cas9-PAM compatibility and cleavage activation, underlining the importance of accounting for local sliding in gRNA design.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.