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Updated: Jan 28, 2026

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution
Published on: February 26, 2019
DNA stretching induces Cas9 off-target activity.
Matthew D Newton1,2, Benjamin J Taylor3, Rosalie P C Driessen4
1Molecular Virology, Department of Medicine, Imperial College London, London, UK.
CRISPR/Cas9 genome editing shows specific DNA binding at low forces. Mechanical stress at higher forces reveals off-target binding, influenced by DNA structure and guide RNA, impacting therapeutic safety.
Area of Science:
- Molecular Biology
- Biophysics
- Genetics
Background:
- CRISPR/Cas9 is a revolutionary genome-editing technology.
- Off-target edits limit its therapeutic potential.
- Understanding target discrimination is crucial for safe applications.
Purpose of the Study:
- To investigate the mechanisms underlying CRISPR/Cas9 target specificity.
- To elucidate how Cas9 differentiates between on-target and off-target DNA sequences.
Main Methods:
- Developed a single-molecule assay combining optical tweezers and fluorescence.
- Monitored Streptococcus pyogenes Cas9 binding and cleavage dynamics on λ-DNA.
- Utilized single-molecule Förster resonance energy transfer (smFRET) and cleavage assays.
Main Results:
- Cas9 exhibits specific binding and cleavage at low forces.
- Increased force induces off-target binding at specific sites, dependent on guide RNA sequence.
- DNA bubbles, formed by mechanical distortion, facilitate off-target binding and cleavage, even with mismatches.
Conclusions:
- Mechanical forces and DNA structural changes (like bubbles) promote Cas9 off-target activity.
- Cellular processes destabilizing DNA may expose cryptic off-target sites.
- Improved algorithms are needed to predict and mitigate CRISPR/Cas9 off-target effects.
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