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Updated: Aug 29, 2025

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
High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs
Tony P Huang1,2,3, Zachary J Heins4,5, Shannon M Miller1,2,3
1Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Researchers engineered novel Cas9 variants to target previously inaccessible pyrimidine-rich PAM sequences in the human genome. These new variants offer improved editing efficiency and reduced off-target activity for gene editing applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- High-activity Cas9 proteins have limitations in targeting certain genomic loci, particularly those with pyrimidine-rich protospacer-adjacent motif (PAM) sequences.
- Engineering Cas9 variants for broader PAM compatibility can sometimes lead to increased off-target activity.
Purpose of the Study:
- To develop novel Cas9 variants capable of targeting a wider range of pyrimidine-rich PAM sequences in the human genome.
- To engineer Cas9 variants with high editing efficiency and reduced off-target activity.
Main Methods:
- Directed evolution, including phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution, was employed to modify Nme2Cas9.
- A selection strategy requiring functional editing with specified target protospacers and PAMs was developed and applied.
Main Results:
- Four high-activity Cas9 variants (eNme2-T.1, eNme2-T.2, eNme2-C, and eNme2-C.NR) were generated.
- Variants eNme2-T.1 and eNme2-T.2 target N4TN PAM sequences with efficiencies comparable to existing variants.
- Variants eNme2-C and eNme2-C.NR exhibit less restrictive PAM requirements, comparable or higher activity in human cells, and lower off-target activity at N4CN PAM sequences.
Conclusions:
- The developed Cas9 variants significantly expand the targeting scope for pyrimidine-rich PAM sequences in the human genome.
- These engineered variants provide efficient and specific gene editing tools, overcoming previous accessibility limitations.
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