Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

EngineeredSpCas9s andAsCas12a cleave fewer off-target genomic sites than wild-type (wt) Cas9. However, understanding their fidelity, mechanisms and cleavage outcomes requires systematic profiling across mispaired target DNAs. Here we describe NucleaSeq-nuclease digestion and deep sequencing-a massively parallel platform that measures the cleavage kinetics and time-resolved cleavage products for over 10,000 targets containing mismatches, insertions and deletions relative to the guide RNA. Combining cleavage rates and binding specificities on the same target libraries, we benchmarked fiveSpCas9 variants andAsCas12a. A biophysical model built from these data sets revealed mechanistic insights into off-target cleavage. Engineered Cas9s, especially Cas9-HF1, dramatically increased cleavage specificity but not binding specificity compared to wtCas9. Surprisingly,AsCas12a cleavage specificity differed little from that of wtCas9. Initial DNA cleavage sites and end trimming varied by nuclease, guide RNA and the positions of mispaired nucleotides. More broadly, NucleaSeq enables rapid, quantitative and systematic comparisons of specificity and cleavage outcomes across engineered and natural nucleases.

Automated summary

The study compares the specificity and cleavage outcomes of engineered and natural nucleases using a massively parallel platform called NucleaSeq, which combines nucleases digestion and deep sequencing. Engineered Cas9s, especially Cas9-HF1, show increased cleavage specificity but not binding specificity compared to wild-type Cas9, while surprisingly AsCas12a cleavage specificity differs little from that of wild-type Cas9. The study also reveals that initial DNA cleavage sites and end trimming vary by nuclease, guide RNA, and the positions of mispaired nucleotides.