Structural basis for mismatch surveillance by CRISPR-Cas9

CRISPR-Cas9 as a programmable genome editing tool is hindered by off-target DNA cleavage(1-4), and the underlying mechanisms by which Cas9 recognizes mismatches are poorly understood(5-7). Although Cas9 variants with greater discrimination against mismatches have been designed(8-10), these suffer from substantially reduced rates of on-target DNA cleavage(5,11). Here we used kinetics-guided cryo-electron microscopy to determine the structure of Cas9 at different stages of mismatch cleavage. We observed a distinct, linear conformation of the guide RNA-DNA duplex formed in the presence of mismatches, which prevents Cas9 activation. Although the canonical kinked guide RNA-DNA duplex conformation facilitates DNA cleavage, we observe that substrates that contain mismatches distal to the protospacer adjacent motif are stabilized by reorganization of a loop in the RuvC domain. Mutagenesis of mismatch-stabilizing residues reduces off-target DNA cleavage but maintains rapid on-target DNA cleavage. By targeting regions that are exclusively involved in mismatch tolerance, we provide a proof of concept for the design of next-generation high-fidelity Cas9 variants.

Automated summary

In this study, the structure of Cas9 during mismatch cleavage was determined using kinetics-guided cryo-electron microscopy. It was found that a linear conformation of the guide RNA-DNA duplex formed in the presence of mismatches, preventing Cas9 activation. Additionally, mismatches distal to the protospacer adjacent motif were stabilized by reorganization of a loop in the RuvC domain. Mutations of mismatch-stabilizing residues reduced off-target DNA cleavage while maintaining rapid on-target DNA cleavage. This study provides proof of concept for the design of next-generation high-fidelity Cas9 variants targeting mismatch tolerance regions.