Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases

Abstract

Targeted knock-in of specific DNA sequences using CRISPR/Cas9 is an advanced technology that enables programmed genome alterations including insertions, deletions, and base substitutions exactly as designed. Despite its utility in life sciences and promise for medical and industrial applications, it remains critical to establish a methodology for highly precise and efficient targeted knock-in to facilitate the practical use of this technology. Tandem paired nicking (TPN) is a genome editing methodology leveraging nicking variants of CRISPR/Cas9 nucleases (Cas9 nickases) to create site-specific nicks within the homologous region of the genome and donor DNA. Such nicking configuration promotes precise and efficient targeted knock-in while repressing the formation of unintended insertions and deletions and p53-mediated DNA damage response. In this study, we conducted a detailed characterization of TPN-based targeted knock-in by performing genome editing assays with various nicking configurations modified from TPN. Our results demonstrated that genomic nicks remarkably contribute to TPN-based targeted knock-in, whereas donor nicks play a less critical role. The introduction of additional nicks beyond the standard two-nick configuration did not further improve the efficiency of TPN-based targeted knock-in. Comparison with other Cas9 nickase-based methodologies for targeted knock-in demonstrated largely equivalent knock-in efficiencies achieved by these methodologies. High-throughput long-read sequencing confirmed a lower incidence of undesired insertions and deletions of various lengths by TPN, in comparison with a conventional Cas9 nuclease-based approach. These findings underscore TPN as a methodology for precise and efficient targeted knock-in, and highlight the broad potential of Cas9 nickase-based targeted knock-in for clinical and industrial applications.