Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency

Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. Previous studies defined an optimal primer binding site (PBS) length for the pegRNA of similar to 13 nucleotides depending on the sequence composition. However, optimal PBS length characterization has been based on prime editing outcomes using plasmid or lentiviral expression systems. In this study, we demonstrate that for prime editor (PE) ribonucleoprotein complexes, the auto-inhibitory interaction between the PBS and the spacer sequence affects pegRNA binding efficiency and target recognition. Destabilizing this auto-inhibitory interaction by reducing the complementarity between the PBS-spacer region enhances prime editing efficiency in multiple prime editing formats. In the case of end-protected pegRNAs, a shorter PBS length with a PBS-target strand melting temperature near 37 degrees C is optimal in mammalian cells. Additionally, a transient cold shock treatment of the cells post PE-pegRNA delivery further increases prime editing outcomes for pegRNAs with optimized PBS lengths. Finally, we show that prime editor ribonucleoprotein complexes programmed with pegRNAs designed using these refined parameters efficiently correct disease-related genetic mutations in patient-derived fibroblasts and efficiently install precise edits in primary human T cells and zebrafish.

Automated summary

This study demonstrates that the length of the primer binding site (PBS) and the interaction between the PBS and the spacer sequence affects the efficiency of prime editing using ribonucleoprotein complexes. By reducing the complementarity between the PBS-spacer region, the auto-inhibitory interaction can be destabilized and prime editing efficiency is enhanced. In mammalian cells, a shorter PBS length with a PBS-target strand melting temperature near 37 degrees C is optimal for prime editing.