Figure 3: Characterization of AsCpf1 and LbCpf1 specificity.

(a) Validated on- and off-target sites for AsCpf1 and LbCpf1 for six separate guide targets as measured by Cpf1-BLISS over two independent biological replicates and validated by targeted NGS (n=3, error bars show s.e.m.). Grey boxes indicate DSB loci not detected within a biological replicate. (b) Evaluating the position-dependent mismatch tolerance of AsCpf1 and LbCpf1 using a repetitive guide with 36,777 predicted genomic loci with single mismatches. (c) A map of mismatch tolerance per position generated by dividing at each base the number of off-targets discovered in BLISS versus the possible single mismatched genomic targets for Cpf1. The grey line plotted on the left y axis is the count of single mismatched targets in the genome for Cpf1 as predicted by Cas OFFinder²⁴. (d) Guide designs for investigating the effect of single base pair mismatches in the RNA guide on AsCpf1 and LbCpf1 specificity by measuring the change in their on-target efficiency versus a matched guide. (e) Composite mismatch tolerance model for AsCpf1 and LbCpf1 based on saturated single base pair mismatches for two guides. Cas9 data (green) modelled from existing Cas9 single mismatch data²⁷.