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Although these proteins are found in many microbes, only a handful of variants are used for these applications. Here, we use bioinformatic and biochemical analyses to explore this largely uncharacterized diversity. PAM recognition spans the entire spectrum of T-, A-, C-, and G-rich nucleotides, from single nucleotide recognition to sequence strings longer than 4 nucleotides.
Characterization of a subset of Cas9 orthologs using purified components reveals additional biochemical diversity, including both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for long stretches of homology between gRNA and DNA target. Easily reprogrammed to recognize different DNA sequences, it has been widely adopted for use in a multitude of applications to edit genomic DNA, modulate gene expression, visualize genetic loci, or detect targets in vitro 5 , 6 , 7 , 8 , 9.
To date, just a handful of variants are used for these applications 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 with the Streptococcus pyogenes Spy Cas9 being used most widely 2. This is further limited by the requirement for careful site selection to minimize off-target binding and cleavage based on the tolerance for mismatches in the gRNA—PAM—target complex 1 , This constraint becomes particularly evident in therapeutic applications where even rare genome alterations resulting from off-targets are undesirable or when targeting more structurally complex plant genomes 22 , Moreover, these restraints impact the use of Cas9 for homology-directed repair HDR , template-free editing, base editing, or prime-editing applications, where the outcome is reliant on the proximity of the desired change to the target sequence 1.
