PAM sequence
PAM stands for Protospacer Adjacent Motif and it is a DNA sequence in the target genome that is recognized by the Cas protein, allowing the Ribonucleoprotein complex to start the process of binding the target DNA.
PAM sequence depends not only on the Cas protein used in the experiment, but also on the species the Cas protein is from and the specific variant. Table 1 shows some examples of PAM sequences.
| Cas protein | PAM sequence |
|---|---|
| Cas9 (Streptococcus pyogenes) | NGG |
| Cas9 EQR variant (Streptococcus pyogenes) | NGAG |
| Cas9 (Staphylococcus aureus) | NNGRRT or NNGRR(N) |
| Cpf1 (Lachnospiraceae bacterium) | TTTV |
| Cpf1 RR variant(Lachnospiraceae bacterium) | TYCV |
Table 1. Examples of PAM sequences. N = any base; R = A or G; V = A or C or G.