What are the steps of editing by a prime editor?

The five steps of editing by prime editor are described below.

1. Nick formation: The Cas9-H840A/pegRNA complex binds to the target region and makes a cut 3 bp before the PAM site, creating a nick on the same strand as the PAM. This releases a 3’ flap.
2. Primer binding: The 3’ flap forms a specific interaction with the 14-16 nt “primer binding site” at the 3’ end of the pegRNA. This forms an RNA/DNA hybrid, functioning as a primer for new DNA synthesis.
3. DNA Synthesis: Using the RNA “edit site” as a template, new DNA synthesis begins at the primer site. The modified RT polymerase copies the template, extending the 3’ flap.
4. Flap Removal: The edited 3’ flap displaces the unedited 5’ flap, which is eliminated by the cellular nuclease FEN1.
5. Mismatch Resolution: Two mismatches remain to be resolved: one in the edited codon (G ≠ T) and one in the modified PAM (C ≠ C). The Mismatch Repair system resolves these, resulting in either precisely edited DNA or reverting to the original sequence. If the PAM sequence remains unmodified, the Cas9-H840A/pegRNA complex can attempt PRIME editing again.