Prime Editing pegRNA Flap Equilibrium

Prime editing writes new DNA sequence directly at a target site without cutting both strands. This simulator renders the molecular choreography step by step: a Cas9 nickase opens one strand, the prime-editing guide RNA's primer-binding site hybridizes to the exposed 3′ end, reverse transcriptase extends a new edited flap from the pegRNA's RT template, and the resulting branched DNA intermediate is resolved by the cell's own flap endonuclease and ligase machinery. Tune the PBS length and RT template (edit) length, toggle the PE3 non-edited-strand nick, and run editing cycles to see how each parameter shifts the balance between a clean edit, a silent reversion to wild type, and an unwanted indel — exactly the trade-offs prime-editing researchers optimize in the lab.