Prime Editing Flap Resolution Simulator

Prime editing's outcome is decided at a single molecular fork: once reverse transcriptase has written the edit onto a new 3′ DNA flap, that flap must out-compete the original, unedited 5′ flap for resolution by the cell's own repair machinery before the edit becomes permanent. This simulator renders that competition in 3D — a Cas9 nickase/pegRNA complex sits on a double helix, and adjustable RT-extension length, flap GC content and PE3 second-strand nicking feed a simplified thermodynamic model of which flap wins. Run individual trials or let them auto-fire to watch the measured editing-efficiency and indel-rate readouts converge toward the model's prediction, exactly the trade-off (short edits install more reliably; PE3 boosts efficiency but raises indels) that drives real prime-editing guide design.