Base editors fuse catalytically dead or nickase Cas9 to a deaminase, converting C→T (or A→G) only within a narrow single-stranded "editing window" exposed roughly 4–8 nt from the PAM-distal end of the R-loop. Prime editors instead fuse a nickase Cas9 to a reverse transcriptase, using a pegRNA whose 3′ extension both primes and templates new DNA sequence written directly into the nicked strand — enabling any substitution, insertion, or deletion, not just transitions.
windowFactor = exp(-(pos-6)^2 / (2*2.5^2))
efficiency = windowFactor * deliveryFrac * pamFactor
offTarget = Σ seedWeight(i) over i mismatch sites
seedWeight(i) = 0.85 if i within 8nt of PAM else 0.25
- Base / Prime Editor buttons — switch editing chemistry; prime editing bypasses the narrow window constraint.
- Target position slider — moves the substrate base along the 20-nt protospacer, shifting it in/out of the deaminase window.
- Off-target mismatches — number of mismatch sites simulated elsewhere in the genome, weighted by seed-region sensitivity.
- Delivery efficiency — fraction of cells receiving functional editor complex (RNP, AAV or LNP delivery).
- Run Edit — triggers the docking + catalysis animation and commits a computed outcome.
These principles underlie real clinical base/prime editing programs correcting single point mutations in diseases such as sickle cell disease and progeria, where minimizing bystander and off-target edits is critical for safety.