A base editor fuses a catalytically-impaired Cas9 (nickase, nCas9, or fully dead dCas9) to a deaminase enzyme and a guide RNA. The gRNA pairs with a 20-nt protospacer next to a PAM; instead of cutting both strands, the deaminase chemically converts one base within a narrow "editing window" while the opposite strand is nicked and repaired using the edited strand as template — so no double-strand break (DSB) ever forms.
Position numbering (Komor et al. 2016):
protospacer nt 1..20, counted from the PAM-distal end
PAM occupies positions 21-23 (NGG for SpCas9)
editing window ≈ positions [start, start+width-1], typically 4-8
Editing efficiency (Gaussian falloff from window center):
center c = start + (width-1)/2, sigma σ = width/2.5
E(p) = exp( -(p-c)² / (2σ²) ) for p inside the window, else 0
Edit happens only if BOTH hold:
1) base(p) matches editor: C for CBE (→T), A for ABE (→G)
2) p is inside the editing window
Bystander edit: any other same-type base inside the window also converts,
with probability ≈ E(p) × (off-target activity / 100).
- Window start / width — slides and resizes where the deaminase can physically reach the exposed single-stranded DNA loop inside the Cas9-gRNA R-loop; positions outside it are untouched.
- Inspect position — pick any of the 20 protospacer nucleotides to see whether the editor's target letter sits there and whether it falls in the window.
- Off-target deaminase activity — models bystander editing: extra C's (CBE) or A's (ABE) inside the same window that get converted as an unwanted side effect, plus rare genome-wide off-target deamination.
Applications: correcting single-nucleotide point mutations (sickle-cell HBB, many inherited metabolic diseases) without relying on error-prone double-strand-break repair. Limitations: only reaches transition mutations (C↔T, A↔G) within a fixed window, bystander edits can create unwanted collateral changes, and delivery (AAV cargo size, mRNA/RNP, nanoparticles) still constrains which tissues can be treated.