The difference in one sentence
Base editing changes one letter into another — but only certain swaps, and it cannot add or remove anything. Prime editing writes new sequence directly, so it can make any letter swap plus small insertions and deletions. Prime editing is more capable and less mature: base editing is in pivotal trials, prime editing has just produced its first published results in patients.
| Aspect | Base editing | Prime editing |
|---|---|---|
| What it can change | Four letter swaps (transitions), plus C→G with lower efficiency | All twelve letter swaps, plus small insertions and deletions |
| Insertions and deletions | No | Yes, short ones |
| Cuts both strands? | No | No |
| Efficiency | Generally high at good sites | Highly variable between sites |
| Size of the machinery | Large | Larger — the hardest mainstream editor to deliver |
| Main risk | Bystander edits in the window | Unintended insertions at the nick; low efficiency at some sites |
| Clinical status | Pivotal trials under way | First-in-human results published |
Which would you choose?
If the change you need is one base editing can make, base editing is usually the better choice today: it is more efficient, easier to deliver and further along clinically. Prime editing is what you reach for when base editing cannot make the change at all — a deletion, an insertion, or a transversion — which is a large fraction of disease-causing variants.
Sources
- Nature (Anzalone et al.) · 2019
Search-and-replace genome editing without double-strand breaks or donor DNA ↗