DNA Repair Pathways and Precision Editing Outcomes
Repair Pathways as the Real Editing Engine
Mechanistic idea
Programmable nucleases create lesions, but cellular repair pathways determine whether the outcome is a knockout, precise correction, insertion, deletion, or rearrangement.
Core repair pathways
Which pathway is most associated with small insertions and deletions after a double-strand break?
NHEJ is error-prone and commonly generates indels at break sites.
Correct answer: Nonhomologous end joining
Why is HDR often less efficient than NHEJ in many cells?
HDR is restricted to specific stages and competes with the more ubiquitous NHEJ pathway.
Correct answer: Because NHEJ is faster and dominates in most cell-cycle contexts
Precision Editing Modalities
Editing outcome classes
Nuclease-driven knockout
- Uses repair by NHEJ
- Efficient gene disruption
- Less precise
HDR-mediated correction
- Can replace exact sequence
- Template dependent
- Typically lower efficiency
Quantitative perspective
If is the probability of precise repair and is the probability of error-prone repair, then design strategy often aims to increase or shift the balance toward the desired product class.
Base editors are especially useful because they:
Base editors enable targeted base conversions while avoiding classical double-strand breaks.
Correct answer: Can change single nucleotides without generating a double-strand break
What is one reason prime editing is considered highly versatile?
Prime editing expands the scope beyond simple base transitions/transversions.
Correct answer: It can introduce small substitutions, insertions, and deletions with programmable specificity