Base & Prime Editing

Mechanism:

1. Target recognition: Cas9 guided by gRNA binds to target DNA
2. DNA cleavage: Cas9 introduces a double-stranded break
3. Cellular Repair: The break is repaired by NHEJ or HDR pathways

Mechanism:

1. Target recognition: nCas9 guided by gRNA binds to the target DNA
2. Deamination: The deaminase converts the target base within the editing window
3. DNA nicking: nCas9 nicks the non-edited DNA strand to stimulate repair
4. Base conversion: Cellular repair replaces the deaminated base, creating a precision conversion

Mechanism:

1. Target recognition: Prime editor guided by pegRNA binds to the target DNA
2. Nicking: Cas9 nickase cuts a single strand of the DNA
3. Reverse transcription: The RT copies the edit encoded in the pegRNA RT template and incorporates it into the target DNA
4. Repair: Edited strand is incorporated. The unedited strand is repaired to match new sequence

Yes

No

No

Often required for precise insertions

No

No

Gene knockouts, insertions, and HDR-mediated modifications

A→G  and C→T base conversions

All base substitutions, small insertions, and deletions

Broad editing outcomes dependent on DNA repair pathways

Highly precise single-base changes

Precise sequence modifications with broad editing flexibility

Broad target accessibility

Limited by editing window and PAM requirements

Broad edit capabilities across many genomic loci

Higher due to double-strand break formation

Lower due to absence of double-strand breaks

Lower due to absence of double-strand breaks

Gene knockout, gene insertion, functional genomics

Precise nucleotide correction, disease modeling, translational research

Disease mutation correction, precision engineering, translational research

Relatively straightforward

Moderate

More complex due to pegRNA design requirements

Creating knockouts or introducing larger insertions

Correcting specific point mutations with high precision

Installing precise substitutions, insertions, or deletions without donor DNA