Table 1 Advantages and disadvantages of gene editing tools
From: Gene therapy for cystic fibrosis: new tools for precision medicine
| ZFN | TALEN | CRISPR/Cas9 | Base Editing | Prime editing | |
|---|---|---|---|---|---|
| Mechanism |
Type IIs restriction enzyme, FokI endonuclease, fused to pair of ZFN DNA binding domains Recognize 18-36 bp of DNA sequence Target DNA sequence break by protein-DNA interaction |
Type IIs restriction enzyme, FokI endonuclease, fused to pair of TALEN DNA binding domains Recognize 30-40 bp of DNA sequence Target DNA sequence break by protein-DNA interaction |
Few Cas endonuclease options for broader specificity and flexibility (Cas9, Cas12) PAM sequence require to design sgRNA Target DNA sequence break by DNA-RNA interaction |
Direct conversion of a DNA base to another without DSBs at a target locus Permanent conversion of C-G to T-A base pairs by cytosin base editor (CBEs) Enzymatically convert A-T base pairs into G-C base pairs by adenine base editors (ABEs) |
Fusion complex composed of a catalytically impaired Cas9 protein and an engineered reverse transcriptase Can recognize DNA of any sequence size |
| Efficiency | Low | Low | High | High | High |
| Advantages |
Currently being used in clinical trials for HIV and Hunter’s syndrome Low immunity and Small protein size |
Target any DNA sequence Less cytotoxic effects |
Highly predictable target sequence Easy to design and possible to target only 1 bp of target sequence Potentially target multiple genes simultaneously |
No random insertion and deletions because do not require DNA break High A > G and C > T conversion |
No random insertion and deletions because do not require DNA break Can be used to generate different mutation types (insertions, deletions, and point mutations) |
| Limitations | Difficult due to extensive cloning needed to link two zinc finger modules together and expensive to design |
Sensitive to DNA methylation Require pair of TALEN with two independent DNA binding sites |
Require PAM site near the target DNA sequence to design gRNA Off-target effect observed Cas9 protein too large for AAV-based delivery |
Only accounts for 4 out of 12 possible base-to-base conversions Too large for AAV-based delivery Difficult to edit DNA sequence that several A or C residues are nearby |
High targeting efficiency but may depend on cell type Too large for AAV-based delivery Detection of undesired off-target effects and on-target mutation |