Table 1.
DNA editing nanomachines
| Name | Target scanning | Use in human cells | Target diversity | Double strand break | Maximum number of simultaneously altered sites* | Maximum observed HDR (%)‡ | Maximum observed NHEJ (%)‡ | Refs |
|---|---|---|---|---|---|---|---|---|
| Unstimulated Endogenous HR | DNA | Yes | High | No | 2 | 10−6 | NA | 158 |
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| MAGE (λ-Red) | DNA | Yes | High | No | 2¶ | NA | NA | 32,159 |
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| CAGE | DNA | No | High | No | NA | NA | NA | 13 |
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| SSOs only | DNA | Yes | High | No | 2 | 10−4 | NA | 33,35 |
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| ZFNs | Protein | Yes | Moderate | Yes§ | 6 | 43 | 65 | 160–162 |
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| TALENs | Protein | Yes | High | Yes§ | 2 | 10 | 50 | 6,163 |
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| Meganucleases | Protein | Yes | Low | Yes | 2 | 1 | 5 | 164,165 |
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| Tyr/Ser-SSRs | Protein | Yes | Low | No|| | 6 | 10−5 | NA | 166 |
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| Group II Introns | RNA | Yes | High | Yes | NA | NA | NA | 58,59 |
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| CRISPR–Cas9 | RNA | Yes | High | Yes§ | 62 | 33 | 79 | 7,70,167 |
In mammalian cells (per individual genome). Homozygous changes counted as two altered sites.
Observed in mammalian stem cells without antibiotic selection.
Can be programmed as nickases (single-strand nucleases).
Although Ser-SSRs utilize double stranded breaks mechanistically, these breaks are probably not exposed to the NHEJ machinery in the manner of the various designer nucleases.
In bacteria, 12 sites have been simultaneously edited.
CAGE, conjugative assembly genome engineering; HDR, homology-directed repair; HR, homologous recombination; MAGE, multiplex automated genome engineering; NA, data not available or not applicable; NHEJ, non-homologous end-joining; SSO, single-stranded oligonucleotides; SSRs, site-specific recombinases; TALENs, transcription activator-like effector nucleases; ZFNs, zinc finger nucleases.