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. Author manuscript; available in PMC: 2015 Sep 1.
Published in final edited form as: Methods. 2014 Apr 2;69(2):137–141. doi: 10.1016/j.ymeth.2014.03.026

Table 1.

Experimental design and outcomes of nuclease-mediated engineering

Desired change Donor Repair
Simple knockout None NHEJ
Specific knock-in ssOligo HR
Long dsDNA HR
Long insertion Long dsDNA HR
Short insertion Long dsDNA HR
dsOligo NHEJ
Long deletion Long dsDNA HR
ssOligo HR
None – 2 nucleases NHEJ
Inversion None – 2 nucleases NHEJ

In each case a targeted nuclease is assumed – a ZFN pair, a TALEN pair, or Cas9 protein plus a guide RNA. More detail is provided in the text, section 4.

Abbreviations: ss, single-stranded; ds, double-stranded; NHEJ, nonhomologous end joining; HR, homologous recombination.