Table 1.
The collections of endonuclease-assisted DNA assembly methods
| Method | REs used in the methodb | RE Sub-type | Scar sequence | Iterative Assembly |
|---|---|---|---|---|
| BioBrick [19] | SpeI ∩ PstI ∩ XbaI ∩ EcoRI | IIP | 8 bp | Yes |
| BglBrick [24] | EcoRI ∩ BglII ∩ BamHI ∩ XhoI | IIP | 6 bp | Yes |
| ePathBrick [22] | SpeI ∩ XbaI ∩ NheI ∩ AvrII | IIP | 6 bp | Yes |
| YaliBrick [28] | SpeI ∩ SalI ∩ XbaI ∩ AvrII | IIP | 6 bp | Yes |
| Quick Gene Assembly [14] | SpeI ∩ EcoRI ∩ XbaI | IIP | 6 bp | Yes |
| iBrick [25] | I-SceI ∩ PI-PspI | Homing endonucleases | 21 bp | Yes |
| C-Brick [17] | FnCpf1 endonuclease | CRISPR–Cas nucleases | 6 bp | Yes |
| CCTL [27] | FnCpf1 endonuclease | CRISPR–Cas nucleases | > 8 bp | Yes |
| PODAC [13] | BsaI | IIS | 8 bp | Yes |
| Golden Gate [30] | BsaI | IIS | 4 bp | No |
| GoldenBraid [12] | BsaI ∩ BsmBI | IIS | 4 bp | Yesc |
| MoClo [32] | BsaI ∩ BpiI | IIS | 4 bp | Yesc |
| Start-Stop Assembly [42] | SapI ∩ BsaI ∩ BbsI | IIS | Scarless | Yes |
| PS-Bricka | (One of hundreds of IIP REs generating overhangs of two or more bases) ∩ (BmrI ∪ BciVI ∪ HphI ∪ MlyI) | IIP and IIS | Scarless | Yes |
aThis study
b∩ Denotes all of the REs before and after this logical AND symbol are simultaneously used, and ∪ denotes only one among the REs before and after this logical OR symbol is used. For example, “SpeI ∩ PstI ∩ XbaI ∩ EcoRI” indicates that the four given REs are simultaneously used in BioBrick standard, and all of the four RE sites are required to be eliminate from the insertion parts. “BmrI ∪ BciVI ∪ HphI ∪ MlyI” indicates that any one of the four REs can be adopted in the PS-Brick, providing broad available options
cElaborate plasmid libraries and complex protocols are required for iterative workflows of Golden Braid and MoClo systems