Plasmids 101: Golden Gate Cloning
Type
Blog Post
... work around this is to "domesticate" your fragment: PCR-based amplification can be used to create silent...and exciting applications, this system is an incredibly powerful tool for cloning complicated constructs...Type IIS sites (such as BsaI or BbsI), that are located on the outside of the cleavage site. As a result...plasmid (Option 1) or added using PCR-based amplification (Option 2).
Advantages of Golden Gate cloning...restriction sites that may not be amenable to "domestication", you might want to consider using an alternative...high-efficiency step.
References:
Sequential amplification of cloned DNA as tandem multimers using class-IIS...