I have been using NEB Hifi Gibson assembly for a couple years now and I've been quite happy with it. I regularly make plasmid constructs with 4-8 fragments, and always >1/4 of the colonies are "perfect," while the remaining ones may have some SNPs at the joining sites, or be misassembled due to a repetitive region.
Some colleagues said that Golden Gate has even higher efficiency. That even with 8 fragments, it is normal for 50-100% of colonies to be perfect. Is that true? Is Golden Gate that perfect?
Hello Gen
Based on my understanding, I believe that it really depends on the kind of experiment that you are doing. Gibson method is considered as a "gold-standard" for assembly of DNA fragments, and has certain advantages over Golden-Gate method and vise versa. Based on the papers and discussions that I had with my colleagues, we find these kinds of questions challenging since we do not absolutely know which is the best method for DNA assembly. Each of them has its own advantages and disadvantages, and may be appropriate on a particular type of study. While most people recognize that Gibson has the gold-standard for assembly, other methods can be explored by conducting experiments.
Hope this helps.
Best.
https://bitesizebio.com/26961/cloning-methods-5-different-ways-to-assemble/