I have my insert in a topo plasmid and I want to change about five of the nt’s. What way is the best you think?
It really depends where you want your mutations. Changing 5 successive (or very close) nucleotides and 5 nt spread over 1 kb are quite different things that will probably require different approaches.
I had 5 that were spread over around 6000kb.
I decided to go with Multi QuikChange from Stratagene