How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product? I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector. The primers I have designed overlap restriction sites of which I plan to use to ligate into the expression vector. The parts between the primers I will try to create mutants with error prone PCR. My concern is the 3' A overhangs that are created from Taq polymerase. How prevalent is this? If it is highly common, what is the best way to account for these additions when trying to ligate my PCR product into the vector?

I am not sure of a case where Taq _doesn't_ add 3' A overhangs.

You could use TA cloning to clone your PCR product. The basic principle is to use a vector with 3' T overhangs. If you have a vector without these overhangs, you can use a terminal transferase + dTTPs to create them (or even Taq, but this is not as great because it adds a purification step to isolate the vectors with overhangs; terminal transferase is much more efficient). You can then ligate your PCR product that has a 3' overhang.

Protocols for adding the 3' T overhangs to your vector are given in Zhou and Gomez-Sanchez 2000.