Which Polymerase for degenerate PCR?

[cat1082]

Hi,

I'm trying to do degenerate PCR and had been using just bog-standard taq. Unfortunately I ran out at a very inconvenient time and had to use Phusion. The phusion is higher fidelity and I'm just wondering if anyone would know if that's a bad choice for degenerate PCR or if it won't really matter too much?

Thanks
Cathy.

[jonoave]

I'm afraid I'm not quite clear on what you mean as "degenerate PCR". Are you doing site-directed mutagenesis or running PCR with degenerate primers since you're unsure of the actual nucleotide sequence?

1. For site-directed mutagenesis - high-fidelity polymerase like PFU is highly recommended.

2. For PCR with degenerate primers - I'm not entirely sure as I have not done this before, but I believe the choice of polymerase depends entirely on what your downstream application is.

[Musty_Hustla]

It doesn't matter which polymerase you use. If anything the high fidelity will help ensure that the region(s) of degeneracy are where you expect them to be.