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Choosing the correct Taq polymerase for your PCR reactionArticle created: Sept 18, 2007
Article by: Jeremiah Faith
I'd guess there is no commercial enzyme in molecular biology with more variants than Taq. I'm using Taq as a generic word for thermostable DNA polymerases (i.e. thermophilic DNA Polymerases). Even though the thermophilic DNA polymerases used for PCR aren't necessarily variants of the polymerase in Thermus aquaticus, in the lab everyone typically calls whatever polymerase they stick in their PCR reaction - Taq. Use Master Mixes Whenever Possible Unless I my reaction needs a rare polymerase that doesn't come in a master mix, I buy a master mix. The downside of master mixes are that the DNA product yields from a mix are slightly lower, and with mixes it becomes more difficult to optimize the concentrations of the reaction components (i.e. the buffer, dNTPs, MgCl2, etc...). However, the odds of the reaction failing because you forgot to add some key component are much smaller with a master mix. General Purpose PCR  Click image for larger - the patent on Taq recently ran out, so it is extremely cheap relative to the other thermophilic DNA polymerases
- it amplifies very effectively - if you have a reasonably sized product (75bp - 3kb) and it doesn't amplify with Taq, you're probably not going to have any better luck with other thermophilic DNA polymerases
- it works with T and U (most DNA polymerases stall at U)
The Taq 2x Master Mix from NEB is conveniently aliquoted into individual screw-top tubes (see photo). The Master Mix is pretty stable at 4C; I leave my stock in the fridge until it's gone, and then I move a new aliquot to the fridge. This way I never have to wait for the master mix to thaw. I've noticed no difference in amplification efficiency even after the mix spent a few months in the fridge.
The problem with the original Taq is that it has no error-correcting ability. Therefore, do NOT use the original Taq for cloning. Otherwise, you'll have to sequence and unnecessarily large number of clones to find one without a mutation. Error-correcting PCR For cloning or other fidelity critical applications, using an error-correcting Taq will save a lot of money, because you won't need to sequence as much (with an error-correcting Taq the large majority of the errors in your sequence will actually be sequencing errors). For error-correcting PCR, I use the Phusion High-Fidelity PCR Master Mix with HF Buffer (the Taq is produced by Finnzymes, but I buy it from NEB: F-531S). This Taq is also pre-aliquoted into eppy tubes. qPCR  Click image for larger PCR for TOPO cloning  Click image for larger
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