PCR & amplification
Taq vs Pfu: choosing a DNA polymerase for research PCR
By Antonio Lamb · Published 2026-10-26 · 8 min read
Taq and Pfu are both thermostable DNA polymerases, but they solve different problems. Taq is fast and robust; Pfu proofreads. The right choice depends on whether the amplicon is only being visualised or whether its sequence is the product.
What proofreading changes
Taq, isolated from Thermus aquaticus, lacks a 3' to 5' exonuclease domain. Misincorporated bases are not removed efficiently, and measured error rates are roughly one per 10^4 to 10^5 bases incorporated, depending on the assay and conditions.
Pfu, isolated from Pyrococcus furiosus, carries a 3' to 5' exonuclease that removes mismatched terminal nucleotides. Direct comparisons report roughly an order of magnitude lower error rate than Taq, though the exact number depends on the reporter gene, template, and cycling conditions.
Speed and yield
Taq extends at roughly 60 to 100 nucleotides per second under standard conditions, and many protocols use one minute per kilobase or less. Pfu is slower, commonly quoted at roughly 20 to 30 nucleotides per second, so longer amplicons may need longer extension.
Pfu can also give lower yield than Taq from the same cycle number. Increasing enzyme, cycle number, or extension time may recover yield, but each change should be tested against the actual template.
When Taq is usually the right choice
Taq is a sensible default when the amplicon is read by size rather than sequence.
- Colony PCR and presence or absence screens.
- Genotyping assays analysed by gel size.
- High-throughput work where cost and speed dominate.
- Templates with strong secondary structure where Taq's robustness helps.
- Work where the product will be re-sequenced and a minority of mutations is acceptable.
When Pfu is usually the right choice
Pfu is the safer default when a single unintended base change can invalidate the construct.
- Cloning a coding sequence that must match the template.
- Site-directed mutagenesis and overlap-extension PCR.
- Assembling a construct from PCR-generated fragments.
- Any amplicon that will be used without sequencing every clone.
A practical checklist
Ask what the amplicon is for, estimate its length and expected error load, and check whether the template is GC-rich or structured. Run a small pilot with the actual template before committing a large batch.
The Renegade Reagents catalog lists the supplied format and handling information for its Taq and Pfu products. It does not currently state enzyme activity in units per volume or a measured fidelity rate, so request those specifications from the supplier before a quantitative comparison.
References
- Tindall and Kunkel (1988). Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27(16), 6008-6013.
- Lundberg et al. (1991). High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108(1), 1-6.
- Cline, Braman, and Hogrefe (1996). PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Research 24(18), 3546-3551.
- NEB PCR protocols and polymerase selection guidance.
Related products
Renegade Reagents products are supplied for research use only. They are not for human or veterinary diagnostic, therapeutic, or clinical applications.