Pfu DNA polymerase

Pfu DNA polymerase is an enzyme found in the hyperthermophilic archaeon Pyrococcus furiosus, where it functions to copy the organism's DNA during cell division. In the laboratory setting, Pfu is used to amplify DNA in the polymerase chain reaction (PCR), where the enzyme serves the central function of copying a new strand of DNA during each extension step.

For the virology term see, see Plaque-forming unit.
Pfu DNA polymerase
Identifiers
OrganismPyrococcus furiosus
Symbolpol
PDB4ahc
UniProtP61875

It is a family B DNA polymerase. It has an RNase H-like 3'-5' exonuclease domain, typical of B-family polymerase such as DNA polymerase II.[1]

Proofreading ability of Pfu polymerase

Pfu DNA polymerase has superior thermostability and proofreading properties compared to Taq DNA polymerase. Unlike Taq DNA polymerase, Pfu DNA polymerase possesses 3' to 5' exonuclease proofreading activity, meaning that as the DNA is assembled from the 5' end to 3' end, the exonuclease activity immediately removes nucleotides misincorporated at the 3' end of the growing DNA strand. Consequently, Pfu DNA polymerase-generated PCR fragments will have fewer errors than Taq-generated PCR inserts.

Commercially available Pfu typically results in an error rate of 1 in 1.3 million base pairs and can yield 2.6% mutated products when amplifying 1 kb fragments using PCR. However, Pfu is slower and typically requires 1–2 minutes per cycle to amplify 1kb of DNA at 72 °C. Using Pfu DNA polymerase in PCR reactions also results in blunt-ended PCR products.[2]

Pfu DNA polymerase is hence superior to Taq DNA polymerase for techniques that require high-fidelity DNA synthesis, but can also be used in conjunction with Taq polymerase to obtain the fidelity of Pfu with the speed of Taq polymerase activity.[3]

History

Scientists led by Eric Mathur at the biotech company Stratagene, based in La Jolla, California, discovered Pfu DNA polymerase which exhibits significantly higher fidelity of replication than Taq DNA polymerase in 1991.[4] They received patents for exonuclease-deficient Pfu and the full Pfu in 1996.[5]

Other polymerases from Pyrococcus strains such as "Deep Vent" (Q51334) from strain GB-D and Pwo DNA polymerase has also seen use.[3]

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References
  1. InterPro protein view: P61875
  2. Agilent Technologies. "PfuTurbo DNA Polymerase Instruction Manual #600250" (PDF).
  3. van Pelt-Verkuil E, van Belkum A, Hays JP (2008). "Taq and Other Thermostable DNA Polymerases". Principles and Technical Aspects of PCR Amplification. pp. 103–18. doi:10.1007/978-1-4020-6241-4_7. ISBN 978-1-4020-6240-7.
  4. Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, Mathur EJ (December 1991). "High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus". Gene. 108 (1): 1–6. doi:10.1016/0378-1119(91)90480-y. PMID 1761218.
  5. U.S. Patent 5,489,523, U.S. Patent 5,545,552
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