We discovered a thermostable enzyme from the archaeon Pyrococcus furiosus (Pfu), which increases yields of PCR product amplified with Pfu DNA polymerase. A high molecular mass (>250 kDa) complex with PCR-enhancing activity was purified from Pfu extracts. The complex is a multimer of two discrete proteins, P45 and P50, with significant similarity to bacterial dCTP deaminase͞dUTPase and DNA flavoprotein, respectively. When tested in PCR, only recombinant P45 exhibited enhancing activity. P45 was shown to function as a dUTPase, converting dUTP to dUMP and inorganic pyrophosphate. Pfu dUTPase improves the yield of products amplified with Pfu DNA polymerase by preventing dUTP incorporation and subsequent inhibition of the polymerase by dU-containing DNA. dUTP was found to accumulate during PCR through dCTP deamination and to limit the efficiency of PCRs carried out with archaeal DNA polymerases. In the absence of dUTP inhibition, the combination of cloned Pfu DNA polymerase and Pfu dUTPase (PfuTurbo DNA polymerase) can amplify longer targets in higher yield than Taq DNA polymerase. In vivo, archaeal dUTPases may play an essential role in preventing dUTP incorporation and inhibition of DNA synthesis by family B DNA polymerases.T he use of high-fidelity DNA polymerases in the polymerase chain reaction (PCR) is important for minimizing amplification errors in products that will be cloned, sequenced, and expressed. Several archaeal DNA polymerases with 3Ј-to 5Ј-exonucleasedependent proofreading activity have been commercialized for high-fidelity PCR amplification. Of the enzymes characterized to date, Pyrococcus furiosus (Pfu) DNA polymerase exhibits the highest fidelity, with an average error rate estimated to be 2-to 60-fold lower than other proofreading enzymes and 6-to 100-fold lower than Taq DNA polymerase (1-4), which lacks proofreading activity.Although inherent high fidelity and other unique biochemical properties of Pfu DNA polymerase have been exploited in numerous molecular biology procedures, including blunt-end cloning (5), amplification of GC-rich targets (6), mutation detection (7), ligation-independent cloning (8), site-directed mutagenesis (9), genotyping (10), and trinucleotide repeat analyses (11), it has been reported that proofreading DNA polymerases tend to perform less reliably than Taq DNA polymerase (4, 12). PCRs conducted with Taq are typically more efficient and require less optimization than reactions carried out with proofreading DNA polymerases. Lower product yields with Pfu DNA polymerase have been attributed to the enzyme's relatively slow polymerization rate (550 vs. 2,800 nucleotides per min for Taq) and interference from its associated 3Ј-to 5Ј-exonuclease activity (13).Improvements in the performance of Pfu DNA polymerase have been achieved by increasing PCR extension times (2 min͞kb of target; Stratagene Pfu DNA polymerase manual), incorporating additives such as DMSO (6,14), and mixing Pfu with Taq DNA polymerase (4). Although DNA polymerase mixtures synthesize higher yields of produ...