Taq polymerase

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Taq polymerase, exonuclease

DNA polymerase bound to a DNA octamer
Identifiers
Symbol Taq-exonuc
Pfam PF09281
InterPro IPR015361
SCOP 1qtm
SUPERFAMILY 1qtm
Taq-exonuc

dna polymerase
Identifiers
Symbol Taq-exonuc
Pfam PF09281
InterPro IPR015361
SCOP 1qtm
SUPERFAMILY 1qtm

Taq polymerase /ˌtæk ˈpɒlɨməreɪz/ is a thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Thomas D. Brock in 1965.[1] It is often abbreviated to "Taq Pol" (or simply "Taq"), and is frequently used in polymerase chain reaction (PCR), a method for greatly amplifying short segments of DNA.

T. aquaticus is a bacterium that lives in hot springs and hydrothermal vents, and Taq polymerase was identified[1] as an enzyme able to withstand the protein-denaturing conditions (high temperature) required during PCR.[2] Therefore it replaced the DNA polymerase from E. coli originally used in PCR.[3] Taq's optimum temperature for activity is 75–80°C, with a half-life of greater than 2 hours at 92.5°C, 40 minutes at 95°C and 9 minutes at 97.5°C, and can replicate a 1000 base pair strand of DNA in less than 10 seconds at 72°C.[4]

One of Taq's drawbacks is its lack of 3' to 5' exonuclease proofreading activity[4] resulting in relatively low replication fidelity. Originally its error rate was measured at about 1 in 9,000 nucleotides.[5] More recent studies, however, found significantly lower error rates like 2.0×10−5 [6] or even 8.0×10−6.[7] The remaining two domains act in coordination, via coupled domain motion.[8] Some thermostable DNA polymerases have been isolated from other thermophilic bacteria and archaea, such as Pfu DNA polymerase, possessing a proofreading activity, and are being used instead of (or in combination with) Taq for high-fidelity amplification.

Taq makes DNA products that have A (adenine) overhangs at their 3' ends. This may be useful in TA cloning, whereby a cloning vector (such as a plasmid) that has a T (thymine) 3' overhang is used, which complements with the A overhang of the PCR product, thus enabling ligation of the PCR product into the plasmid vector.

Taq polymerase in PCR

In the early 1980s, Kary Mullis was working at Cetus Corporation on the application of synthetic DNAs to biotechnology. He was familiar with the use of DNA oligonucleotides as probes for binding to target DNA strands, as well as their use as primers for DNA sequencing and cDNA synthesis. In 1983, he began using two primers, one to hybridize to each strand of a target DNA, and adding DNA polymerase to the reaction. This led to exponential DNA replication,[9] greatly amplifying the amounts of DNA between the primers.[3]

However, after each round of replication the mixture needs to be heated above 90°C to denature the newly formed DNA, allowing the strands to separate and act as templates in the next round of amplification. This heating step also inactivates the DNA polymerase that was in use before the discovery of Taq polymerase, the Klenow fragment of the DNA Polymerase I from E. coli.

Use of the thermostable Taq enables running the PCR at high temperature (~60°C and above), which facilitates high specificity of the primers and reduces the production of unspecific products, such as primer dimer. Moreover, use of the thermostable polymerase eliminates the need for having to add new enzyme to the PCR reaction during the thermocycling process. A single closed tube in a relatively simple machine can be used to carry out the entire process. Thus, the use of Taq polymerase was the key idea that made PCR applicable to a large variety of molecular biology problems concerning DNA analysis.[2]

Patent issues

Hoffmann-La Roche eventually bought the PCR and Taq patents from Cetus for $330 million, from which it may have received up to $2 billion in royalties.[10] In 1989, Science Magazine named Taq polymerase its first "Molecule of the Year". Kary Mullis received the Nobel Prize in 1993, the only one awarded for research performed at a biotechnology company. By the early 1990s, the PCR technique with Taq polymerase was being used in many areas, including basic molecular biology research, clinical testing, and forensics. It also began to find a pressing application in direct detection of the HIV in AIDS.[11]

In December 1999, U.S. District Judge Vaughn Walker ruled that the 1990 patent involving Taq polymerase was issued, in part, on misleading information and false claims by scientists with Cetus Corporation. The ruling supported a challenge by Promega Corporation against Hoffman-La Roche, which purchased the Taq patents in 1991. Judge Walker cited previous discoveries by other laboratories, including the laboratory of Professor John Trela in the University of Cincinnati department of biological sciences, as the basis for the ruling.[12]

Protein domain

Function

In molecular biology, this protein domain, Taq polymerase exonuclease, refers to a domain found in prokaryotic Taq DNA polymerase (thermostable).

Structure

This domain where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase.[13]

See also

References

  1. ↑ 1.0 1.1 Chien A, Edgar DB, Trela JM (1976). "Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus". J. Bact. 127 (3): 1550–7. PMC 232952. PMID 8432. 
  2. ↑ 2.0 2.1 Saiki, RK; et al. (1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.". Science 239 (4839): 487–91. doi:10.1126/science.2448875. PMID 2448875. 
  3. ↑ 3.0 3.1 Saiki, RK; et al. (1985). "Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia". Science 230 (4732): 1350–4. doi:10.1126/science.2999980. PMID 2999980. 
  4. ↑ 4.0 4.1 Lawyer FC, et al. (1993). "High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase ...". PCR Methods Appl. 2 (4): 275–87. PMID 8324500. 
  5. ↑ Tindall KR and Kunkel TA (1988). "Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase". Biochemistry 27 (16): 6008–13. doi:10.1021/bi00416a027. PMID 2847780. 
  6. ↑ Lundberg KS, et al. (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. 
  7. ↑ Cline J, et al. (1996). "PCR Fidelity of Pfu DNA Polymerase and Other Thermostable DNA Polymerases". Nucleic Acids Research 24 (18): 3546–3551. doi:10.1093/nar/24.18.3546. PMID 8836181. 
  8. ↑ Bu Z, Biehl R, Monkenbusch M, Richter D, Callaway DJ (December 2005). "Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy". Proc. Natl. Acad. Sci. U.S.A. 102 (49): 17646–51. doi:10.1073/pnas.0503388102. PMC 1345721. PMID 16306270. 
  9. ↑ Mullis KB (April 1990). "The unusual origin of the polymerase chain reaction". Sci. Am. 262 (4): 56–61, 64–5. doi:10.1038/scientificamerican0490-56. PMID 2315679. 
  10. ↑ Fore J, Wiechers IR, Cook-Deegan R (2006). "The effects of business practices, licensing, and intellectual property on development and dissemination of the polymerase chain reaction: case study". J Biomed Discov Collab 1: 7. doi:10.1186/1747-5333-1-7. PMC 1523369. PMID 16817955. 
    Detailed history of Cetus Corporation and the commercial aspects of PCR.
  11. ↑ Guatelli JC, Gingeras TR, Richman DD (1 April 1989). "Nucleic acid amplification in vitro: detection of sequences with low copy numbers and application to diagnosis of human immunodeficiency virus type 1 infection". Clin. Microbiol. Rev. 2 (2): 217–26. PMC 358112. PMID 2650862. 
  12. ↑ Curran, Chris, Bio-Medicine, Dec. 7, 1999
  13. ↑ Li Y, Mitaxov V, Waksman G (August 1999). "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation". Proc. Natl. Acad. Sci. U.S.A. 96 (17): 9491–6. PMC 22236. PMID 10449720. 
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