Skip to main content

Proteins of DNA Replication from Extreme Thermophiles: PCR and Beyond

  • Chapter
  • First Online:
Biotechnology of Extremophiles:

Part of the book series: Grand Challenges in Biology and Biotechnology ((GCBB,volume 1))

Abstract

PCR remains one of the most versatile and widely used techniques in molecular biology, yet the capabilities of PCR seem rudimentary when compared to genome replication in living cells. Modifying Taq polymerase, or supplementing or replacing it with other proteins of thermophilic archaea or bacteria, has enhanced the functional properties of PCR and created other techniques with extended or complementary capabilities. The enhancements to PCR include increased fidelity, the ability to amplify damaged template, and tolerance of otherwise inhibitory substances in analytical samples, whereas the complementary techniques include whole-genome amplification, high-resolution genotyping, and improved performance of massively parallel sequencing. A tremendous functional diversity of thermostable DNA-replication enzymes is provided by (i) the native proteins of thermophiles currently in culture, (ii) those cloned from uncultivated thermophiles, and (iii) molecular engineering of clones obtained from both these sources. The extent and depth of this molecular diversity argues that the pace of technological innovation involving DNA synthesis at elevated temperatures will continue to accelerate.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Alsmadi OA, Bornarth CJ, Song W, Wisniewski M, Du J, Brockman JP, Faruqi AF, Hosono S, Sun Z, Du Y, Wu X, Egholm M, Abarzua P, Lasken RS, Driscoll MD (2003) High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay. BMC Genomics 4:21

    Article  PubMed  PubMed Central  Google Scholar 

  • Arezi B, McKinney N, Hansen C, Cayouette M, Fox J, Chen K, Lapira J, Hamilton S, Hogrefe H (2014) Compartmentalized self-replication under fast PCR cycling conditions yields Taq DNA polymerase mutants with increased DNA-binding affinity and blood resistance. Front Microbiol 5:408

    Article  PubMed  PubMed Central  Google Scholar 

  • Baar C, d'Abbadie M, Vaisman A, Arana ME, Hofreiter M, Woodgate R, Kunkel TA, Holliger P (2011) Molecular breeding of polymerases for resistance to environmental inhibitors. Nucleic Acids Res 39, e51

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barnes WM, Rowlyk KR (2002) Magnesium precipitate hot start method for PCR. Mol Cell Probes 16:167–171

    Article  CAS  PubMed  Google Scholar 

  • Chander Y, Koelbl J, Puckett J, Moser MJ, Klingele AJ, Liles MR, Carrias A, Mead DA, Schoenfeld TW (2014) A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP). Front Microbiol 5:395

    Article  PubMed  PubMed Central  Google Scholar 

  • Chang K, Deng S, Chen M (2015) Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 66:297–307

    Article  CAS  PubMed  Google Scholar 

  • Cho M, Chung S, Heo SD, Ku J, Ban C (2007) A simple fluorescent method for detecting mismatched DNAs using a MutS-fluorophore conjugate. Biosens Bioelectron 22:1376–1381

    Article  CAS  PubMed  Google Scholar 

  • Cozens C, Pinheiro VB, Vaisman A, Woodgate R, Holliger P (2012) A short adaptive path from DNA to RNA polymerases. Proc Natl Acad Sci USA 109:8067–8072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • d’Abbadie M, Hofreiter M, Vaisman A, Loakes D, Gasparutto D, Cadet J, Woodgate R, Paabo S, Holliger P (2007) Molecular breeding of polymerases for amplification of ancient DNA. Nat Biotechnol 25:939–943

    Article  PubMed  PubMed Central  Google Scholar 

  • Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99:5261–5266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fogg MJ, Pearl LH, Connolly BA (2002) Structural basis for uracil recognition by archaeal family-B DNA polymerases. Nat Struct Biol 9:922–927

    Article  CAS  PubMed  Google Scholar 

  • Gaidamaviciute E, Tauraite D, Gagilas J, Lagunavicius A (2010) Site-directed chemical modification of archaeal Thermococcus litoralis Sh1B DNA polymerase: acquired ability to read through template-strand uracils. Biochim Biophys Acta 1804:1385–1393

    Article  CAS  PubMed  Google Scholar 

  • Gardner AF, Jack WE (2002) Acyclic and dideoxy terminator preferences denote divergent sugar recognition by archaeon and Taq DNA polymerases. Nucleic Acids Res 30:605–613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghadessy FJ, Ong JL, Holliger P (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 98:4552–4557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol 22:755–759

    Article  CAS  PubMed  Google Scholar 

  • Gruz P, Shimizu M, Pisani FM, De Felice M, Kanke Y, Nohmi T (2003) Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus. Nucleic Acids Res 31:4024–4030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hafner GJ, Yang IC, Wolter LC, Stafford MR, Giffard PM (2001) Isothermal amplification and multimerization of DNA by Bst DNA polymerase. Biotechniques 30:852–856

    CAS  PubMed  Google Scholar 

  • Hogrefe HH, Hansen CJ, Scott BR, Nielson KB (2002) Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc Natl Acad Sci USA 99:596–601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jozwiakowski SK, Keith BJ, Gilroy L, Doherty AJ, Connolly BA (2014) An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family. Nucleic Acids Res 42:9949–9963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaboev OK, Luchkina LA, Tretiakov AN, Bahrmand AR (2000) PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). Nucleic Acids Res 28, e94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kermekchiev MB, Tzekov A, Barnes WM (2003) Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic Acids Res 31:6139–6147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM (2009) Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res 37, e40

    Article  PubMed  PubMed Central  Google Scholar 

  • Laos R, Shaw R, Leal NA, Gaucher E, Benner S (2013) Directed evolution of polymerases to accept nucleotides with nonstandard hydrogen bond patterns. Biochemistry 52:5288–5294

    Article  CAS  PubMed  Google Scholar 

  • Laos R, Thomson JM, Benner SA (2014) DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front Microbiol 5:565

    Article  PubMed  PubMed Central  Google Scholar 

  • Lasken RS, Schuster DM, Rashtchian A (1996) Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J Biol Chem 271:17692–17696

    Article  CAS  PubMed  Google Scholar 

  • Li GM (2008) Mechanisms and functions of DNA mismatch repair. Cell Res 18:85–98

    Article  CAS  PubMed  Google Scholar 

  • Liu XP, Liu JH (2011) Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase. PLoS ONE 6, e27248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19:225–232

    Article  CAS  PubMed  Google Scholar 

  • Louwrier A, van der Valk A (2005) Thermally reversible inactivation of Taq polymerase in an organic solvent for application in hot start PCR. Enzyme Microb Technol 36:947–952

    Article  CAS  Google Scholar 

  • McDonald JP, Hall A, Gasparutto D, Cadet J, Ballantyne J, Woodgate R (2006) Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs. Nucleic Acids Res 34:1102–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Motz M, Kober I, Girardot C, Loeser E, Bauer U, Albers M, Moeckel G, Minch E, Voss H, Kilger C, Koegl M (2002) Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes. J Biol Chem 277:16179–16188

    Article  CAS  PubMed  Google Scholar 

  • Nilsson M, Dahl F, Larsson C, Gullberg M, Stenberg J (2006) Analyzing genes using closing and replicating circles. Trends Biotechnol 24:83–88

    Article  CAS  PubMed  Google Scholar 

  • O’Donnell M, Langston L, Stillman B (2013) Principles and concepts of DNA replication in bacteria, Erchaea, and Eukarya. Cold Spring Harb Perspect Biol 5:pii: a010108. doi:10.1101/cshperspect.a010108

    Google Scholar 

  • Pata JD (2010) Structural diversity of the Y-family DNA polymerases. Biochim Biophys Acta 1804:1124–1135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paul N, Shum J, Le T (2010) Hot start PCR. Methods Mol Biol 630:301–318

    Article  CAS  PubMed  Google Scholar 

  • Potapova O, Grindley ND, Joyce CM (2002) The mutational specificity of the Dbh lesion bypass polymerase and its implications. J Biol Chem 277:28157–28166

    Article  CAS  PubMed  Google Scholar 

  • Ramsay N, Jemth AS, Brown A, Crampton N, Dear P, Holliger P (2010) CyDNA: synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase. J Am Chem Soc 132:5096–5104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rasila TS, Pajunen MI, Savilahti H (2009) Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. Anal Biochem 388:71–80

    Article  CAS  PubMed  Google Scholar 

  • Ribble W, Kane SD, Bullard JM (2015) Long-range PCR amplification of DNA by DNA polymerase III holoenzyme from Thermus thermophilus. Enzyme Res 2015:837–842

    Article  Google Scholar 

  • Tindall KR, Kunkel TA (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008–6013

    Article  CAS  PubMed  Google Scholar 

  • Trombley-Hall A, McKay Zovanyi A, Christensen DR, Koehler JW, Devins Minogue T (2013) Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples. PLoS One 8, e73845

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Prosen DE, Mei L, Sullivan JC, Finney M, Vander Horn PB (2004) A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Res 32:1197–1207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waters LS, Minesinger BK, Wiltrout ME, D’Souza S, Woodruff RV, Walker GC (2009) Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance, Microbiol Mol Biol Rev 73:134–154

    Google Scholar 

  • White MF, Grogan DW (2008) DNA stability and repair. In: Robb FT, Antranikian G, Grogan DW, Driessen AJ (eds) Thermophiles: biology and technology at high temperatures. CRC Press, Boca Raton, pp 179–188

    Google Scholar 

  • Wiedmann M, Wilson WJ, Czajka J, Luo J, Barany F, Batt CA (1994) Ligase chain reaction (LCR) – overview and applications. PCR Methods Appl 3:S51–S64

    Article  CAS  PubMed  Google Scholar 

  • Wilson RC, Pata JD (2008) Structural insights into the generation of single-base deletions by the Y-family DNA polymerase Dbh. Mol Cell 29:767–779

    Article  CAS  PubMed  Google Scholar 

  • Yamagami T, Ishino S, Kawarabayasi Y, Ishino Y (2014) Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering. Front Microbiol 5:461

    Article  PubMed  PubMed Central  Google Scholar 

  • Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO (2014) Isothermal amplified detection of DNA and RNA. Mol Biosyst 10:970–1003

    Article  CAS  PubMed  Google Scholar 

  • Yang W, Woodgate R (2007) What a difference a decade makes: insights into translesion DNA synthesis. Proc Natl Acad Sci USA 104:15591–15598

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Dennis W. Grogan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Grogan, D.W. (2016). Proteins of DNA Replication from Extreme Thermophiles: PCR and Beyond. In: Rampelotto, P. (eds) Biotechnology of Extremophiles:. Grand Challenges in Biology and Biotechnology, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-319-13521-2_18

Download citation

Publish with us

Policies and ethics