Molecular breeding of polymerases for amplification of ancient DNA

Nature Biotechnology

Volumn 25, Issue 8, 2007, Pages 939-943

  D'Abbadie, Marc ^a   Hofreiter, Michael ^b   Vaisman, Alexandra ^c   Loakes, David ^a   Gasparutto, Didier ^d   Cadet, Jean ^d   Woodgate, Roger ^c   Pääbo, Svante ^b   Holliger, Philipp ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^c EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^d DIF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; MOLECULAR DYNAMICS; ONTOLOGY;

FORENSIC MEDICINE; GENETIC INFORMATION; PLEISTOCENE SPECIMENS; POLYMERASES;

ENZYMES;

DNA POLYMERASE; HYDANTOIN;

ARTICLE; BREEDING; CONTROLLED STUDY; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; GENE AMPLIFICATION; NONHUMAN; PLEISTOCENE; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; THERMUS AQUATICUS; THERMUS THERMOPHILUS;

DNA; DNA DAMAGE; DNA FINGERPRINTING; DNA-DIRECTED DNA POLYMERASE; FORENSIC GENETICS; FOSSILS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING;

THERMUS; THERMUS AQUATICUS; THERMUS THERMOPHILUS; URSUS SPELAEUS;

EID: 34547769773     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1321     Document Type: Article

References (30)

1. Pääbo, S. et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645-679 (2004).
2. Crameri, A., Raillard, S.A., Bermudez, E. & Stemmer, W.P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291 (1998).
3. Ghadessy, F.J., Ong, J.L. & Holliger, P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl. Acad. Sci. USA 98, 4552-4557 (2001).
4. Ghadessy, F.J. et al. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat. Biotechnol. 22, 755-759 (2004).
5. Leonard, J.A. et al. Ancient DNA evidence for Old World origin of New World dogs. Science 298, 1613-1616 (2002).
6. Jaenicke-Despres, V. et al. Early allelic selection in maize as revealed by ancient DNA. Science 302, 1206-1208 (2003).
7. Anderung, C. et al. Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle. Proc. Natl. Acad. Sci. USA 102, 8431-8435 (2005).
8. Green, R.E. et al. Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330-336 (2006).
9. Krings, M. et al. Neandertal DNA sequences and the origin of modern humans. Cell 90, 19-30 (1997).
10. Geigl, E.M. Inadequate use of molecular hybridization to analyze DNA in Neanderthal fossils. Am. J. Hum. Genet. 68, 287-291 (2001).
11. Plosky, B.S. & Woodgate, R. Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases. Curr. Opin. Genet. Dev. 14, 113-119 (2004).
12. Poinar, H.N. et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392-394 (2005).
13. Huang, M.-M., Arnheim, N. & Goodman, M.F. Extension of base mispairs by Taq polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res. 20, 4567-4573 (1992).
14. Miller, H. & Grollman, A.P. Kinetics of DNA polymerase I (Klenow fragment exo-) activity on damaged DNA templates: effect of proximal and distal template damage on DNA synthesis. Biochemistry 36, 15336-15342 (1997).
15. Suzuki, M., Baskin, D., Hood, L. & Loeb, L.A. Random mutagenesis of Thermus aquaticus DNA polymerase I: concordance of immutable sites in vivo with the crystal structure. Proc. Natl. Acad. Sci. USA 93, 9670-9675 (1996).
16. Xia, G. et al. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl. Acad. Sci. USA 99, 6597-6602 (2002).
17. Ong, J.L., Loakes, D., Jaroslawski, S., Too, K. & Holliger, P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J. Mol. Biol. 361, 537-550 (2006).
18. Matsuda, T. et al. Error rate and specificity of human and murine DNA polymerase eta. J. Mol. Biol. 312, 335-346 (2001).
19. Frank, E.G. et al. Altered nucleotide misinsertion fidelity associated with poliota-dependent replication at the end of a DNA template. EMBO J. 20, 2914-2922 (2001).
20. Höss, M., Jaruga, P., Zastawny, T.H., Dizdaroglu, M. & Pääbo, S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304-1307 (1996).
21. Lindahl, T. & Karlstrom, O. Heat-induced depyrimidination of deoxyribonucleic acid in neutral solution. Biochemistry 12, 5151-5154 (1973).
22. Lindahl, T. & Nyberg, B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610-3618 (1972).
23. Hansen, A.J. et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173, 1175-1179 (2006).
24. Bloom, J.D., Labthavikul, S.T., Otey, C.R. & Arnold, F.H. Protein stability promotes evolvability. Proc. Natl. Acad. Sci. USA 103, 5869-5874 (2006).
25. Zhao, H., Giver, L., Shao, Z., Affholter, J.A. & Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 16, 258-261 (1998) [see comments].
26. Ghadessy, F.J. & Holliger, P. Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes. Methods Mol. Biol. 352, 237-248 (2007).
27. Debbie, P. et al. Allele identification using immobilized mismatch binding protein: detection and identification of antibiotic resistant bacteria and determination of sheep susceptibility to scrapie. Nucleic Acids Res. 25, 4825-4829 (1997).
28. McDonald, J.P. et al. Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs. Nucleic Acids Res. 34, 1102-1111 (2006).
29. Hofreiter, M. et al. Evidence for reproductive isolation between cave bear populations. Curr. Biol. 14, 40-43 (2004).
30. Tawfik, D.S. & Griffiths, A.D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 16, 652-656 (1998).