In vitro production and screening of DNA polymerase η mutants for catalytic diversity

BioTechniques

Volumn 33, Issue 5, 2002, Pages 1136-1144

  Glick, Eitan ^a   Anderson, Jon P ^a   Loeb, Lawrence A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; BIOTECHNOLOGY; DNA; DRUG PRODUCTS; ENZYME INHIBITION; MUTAGENESIS; SCREENING;

CATALYTIC DIVERSITY;

ENZYMES;

DNA DIRECTED DNA POLYMERASE ETA; DNA POLYMERASE; MUTANT PROTEIN; NUCLEOTIDE DERIVATIVE; RECOMBINANT ENZYME; UNCLASSIFIED DRUG; DEOXYURIDINE PHOSPHATE; DEOXYURIDINE TRIPHOSPHATE; DNA DIRECTED DNA POLYMERASE; FLUORESCENT DYE; HYBRID PROTEIN; NUCLEOTIDE; RHODAMINE;

ARTICLE; BIODIVERSITY; CATALYSIS; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME ENGINEERING; ENZYME SYNTHESIS; FLUORESCENCE ANALYSIS; IN VITRO STUDY; MUTANT; SCREENING; AUTOMATION; COMPARATIVE STUDY; DNA ADDUCT; DNA DAMAGE; ENZYME SPECIFICITY; EVALUATION; GENE LIBRARY; GENETICS; HUMAN; METABOLISM; MUTAGENESIS;

AUTOMATION; CATALYSIS; DEOXYURACIL NUCLEOTIDES; DNA ADDUCTS; DNA DAMAGE; DNA-DIRECTED DNA POLYMERASE; FLUORESCENT DYES; GENE LIBRARY; HUMANS; MUTAGENESIS; NUCLEOTIDES; RECOMBINANT FUSION PROTEINS; RHODAMINES; SUBSTRATE SPECIFICITY;

EID: 1842864795     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/02335dd08     Document Type: Article

References (31)

1. Adhami, F., S. Muller, and M.T. Hauser. 1999. Nonradioactive labeling of large DNA fragments for genome walking, RFLP and northern blot analysis. BioTechniques 27:314-320.
2. Arnold, F.H. 1998. When blind is better: Protein design by evolution. Nat. Biotechnol. 16:617-618.
3. Augustin, M.A., W. Ankenbauer, and B. Angerer. 2001. Progress towards single-molecule sequencing: Enzymatic synthesis of nucleotide-specifically labeled DNA. J. Biotechnol. 86:289-301.
4. Ausubel, F.M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl. 1998. Current Protocols in Molecular Biology. John Wiley & Sons, New York.
5. Bedford, E., S. Tabor, and C.C. Richardson. 1997. The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Proc. Natl. Acad. Sci. USA 94:479-484.
6. Crameri, A., S.-A. Raillard, E. Bermudez, and W.P.C. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288-291.
7. Davidson, J.F., J.P. Anderson, H. Guo, D. Landis, and L.A. Loeb. 2002. Applied molecular evolution of enzymes involved in synthesis and repair of DNA, p. 281-307. In S. Brakmann and K. Johnsson (Eds.), Directed Molecular Evolution of Proteins. Weiley, Weinheim.
8. Foldes-Papp, Z., B. Angerer, W. Ankenbauer, and R. Rigler. 2001. Fluorescent highdensity labeling of DNA: Error-free substitution for a normal nucleotide. J. Biotechnol. 86:237-253.
9. Fortina, P., K. Delgrosso, T. Sakazume, R. Santacroce, S. Moutereau, H.J. Su, D. Graves, S. McKenzie, et al. 2000. Simple two-color array-based approach for mutation detection. Eur. J. Hum. Genet. 8:884-894.
10. Ghadessy, F.J., J.L. Ong, and P. Holliger. 2001. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl. Acad. Sci. USA 98:4552-4557.
11. Glick, E., K.L. Vigna, and L.A. Loeb. 2001. Mutations in human DNA polymerase eta motif II alter bypass of DNA lesions. EMBO J. 20:7303-7312.
12. Hamilton, S.C., J.W. Farchaus, and M.C. Davis. 2001. DNA polymerases as engines for biotechnology. BioTechniques 31:370-383.
13. Holtke, H.J., G. Sagner, C. Kessler, and G. Schmitz. 1992. Sensitive chemiluminescent detection of digoxigenin-labeled nucleic acids: A fast and simple protocol and its applications. BioTechniques 12:104-113.
14. Kebelmann-Betzing, C., K. Seeger, S. Dragon, G. Schmitt, A. Moricke, T.A. Schild, G. Henze, and B. Beyermann. 1998. Advantages of a new Taq DNA polymerase in multiplex PCR and time-release PCR. BioTechniques 24:154-158.
15. Kessler, C., H.J. Holtke, R. Seibl, J. Burg, and K. Muhlegger. 1990. Non-radioactive labeling and detection of nucleic acids. I. A novel DNA labeling and detection system based on digoxigenin: Anti-digoxigenin ELISA principle (digoxigenin system). Biol. Chem. Hoppe Seyler 371:917-927.
16. Kim, B. and L.A. Loeb. 1995. Human immunodeficiency virus reverse transcriptase substitutes for DNA polymerase I in Escherichia coli. Proc. Natl. Acad. Sci. USA 92:684-688.
17. Kornberg, A. and T. Baker. 1992. DNA Replication. W.H. Freeman and Co., New York.
18. Li, Y., V. Mitaxov, and G. Waksman. 1999. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc. Natl. Acad. Sci. USA 96:9491-9496.
19. Ling, H., F. Boudsocq, R. Woodgate, and W. Yang. 2001. Crystal structure of a y-family dna polymerase in action. A mechanism for error-prone and lesion-bypass replication. Cell 107:91-102.
20. Martin, R., C. Hoover, S. Grimme, C. Grogan, J. Holtke, and C. Kessler. 1990. A highly sensitive, nonradioactive DNA labeling and detection system. BioTechniques 9:762-768.
21. Martzen, M.R., S.M. McCraith, S.L. Spinelli, F.M. Torres, S. Fields, E.J. Grayhack, and E.M. Phizicky. 1999. A biochemical genomics approach for identifying genes by the activity of their products. Science 286:1153-1155.
22. McDonald, J.P., A.S. Levine, and R. Woodgate. 1997. The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free postreplication repair mechanism. Genetics 147:1557-1568.
23. Parker, L.T., H. Zakeri, Q. Deng, S. Spurgeon, P.Y. Kwok, and D.A. Nickerson. 1996. AmpliTaq DNA polymerase, FS dye-terminator sequencing: Analysis of peak height patterns. BioTechniques 21:694-699.
24. Patel, P.H. and L.A. Loeb. 2000. DNA polymerase active site is highly mutable: Evolutionary consequences. Proc. Natl. Acad. Sci. USA 97:5095-5100.
25. Randolph, J.B. and A.S. Waggoner. 1997. Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes. Nucleic Acids Res. 25:2923-2929.
26. Seela, F., E. Feiling, J. Gross, F. Hillenkamp, N. Ramzaeva, H. Rosemeyer, and M. Zulauf. 2001. Fluorescent DNA: The development of 7-deazapurine nucleoside triphosphates applicable for sequencing at the single molecule level. J. Biotechnol. 86:269-279.
27. Shinkai, A. and L.A. Loeb. 2001. In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile709 in motif A functions in base selection. J. Biol. Chem. 15:15.
28. Sweasy, J.B. and L.A. Loeb. 1992. Mammalian DNA polymerase β can substitute for DNA polymerase I during DNA replication in Escherichia coli. J. Biol. Chem. 267:1407-1410.
29. Sweasy, J.B. and L.A. Loeb. 1993. Detection and characterization of mammalian DNA polymerase β mutants by functional complementation in Escherichia coli. Proc. Natl. Acad. Sci. USA 90:4626-4630.
30. Trincao, J., R.E. Johnson, C.R. Escalante, S. Prakash, L. Prakash, and A.K. Aggarwal. 2001. Structure of the catalytic core of S. cerevisiae DNA polymerase eta: Implications for translesion DNA synthesis. Mol. Cell 8:417-426.
31. Wildsmith, S.E., G.E. Archer, A.J. Winkley, P.W. Lane, and P.J. Bugelski. 2001. Maximization of signal derived from cDNA microarrays. BioTechniques 30:202-208.