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Protein Engineering Protocols - Mycobacteriology research center

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NExT DNA Shuffling 1894. Zhao, H., Giver, L., Shao, Z., Affholter, J. A., and Arnold, F. H. (1998) Molecular evolutionby staggered extension process (StEP) in vitro recombination. Nat. Biotechnol.16, 258–261.5. Shao, Z., Zhao, H., Giver, L., and Arnold, F. H. (1998) Random-priming in vitrorecombination: an effective tool for directed evolution. Nucleic Acids Res. 26,681–683.6. Cadwell, R. C. and Joyce, G. F. (1992) Randomization of genes by PCR mutagenesis.PCR Methods Appl. 2, 28–33.7. Arndt, K. M., Müller, K. M., and Plückthun, A. (2001) Helix-stabilized Fv (hsFv)antibody fragments: substituting the constant domains of a Fab fragment for a heterodimericcoiled-coil domain. J. Mol. Biol. 312, 221–228.8. Sambrook, J. and Russel, D. W. (2001) Molecular Cloning: A Laboratory Manual.3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.9. Patel, P. H. and Loeb, L. A. (2000) Multiple amino acid substitutions allow DNApolymerases to synthesize RNA. J. Biol. Chem. 275, 40,266–40,272.10. Boiteux, S., O’Connor, T. R., and Laval, J. (1987) Formamidopyrimidine-DNAglycosylase of Escherichia coli: cloning and sequencing of the fpg structural geneand overproduction of the protein. Embo J. 6, 3177–3183.11. Friedberg, E. C., Walker, G. C., and Siede, W. (1995) DNA Repair and Mutagenesis.American Society of Microbiology, Washington, DC.12. Drohat, A. C., Jagadeesh, J., Ferguson, E., and Stivers, J. T. (1999) Role of electrophilicand general base catalysis in the mechanism of Escherichia coli uracilDNA glycosylase. Biochemistry 38, 11,866–11,875.13. Maxam, A. M. and Gilbert, W. (1980) Sequencing end-labeled DNA with basespecificchemical cleavages. Methods Enzymol. 65, 499–560.14. Ljungquist, S. (1977) A new endonuclease from Escherichia coli acting at apurinicsites in DNA. J. Biol. Chem. 252, 2808–2814.15. Richardson, C. C. and Kornberg, A. (1964) A deoxyribonucleic acid phosphataseexonucleasefrom Escherichia coli. I. Purification of the enzyme and characterizationof the phosphatase activity. J. Biol. Chem. 239, 242–250.16. Dodson, M. L., Schrock, R. D., 3rd, and Lloyd, R. S. (1993) Evidence for an iminointermediate in the T4 endonuclease V reaction. Biochemistry 32, 8284–8290.17. Levin, J. D. and Demple, B. (1990) Analysis of class II (hydrolytic) and class I(beta-lyase) apurinic/apyrimidinic endonucleases with a synthetic DNA substrate.Nucleic Acids Res. 18, 5069–5075.18. Miyazaki, K. (2002) Random DNA fragmentation with endonuclease V: applicationto DNA shuffling. Nucleic Acids Res. 30, e139.19. Mattila, P., Korpela, J., Tenkanen, T., and Pitkanen, K. (1991) Fidelity of DNA synthesisby the Thermococcus litoralis DNA polymerase—an extremely heat stableenzyme with proofreading activity. Nucleic Acids Res. 19, 4967–4973.20. Kong, H., Kucera, R. B., and Jack, W. E. (1993) Characterization of a DNA polymerasefrom the hyperthermophile archaea Thermococcus litoralis. Vent DNApolymerase, steady state kinetics, thermal stability, processivity, strand displacement,and exonuclease activities. J. Biol. Chem. 268, 1965–1975.

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