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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METHODS IN MOLECULAR BIOLOGY 352Pr
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M E T H O D S I N M O L E C U L A R
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PrefaceProtein engineering is a fas
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ContentsPreface ...................
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ContributorsKATJA M. ARNDT • Inst
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Contributors xiKAZUNARI TAIRA • D
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1Combinatorial Protein Design Strat
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Combinatorial Protein Design Strate
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2Global Incorporation of Unnatural
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Incorporation of Unnatural Amino Ac
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3Considerations in the Design and O
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Design of Coiled Coil Structures 37
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4Calcium Indicators Based on Calmod
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Protein-Based Ca 2+ Indicators 73Fi
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Protein-Based Ca 2+ Indicators 7512
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Protein-Based Ca 2+ Indicators 8145
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5Design and Synthesis of Artificial
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Design of Zinc Finger Proteins 853.
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Design of Zinc Finger Proteins 89pr
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Design of Zinc Finger Proteins 91Fi
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96 Koide and Koidewhile retaining t
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98 Koide and Koide5. M9-tryptone: M
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100 Koide and Koidetarget-binding s
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102 Koide and Koide4. Discard the s
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104 Koide and Koideup to 1 mM for h
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106 Koide and Koideplate. Incubate
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108 Koide and Koide1. Perform steps
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7Engineering Site-Specific Endonucl
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Engineering Site-Specific Endonucle
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115Fig. 1. Mapping group-specific r
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8Protein Library Design and Screeni
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Protein Library Design and Screenin
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135Fig. 2. Excel worksheet describi
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137Fig. 4. Excel worksheet describi
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Page 170 and 171: Protein Design by Binary Patterning
Page 180 and 181: 10Versatile DNA Fragmentation and D
Page 182 and 183: NExT DNA Shuffling 169This chapter
Page 184 and 185: NExT DNA Shuffling 1713. Methods3.1
Page 186 and 187: NExT DNA Shuffling 17372°C, 4 min.
Page 188 and 189: NExT DNA Shuffling 175Fig. 2. Varia
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Page 192 and 193: NExT DNA Shuffling 179Fig. 3. Reass
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Page 196 and 197: NExT DNA Shuffling 183likelihood of
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Page 200 and 201: NExT DNA Shuffling 187staining. Bec
Page 204 and 205: 11Degenerate Oligonucleotide Gene S
Page 206 and 207: Degenerate Oligonucleotide Gene Shu
Page 218 and 219: 12M13 Bacteriophage Coat Proteins E
Page 220 and 221: Engineered M13 Bacteriophage Coat P
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Page 235 and 236: 222 Fujita et al.The methods that h
Page 237 and 238: 224 Fujita et al.3. Streptavidin an
Page 239 and 240: 226 Fujita et al.Fig. 2. (Continued
Page 241 and 242: 228 Fujita et al.Fig. 3. (Continued
Page 243 and 244: 230 Fujita et al.Fig. 3. (A) Schema
Page 245 and 246: 232 Fujita et al.1. Add 2 µg mRNA
Page 247 and 248: 234 Fujita et al.Innovative Bioscie
Page 249 and 250: 236 Fujita et al.30. Kim, Y., Mlsa,
Page 251 and 252: 238 Ghadessy and Holligeraffinity m
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240 Ghadessy and HolligerFig. 1. (A
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242 Ghadessy and HolligerFinally, t
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244 Ghadessy and Holliger2. Prepare
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246 Ghadessy and Holliger2. After 6
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248 Ghadessy and Holliger21. Oberho
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250 Campbell-Valois and Michnickscr
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252 Campbell-Valois and Michnickfol
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254 Campbell-Valois and Michnick7.
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256 Campbell-Valois and MichnickFig
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258 Campbell-Valois and Michnickres
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260Fig. 3. BL21 pREP4 cells were co
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262 Campbell-Valois and MichnickFig
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264 Campbell-Valois and Michnickvar
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276 Hecky et al.improved half-life
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278 Hecky et al.Fig. 1. (A) Scheme
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280 Hecky et al.11. Reverse primer
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282 Hecky et al.high variability in
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284 Hecky et al.coding sequence for
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286 Hecky et al.4. Analyze the resu
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Table 1Amino Acid Substitutions Sel
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290 Hecky et al.Fig. 4. Structure o
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292 Hecky et al.Fig. 5. Expression
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294 Hecky et al.Table 2Kinetic Para
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296 Hecky et al.The thermoactivity
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298 Hecky et al.Fig. 8. Unfolding o
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300 Hecky et al.for the first trans
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302 Hecky et al.7. Thompson, M. J.
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304 Hecky et al.40. Wang, X., Minas
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306 IndexCCalcium indicators, see C
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308 Indexchemiocompetent cellprepar
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310 Indexmaterials, 169, 170mutatio
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312 IndexTerminal truncation, see a
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