Microbeads display of proteins using emulsion PCR and cell-free protein synthesis

Biotechnology Progress

Volumn 24, Issue 5, 2008, Pages 1107-1114

  Gan, Rui ^a   Yamanaka, Yumiko ^a   Kojima, Takaaki ^a   Nakano, Hideo ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Directed evolution; Flow cytometry; In vitro branscription translation

Indexed keywords

BIOTINYLATED; DIRECTED EVOLUTION; DNA LIBRARIES; DNA TEMPLATES; FLUORESCEIN ISOTHIOCYANATE; GLUTATHIONE; IN VITRO BRANSCRIPTION/TRANSLATION; MAGNETIC MICROBEADS; MICRO BEADS; PROTEIN SYNTHESES; RANDOMIZED SEQUENCES; STREPTAVIDIN; TEMPLATE MOLECULES; TWO TYPES; W/O EMULSIONS;

AMINES; AMPLIFICATION; COSMIC RAYS; DNA; EMULSIONS; FLOW CYTOMETRY; GENES; MICROSCOPIC EXAMINATION; NUCLEIC ACIDS; ORGANIC ACIDS; PROGRAMMING THEORY; PROTEINS; SYSTEM THEORY;

EMULSIFICATION;

DNA; MICROSPHERE; PROTEIN; STREPTAVIDIN;

ARTICLE; CELL FREE SYSTEM; CHEMISTRY; EMULSION; GENE LIBRARY; MAGNETISM; METHODOLOGY; POLYMERASE CHAIN REACTION; SURFACE PROPERTY; SYNTHESIS;

CELL-FREE SYSTEM; DNA; EMULSIONS; GENE LIBRARY; MAGNETICS; MICROSPHERES; POLYMERASE CHAIN REACTION; PROTEINS; STREPTAVIDIN; SURFACE PROPERTIES;

EID: 56249117019     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1002/btpr.43     Document Type: Article

References (28)

1. Scott JK, Smith GP. Searching for peptide ligands with an epitope library. Science. 1990;249:386-390.
2. Mattheakis LC, Bhatt RR, Dower WJ. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci USA. 1994;91:9022-9026.
3. Nemoto N, Miyamoto-Sato E, Husimi Y, Yanagawa H. In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett. 1997;414:405-408.
4. Roberts RW, Szostak JW. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA. 1997;94:12297-12302.
5. Ihara H, Mie M, Funabashi H, Takabashi F, Sawasaki T, Endo Y, Kobatake E. In vitro selection of zinc finger DNA-binding proteins through ribosome display. Biochem Biophys Res Commun. 2006;345:1149-1154.
6. Nilsson MTI, Mossing MC, Widersten M. Functional expression and affinity selection of single-chain Cro by phage display: isolation of novel DNA-binding proteins. Protein Eng. 2000;13:519-526.
7. Krag DN, Shukla GS, Shen GP, Pero S, Ashikaga T, Fuller S, Weaver DL, Burdette-Radoux S, Thomas C. Selection of tumor-binding ligands in cancer patients with phage display libraries. Cancer Res. 2006;66:7724-7733.
8. Hu S, Guo X, Xie H, Du Y, Pan Y, Shi Y, Wang J, Hong L, Han S, Zhang D, Huang D, Zhang K, Bai F, Jiang H, Zhai H, Nie Y, Wu K, Fan D. Phage display selection of peptides that inhibit metastasis ability of gastric cancer cells with high liver-metastatic potential. Biochem Biophys Res Commun. 2006;341:964-972.
9. Yan X, Xu Z. Ribosome-display technology: applications for directed evolution of functional proteins. Drug Discov Today. 2006;11:911-916.
10. Steiner D, Forrer P, Stumpp MT, Plückthun A. Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat Biotechnol. 2006;24:823-831.
11. Brinkmann U, Chowdhury PS, Roscoe DM, Pastan I. Phage display of disulfide-stabilized Fv fragments. J Immunol Methods. 1995;182:41-50.
12. Calhoun KA, Swartz JR. Energy systems for ATP regeneration in cell-free protein synthesis reactions. Methods Mol Biol. 2007;375:3-17.
13. Ohashi H, Shimizu Y, Ying B, Ueda T. Efficient protein selection based on ribosome display system with purified components. Biochem Biophys Res Commun. 2007;352:270-276.
14. Tawfik DS, Griffiths AD. Man-made cell-like compartments for molecular evolution. Nat Biotechnol. 1998;16:652-656.
15. Doi N, Yanagawa H. STABLE: protein-DNA fusion system for screening of combinatorial protein libraries in vitro. FEBS Lett. 1999;457:227-230.
16. Sepp A, Choo Y. Cell-free selection of zinc finger dna-binding proteins using in vitro compartmentalization. J Mol Biol. 2005;354:212-219.
17. Zheng Y, Roberts RJ. Selection of restriction endonucleases using artificial cells. Nucl Acids Res. 2007;35:e83.
18. Ong JL, 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. 2006;361:537-550.
19. Bernath K, Hai M, Mastrobattista E, Griffiths AD, Magdassi S, Tawfik DS. In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem. 2004;325:151-157.
20. Bernath K, Magdassi S, Tawfik DS. Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery. J Mol Biol. 2005;345:1015-1026.
21. Sepp A, Tawfik DS, Griffiths AD. Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett. 2002;532:455-458.
22. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376-380.
23. Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'Neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med. 2006;12:852-855.
24. Kojima T, Takei Y, Ohtsuka M, Kawarasaki Y, Yamane T, Nakano H. PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets. Nucl Acids Res. 2005;33:e150.
25. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001.
26. Griffiths AD, Tawfik DS. Miniaturising the laboratory in emulsion droplets. Trends Biotechnol. 2006;24:395-402.
27. Famm K, Winter G. Engineering aggregation-resistant proteins by directed evolution. Protein Eng Des Sel. 2006;19:479-481.
28. Kaufmann M, Lindner P, Honegger A, Blank K, Tschopp M, Capitani G, Plückthun A, Grüner MG. Crystal Structure of the anti-His tag antibody 3D5 single-chain fragment complexed to its antigen. J Mol Biol. 2002;318:135-147.