Droplets as reaction compartments for protein nanotechnology

Methods in Molecular Biology

Volumn 996, Issue , 2013, Pages 269-286

  Devenish, Sean R A ^a   Kaltenbach, Miriam ^a   Fischlechner, Martin ^a   Hollfelder, Florian ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Directed evolution; In vitro compartmentalization; Microfluidics; Protein engineering; Water in oil emulsion

Indexed keywords

MINERAL OIL; OIL; SURFACTANT;

ARTICLE; COMPUTER AIDED DESIGN; CONCENTRATION (PARAMETERS); DNA TEMPLATE; DOWNSTREAM PROCESSING; EMULSION; FLUORESCENCE ANALYSIS; IN VITRO STUDY; MICROFLUIDICS; MICROSCOPY; NANOTECHNOLOGY; PRIORITY JOURNAL; SCIENTIST;

EID: 84877123797     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-354-1_16     Document Type: Article

References (50)

1. Schaerli Y, Hollfelder F (2009) The potential of micro fluidic water-in-oil droplets in experimental biology. Mol Biosyst 5: 1392-1404
2. Chen DL, Gerdts CJ, Ismagilov RF (2005) Using Micro fluidics to Observe the Effect of Mixing on Nucleation of Protein Crystals. J Am Chem Soc 127:9672-9673
3. Huebner A, Bratton D, Whyte G, Yang M, deMello AJ, Abell C, Hollfelder F (2009) Static microdroplet arrays: A micro fluidic device for droplet trapping, incubation and release for enzymatic and cell-based assays. Lab Chip 9:692-698
4. Huebner A, Srisa-Art M, Holt D, Abell C, Hollfelder F, Demello AJ, Edel JB (2007) Quantitative detection of protein expression in single cells using droplet micro fluidics. Chem Commun 2007:1218-1220
5. Hufnagel H, Huebner A, Gulch C, Guse K, Abell C, Hollfelder F (2009) An integrated cell culture lab on a chip: Modular microdevices for cultivation of mammalian cells and delivery into micro fluidic microdroplets. Lab Chip 9:1576-1582
6. Köster S, Angile FE, Duan H, Agresti JJ, Wintner A, Schmitz C, Rowat AC, Merten CA, Pisignano D, Griffiths AD, Weitz DA (2008) Drop-based micro fluidic devices for encapsulation of single cells. Lab Chip 8:1110-1115
7. Clausell-Tormos J, Lieber D, Baret J-C, El-Harrak A, Miller OJ, Frenz L, Blouwolff J, Humphry KJ, Köster S, Duan H, Holtze C, Weitz DA, Griffiths AD, Merten CA (2008) Droplet-Based Micro fluidic Platforms for the Encapsulation and Screening of Mammalian Cells and Multicellular Organisms. Chem Biol 15:427-437
8. Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, Hutchison JB, Rothberg JM, Link DR, Perrimon N, Samuels ML (2009) Droplet micro fluidic technology for single-cell high-throughput screening. Proc Natl Acad Sci USA 106:14195-14200
9. Shim JU, Olguin LF, Whyte G, Scott D, Babtie A, Abell C, Huck WTS, Hollfelder F (2009) Simultaneous determination of gene expression and enzymatic activity in individual bacterial cells in microdroplet compartments. J Am Chem Soc 131:15251-15256
10. El Debs BW, Tschulena U, Griffiths AD, Merten CA (2011) A competitive co-cultivation assay for cancer drug speci ficity evaluation. J Biomol Screen 16:818-824
11. Shim J-u, Patil SN, Hodgkinson JT, Bowden SD, Spring DR, Welch M, Huck WTS, Hollfelder F, Abell C (2011) Controlling the contents of microdroplets by exploiting the permeability of PDMS. Lab Chip 11:1132-1137
12. Huebner A, Olguin LF, Bratton D, Whyte G, Huck WTS, deMello AJ, Edel JB, Abell C, Hollfelder F (2008) Development of quantitative cell-based enzyme assays in microdroplets. Anal Chem 80:3890-3896
13. Damean N, Olguin LF, Hollfelder F, Abell C, Huck WTS (2009) Simultaneous measurement of reactions in microdroplets filled by concentration gradients. Lab Chip 9:1707-1713
14. Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, Baret JC, Marquez M, Klibanov AM, Griffiths AD, Weitz DA (2010) Ultrahighthroughput screening in drop-based micro fluidics for directed evolution. Proc Natl Acad Sci USA 107:4004-4009
15. Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS (2005) High-throughput screening of enzyme libraries: Thiolactonases evolved by fl uorescence-activated sorting of single cells in emulsion compartments. Chem Biol 12: 1281-1289
16. Mastrobattista E, Taly V, Chanudet E, Treacy P, Kelly BT, Griffiths AD (2005) Highthroughput screening of enzyme libraries: In vitro evolution of a beta-galactosidase by fl uorescence-activated sorting of double emulsions. Chem Biol 12:1291-1300
17. Cohen HM, Tawfik DS, Griffiths AD (2004) Altering the sequence speci ficity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization. Prot Eng Des Sel 17:3-11
18. Kintses B, Hein C, Mohamed MF, Fischlechner M, Courtois F, Lainé C, Hollfelder F (2012) Picoliter cell lysate assays in micro fluidic droplet compartments for directed enzyme evolution. Chem Biol 19:1001-1009
19. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145
20. Umbanhowar PB, Prasad V, Weitz DA (2000) Monodisperse Emulsion Generation via Drop Break Off in a Co fl owing Stream. Langmuir 16:347-351
21. Theberge AB, Courtois F, Schaerli Y, Fischlechner M, Abell C, Hollfelder F, Huck WTS (2010) Microdroplets in Micro fluidics: An Evolving Platform for Discoveries in Chemistry and Biology. Angew Chem Int Ed Engl 49:5846-5868
22. Kintses B, van Vliet LD, Devenish SR, Hollfelder F (2010) Micro fluidic droplets: New integrated work fl ows for biological experiments. Curr Opin Chem Biol 14: 548-555
23. Holtze C, Rowat AC, Agresti JJ, Hutchison JB, Angilè FE, Schmitz CHJ, Köster S, Duan H, Humphry KJ, Scanga RA, Johnson JS, Pisignano D, Weitz DA (2008) Biocompatible surfactants for water-in- fl uorocarbon emulsions. Lab Chip 8:1632
24. Chen C-H, Sarkar A, Song Y-A, Miller MA, Kim SJ, Griffith LG, Lauffenburger DA, Han J (2011) Enhancing Protease Activity Assay in Droplet-Based Micro fluidics Using a Biomolecule Concentrator. J Am Chem Soc 133:10368-10371
25. Courtois F, Olguin LF, Whyte G, Theberge AB, Huck WTS, Hollfelder F, Abell C (2009) Controlling the retention of small molecules in emulsion microdroplets for use in cell-based assays. Anal Chem 81:3008-3016
26. Stein V, Johnsson K, Hollfelder F (2007) A Covalent Chemical Genotype- Phenotype Linkage for in vitro Protein Evolution. Chembiochem 8:2191-2194
27. Kaltenbach M, Stein V, Hollfelder F (2011) SNAP Dendrimers: Multivalent Protein Display on Dendrimer-Like DNA for Directed Evolution. Chembiochem 12:2208-2216
28. Huebner A, Srisa-Art M, Holt D, Abell C, Hollfelder F, deMello AJ, Edel JB (2007) Quantitative detection of protein expression in single cells using droplet micro fluidics. Chem Commun (12):1218-1220
29. Tawfik DS, Griffiths AD (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16:652-656
30. Courtois F, Olguin LF, Whyte G, Bratton D, Huck WTS, Abell C, Hollfelder F (2008) An integrated device for monitoring time-dependent in vitro expression from single genes in picolitre droplets. Chembiochem 9:439-446
31. Agresti JJ, Kelly BT, Jäschke A, Griffiths AD (2005) Selection of ribozymes that catalyse multiple-turnover Diels- Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci USA 102:16170-16175
32. Griffiths AD, Tawfik DS (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. EMBO J 22:24-35
33. Stein V, Sielaff I, Johnsson K, Hollfelder F (2007) A covalent chemical genotype-phenotype linkage for in vitro protein evolution. Chembiochem 8:2191-2194
34. Miller OJ, Bernath K, Agresti JJ, Amitai G, Kelly BT, Mastrobattista E, Taly V, Magdassi S, Tawfik DS, Griffiths AD (2006) Directed evolution by in vitro compartmentalization. Nat Meth 3:561-570
35. Kaltenbach M, Devenish SRA, Hollfelder F (2012) A simple method to evaluate the biochemical compatibility of oil/surfactant mixtures for experiments in microdroplets. Lab Chip 12:4185-92
36. Schaerli Y, Wootton RC, Robinson T, Stein V, Dunsby C, Neil MA, French PM, deMello AJ, Abell C, Hollfelder F (2009) Continuous- fl ow polymerase chain reaction of single-copy DNA in micro fluidic microdroplets. Anal Chem 81:302-306
37. Frenz L, Blank K, Brouzes E, Griffiths AD (2009) Reliable micro fluidic on-chip incubation of droplets in delay-lines. Lab Chip 9:1344-1348
38. Bertschinger J, Grabulovski D, Neri D (2007) Selection of single domain binding proteins by covalent DNA display. Prot Eng Des Sel 20:57
39. Bertschinger J, Neri D (2004) Covalent DNA display as a novel tool for directed evolution of proteins in vitro. Prot Eng Des Sel 17:699
40. Doi N, Yanagawa H (1999) STABLE: Protein-DNA fusion system for screening of combinatorial protein libraries in vitro. FEBS Lett 457:227-230
41. Yonezawa M, Doi N, Higashinakagawa T, Yanagawa H (2004) DNA display of biologically active proteins for in vitro protein selection. J Biochem 135:285
42. Yonezawa M, Doi N, Kawahashi Y, Higashinakagawa T, Yanagawa H (2003) DNA display for in vitro selection of diverse peptide libraries. Nuc Acids Res 31:e118
43. Kaltenbach M, Hollfelder F (2011) SNAP display: In vitro protein evolution in microdroplets. In: Jackson RH, Douthwaite JA (eds) Ribosome Display and Related Technologies: Methods and Protocols. Humana Press (Springer Protocols), London
44. Kiss MM, Ortoleva-Donnelly L, Beer NR, Warner J, Bailey CG, Colston BW, Rothberg JM, Link DR, Leamon JH (2011) High-Throughput Quantitative Polymerase Chain Reaction in Picoliter Droplets. Anal Chem 80:8975-8981
45. Ghadessy FJ, Ong JL, Holliger P (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 98:4552-4557
46. d' Abbadie M, Hofreiter M, Vaisman A, Loakes D, Gasparutto D, Cadet J, Woodgate R, Pääbo S, Holliger P (2007) Molecular breeding of polymerases for ampli fication of ancient DNA. Nat Biotechnol 25:939-943
47. Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol 22:755-759
48. Mazutis L, Araghi AF, Miller OJ, Baret JC, Frenz L, Janoshazi A, Taly V, Miller BJ, Hutchison JB, Link D, Griffiths AD, Ryckelynck M (2009) Droplet-based micro fluidic systems for high-throughput single DNA molecule isothermal ampli fication and analysis. Anal Chem 81:4813-4821
49. Paegel BM, Joyce GF (2010) Micro fluidic Compartmentalized Directed Evolution. Chem Biol 17:717-724
50. Jousse F, Farr R, Link DR, Fuerstman MJ, Garstecki P (2006) Bifurcation of droplet fl ows within capillaries. Phys Rev E 74:036311