From fluorescence polarization to Quenchbody: Recent progress in fluorescent reagentless biosensors based on antibody and other binding proteins

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 11, 2014, Pages 1951-1959

  Ueda, Hiroshi ^a   Dong, Jinhua ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

DARPin; Fluorescence quenching; In vitro translation; Position specific labeling; Q body; Reagentless biosensor

Indexed keywords

ANTIBODY; BINDING PROTEIN; FLUORESCENT DYE; IMMUNOGLOBULIN F(AB) FRAGMENT; VIMENTIN;

ARTICLE; BIOSENSOR; BIOSENSOR QUENCHBODY; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT ANTIBODY TECHNIQUE; IMAGING; IMMUNOASSAY; PHOTOCHEMICAL QUENCHING; POLARIZATION; PROTEIN PHOSPHORYLATION;

EID: 84907943065     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2014.06.005     Document Type: Review

References (81)

1. D. Wild The Immunoassay Handbook, Fourth Edition: Theory and Applications of Ligand Binding, ELISA and Related Techniques 4th ed. 2013 Elsevier Oxford
2. FDA Draft Guidance for Industry and Food and Drug Administration Staff: In Vitro Companion Diagnostic Devices 2011
3. L.J. Clark, and C. Lyons Electrode systems for continuous monitoring in cardiovascular surgery Ann. N. Y. Acad. Sci. 102 1962 29 45
4. G.A. Rechnitz, R.K. Kobos, S.J. Riechel, and C.R. Gebauer A bio-selective membrane electrode prepared with living bacterial cells Anal. Chim. Acta. 94 1977 357 365
5. V. Sanz, S. de Marcos, and J. Galbán Hydrogen peroxide and peracetic acid determination in waste water using a reversible reagentless biosensor Anal. Chim. Acta. 583 2007 332 339
6. D.J. Weiss, M. Dorris, A. Loh, and L. Peterson Dehydrogenase based reagentless biosensor for monitoring phenylketonuria Biosens. Bioelectron. 22 2007 2436 2441
7. V. Laurinavicius, B. Kurtinaitien, V. Liauksminas, A. Jankauskait, R. Simkus, R. Meskys, L. Boguslavsky, T. Skotheim, and S. Tanenbaum Reagentless biosensor based on PQQ-depended glucose dehydrogenase and partially hydrolyzed polyarbutin Talanta 52 2000 485 493
8. I.L. Medintz, E.R. Goldman, M.E. Lassman, A. Hayhurst, A.W. Kusterbeck, and J.R. Deschamps Self-assembled TNT biosensor based on modular multifunctional surface-tethered components Anal. Chem. 77 2005 365 372
9. C. McDonagh, C.S. Burke, and B.D. MacCraith Optical chemical sensors Chem. Rev. 108 2008 400 422
10. D. Grieshaber, R. MacKenzie, J. Voros, and E. Reimhult Electrochemical biosensors - sensor principles and architectures Sensors 8 2008 1400 1458
11. X. Fan, I.M. White, S.I. Shopova, H. Zhu, J.D. Suter, and Y. Sun Sensitive optical biosensors for unlabeled targets: a review Anal. Chim. Acta. 620 2008 8 26
12. K.A. Marx Quartz crystal microbalance: a useful tool for studying thin polymer films and complex biomolecular systems at the solution-surface interface Biomacromolecules 4 2003 1099 1120
13. K. Ren, P. Kao, M. Pisani, and S. Tadigadapa Monitoring biochemical reactions using Y-cut quartz thermal sensors Analyst 136 2011 2904 2911
14. I. Lopez Arbeloa, and P. Ruiz Ojeda Dimeric states of rhodamine B Chem. Phys. Lett. 87 1982 556 560
15. W.B. Dandliker, and G.A. Feigen Quantification of the antigen-antibody reaction by the polarization of fluorescence Biochem. Biophys. Res. Commun. 5 1961 299 304
16. W.B. Dandliker, R.J. Kelly, J. Dandliker, J. Farquahar, and J. Levin Fluorescence polarization immunoassay. Theory and experimental method Immunochemistry 10 1973 219 227
17. X.Q. Guo, F.N. Castellano, L. Li, and J.R. Lakowicz Use of a long-lifetime Re(I) complex in fluorescence polarization immunoassays of high-molecular-weight analytes Anal. Chem. 70 1998 632 637
18. J.A. Fitzpatrick, and B.F. Lillemeier Fluorescence correlation spectroscopy: linking molecular dynamics to biological function in vitro and in situ Curr. Opin. Struct. Biol. 21 2011 650 660
19. Y. Takahashi, J. Nishimura, A. Suzuki, K. Ishibashi, M. Kinjo, and A. Miyawaki Cross-talk-free fluorescence cross-correlation spectroscopy by the switching method Cell Struct. Funct. 33 2008 143 150
20. L.C. Hwang, and T. Wohland Recent advances in fluorescence cross-correlation spectroscopy Cell Biochem. Biophys. 49 2007 1 13
21. T. Förster Zwischen molekulare energiewanderung und fluoreszenz Ann. Phys. 2 1948 55 75
22. E.F. Ullman, and P.L. Khanna Fluorescence excitation transfer immunoassay (FETI) Methods Enzymol. 74 Pt C 1981 28 60
23. E.F. Ullman, M. Schwarzberg, and K.E. Rubenstein Fluorescent excitation transfer immunoassay. A general method for determination of antigens J. Biol. Chem. 251 1976 4172 4178
24. K. Blomberg, P. Hurskainen, and I. Hemmila Terbium and rhodamine as labels in a homogeneous time-resolved fluorometric energy transfer assay of the beta subunit of human chorionic gonadotropin in serum Clin. Chem. 45 1999 855 861
25. H. Ueda Open sandwich immunoassay: a novel immunoassay approach based on the interchain interaction of an antibody variable region J. Biosci. Bioeng. 94 2002 614 619
26. H. Ueda, K. Tsumoto, K. Kubota, E. Suzuki, T. Nagamune, H. Nishimura, P.A. Schueler, G. Winter, I. Kumagai, and W.C. Mahoney Open sandwich ELISA: a novel immunoassay based on the interchain interaction of antibody variable region Nat. Biotechnol. 14 1996 1714 1718
27. R. Arai, H. Ueda, K. Tsumoto, W.C. Mahoney, I. Kumagai, and T. Nagamune Fluorolabeling of antibody variable domains with green fluorescent protein variants: application to an energy transfer-based homogeneous immunoassay Protein Eng. 13 2000 369 376
28. H. Ueda, K. Kubota, Y. Wang, K. Tsumoto, W. Mahoney, I. Kumagai, and T. Nagamune Homogeneous non-competitive immunoassay based on the energy transfer between fluorolabeled antibody variable domains (open sandwich FIA) Biotechniques 27 1999 738 742
29. Y. Sasajima, T. Aburatani, K. Sakamoto, and H. Ueda Detection of protein tyrosine phosphorylation by open sandwich fluoroimmunoassay Biotechnol. Prog. 22 2006 968 973
30. J.D. Dattelbaum, and J.R. Lakowicz Optical determination of glutamine using a genetically engineered protein Anal. Biochem. 291 2001 89 95
31. A. Wada, M. Mie, M. Aizawa, P. Lahoud, A.E. Cass, and E. Kobatake Design and construction of glutamine binding proteins with a self-adhering capability to unmodified hydrophobic surfaces as reagentless fluorescence sensing devices J. Am. Chem. Soc. 125 2003 16228 16234
32. S. Aoyagi, R. Imai, K. Sakai, and M. Kudo Reagentless and regenerable immunosensor for monitoring of immunoglobulin G based on non-separation immunoassay Biosens. Bioelectron. 18 2003 791 795
33. R.M. de Lorimier, J.J. Smith, M.A. Dwyer, L.L. Looger, K.M. Sali, C.D. Paavola, S.S. Rizk, S. Sadigov, D.W. Conrad, L. Loew, and H.W. Hellinga Construction of a fluorescent biosensor family Protein Sci. 11 2002 2655 2675
34. J.D. Dattelbaum, L.L. Looger, D.E. Benson, K.M. Sali, R.B. Thompson, and H.W. Hellinga Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor Protein Sci. 14 2005 284 291
35. S.S. Rizk, M.J. Cuneo, and H.W. Hellinga Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates Protein Sci. 15 2006 1745 1751
36. E.J. Choi, J. Mao, and S.L. Mayo Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications Protein Sci. 16 2007 582 588
37. Y. Tian, M.J. Cuneo, A. Changela, B. Hocker, L.S. Beese, and H.W. Hellinga Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein Protein Sci. 16 2007 2240 2250
38. B.S. Der, and J.D. Dattelbaum Construction of a reagentless glucose biosensor using molecular exciton luminescence Anal. Biochem. 375 2008 132 140
39. K. Hedgethorne, and M.R. Webb Fluorescent SSB as a reagentless biosensor for single-stranded DNA Methods Mol. Biol. 922 2012 219 233
40. Y. Rahimi, S. Shrestha, T. Banerjee, and S.K. Deo Copper sensing based on the far-red fluorescent protein, HcRed, from Heteractis crispa Anal. Biochem. 370 2007 60 67
41. H. Wang, E. Nakata, and I. Hamachi Recent progress in strategies for the creation of protein-based fluorescent biosensors ChemBioChem 10 2009 2560 2577
42. T. Ozawa, H. Yoshimura, and S.B. Kim Advances in fluorescence and bioluminescence imaging Anal. Chem. 85 2013 590 609
43. M. Renard, L. Belkad, N. Hugo, P. England, D. Altschuh, and H. Bedouelle Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies J. Mol. Biol. 318 2002 429 442
44. M. Renard, and H. Bedouelle Improving the sensitivity and dynamic range of reagentless fluorescent immunosensors by knowledge-based design Biochemistry 43 2004 15453 15462
45. M. Renard, L. Belkadi, and H. Bedouelle Deriving topological constraints from functional data for the design of reagentless fluorescent immunosensors J. Mol. Biol. 326 2003 167 175
46. L. Jespers, T.P. Bonnert, and G. Winter Selection of optical biosensors from chemisynthetic antibody libraries Protein Eng. Des. Sel. 17 2004 709 713
47. Y. Hayashi-Takanaka, K. Yamagata, N. Nozaki, and H. Kimura Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase J. Cell Biol. 187 2009 781 790
48. Y. Sato, M. Mukai, J. Ueda, M. Muraki, T.J. Stasevich, N. Horikoshi, T. Kujirai, H. Kita, T. Kimura, S. Hira, Y. Okada, Y. Hayashi-Takanaka, C. Obuse, H. Kurumizaka, A. Kawahara, K. Yamagata, N. Nozaki, and H. Kimura Genetically encoded system to track histone modification in vivo Sci. Rep. 3 2013 2436
49. A. Gulyani, E. Vitriol, R. Allen, J. Wu, D. Gremyachinskiy, S. Lewis, B. Dewar, L.M. Graves, B.K. Kay, B. Kuhlman, T. Elston, and K.M. Hahn A biosensor generated via high-throughput screening quantifies cell edge Src dynamics Nat. Chem. Biol. 7 2011 437 444
50. P. Nalbant, L. Hodgson, V. Kraynov, A. Toutchkine, and K.M. Hahn Activation of endogenous Cdc42 visualized in living cells Science 305 2004 1615 1619
51. M.R. Groves, and D. Barford Topological characteristics of helical repeat proteins Curr. Opin. Struct. Biol. 9 1999 383 389
52. M.A. Andrade, C. Perez-Iratxeta, and C.P. Ponting Protein repeats: structures, functions, and evolution J. Struct. Biol. 134 2001 117 131
53. O. Valdes-Aguilera, and D.C. Neckers Aggregation phenomena in xanthene dyes Acc. Chem. Res. 22 1989 171 177
54. M. Inagaki, Y. Nishi, K. Nishizawa, M. Matsuyama, and C. Sato Site-specific phosphorylation induces disassembly of vimentin filaments in vitro Nature 328 1987 649 652
55. H. Goto, and M. Inagaki Production of a site- and phosphorylation state-specific antibody Nat. Protoc. 2 2007 2574 2581
56. J. Ivaska, H.M. Pallari, J. Nevo, and J.E. Eriksson Novel functions of vimentin in cell adhesion, migration, and signaling Exp. Cell Res. 313 2007 2050 2062
57. I.L. Medintz, G.P. Anderson, M.E. Lassman, E.R. Goldman, L.A. Bettencourt, and J.M. Mauro General strategy for biosensor design and construction employing multifunctional surface-tethered components Anal. Chem. 76 2004 5620 5629
58. J. Li, A. Mahajan, and M.D. Tsai Ankyrin repeat: a unique motif mediating protein-protein interactions Biochemistry 45 2006 15168 15178
59. L.K. Mosavi, D.L. Minor Jr., and Z.Y. Peng Consensus-derived structural determinants of the ankyrin repeat motif Proc. Natl. Acad. Sci. U. S. A. 99 2002 16029 16034
60. H.K. Binz, M.T. Stumpp, P. Forrer, P. Amstutz, and A. Pluckthun Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins J. Mol. Biol. 332 2003 489 503
61. A. Kohl, H.K. Binz, P. Forrer, M.T. Stumpp, A. Pluckthun, and M.G. Grutter Designed to be stable: crystal structure of a consensus ankyrin repeat protein Proc. Natl. Acad. Sci. U. S. A. 100 2003 1700 1705
62. E. Brient-Litzler, A. Pluckthun, and H. Bedouelle Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein Protein Eng. Des. Sel. 23 2010 229 241
63. H.K. Binz, P. Amstutz, A. Kohl, M.T. Stumpp, C. Briand, P. Forrer, M.G. Grutter, and A. Pluckthun High-affinity binders selected from designed ankyrin repeat protein libraries Nat. Biotechnol. 22 2004 575 582
64. F.F. Miranda, E. Brient-Litzler, N. Zidane, F. Pecorari, and H. Bedouelle Reagentless fluorescent biosensors from artificial families of antigen binding proteins Biosens. Bioelectron. 26 2011 4184 4190
65. L. Kummer, C.W. Hsu, O. Dagliyan, C. MacNevin, M. Kaufholz, B. Zimmermann, N.V. Dokholyan, K.M. Hahn, and A. Pluckthun Knowledge-based design of a biosensor to quantify localized ERK activation in living cells Chem. Biol. 20 2013 847 856
66. R. Abe, H. Ohashi, I. Iijima, M. Ihara, H. Takagi, T. Hohsaka, and H. Ueda "Quenchbodies": quench-based antibody probes that show antigen-dependent fluorescence J. Am. Chem. Soc. 133 2011 17386 17394
67. T. Hohsaka, D. Kajihara, Y. Ashizuka, H. Murakami, and M. Sisido Efficient incorporation of nonnatural amino acids with large aromatic groups into streptavidin in in vitro protein synthesizing systems J. Am. Chem. Soc. 121 1999 34 40
68. R. Abe, K. Shiraga, S. Ebisu, H. Takagi, and T. Hohsaka Incorporation of fluorescent non-natural amino acids into N-terminal tag of proteins in cell-free translation and its dependence on position and neighboring codons J. Biosci. Bioeng. 110 2010 32 38
69. D. Kajihara, T. Hohsaka, and M. Sisido Synthesis and sequence optimization of GFP mutants containing aromatic nonnatural amino acids at the Tyr66 position Protein Eng. Des. Sel. 18 2005 273 278
70. I. Iijima, and T. Hohsaka Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching ChemBioChem 10 2009 999 1006
71. S.-L. Lim, H. Ichinose, T. Shinoda, and H. Ueda Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay Anal. Chem. 79 2007 6193 6200
72. N. Marmé, J.-P. Knemeyer, M. Sauer, and J. Wolfrum Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan Bioconjug. Chem. 14 2003 1133 1139
73. H.-J. Jeong, Y. Ohmuro-Matsuyama, H. Ohashi, F. Ohsawa, Y. Tatsu, M. Inagaki, and H. Ueda Detection of vimentin serine phosphorylation by multicolor Quenchbodies Biosens. Bioelectron. 40 2013 17 23
74. M. Ogawa, N. Kosaka, P.L. Choyke, and H. Kobayashi H-type dimer formation of fluorophores: a mechanism for activatable, in vivo optical molecular imaging ACS Chem. Biol. 4 2009 535 546
75. S. Kunzelmann, and M.R. Webb A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM ACS Chem. Biol. 5 2010 415 425
76. R. Abe, H.J. Jeong, D. Arakawa, J.H. Dong, H. Ohashi, R. Kaigome, F. Saiki, K. Yamane, H. Takagi, and H. Ueda Ultra Q-bodies: quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence Sci. Rep. 4 2014 4640
77. R.A. Scheck, and M.B. Francis Regioselective labeling of antibodies through N-terminal transamination ACS Chem. Biol. 2 2007 247 251
78. L.S. Witus, C. Netirojjanakul, K.S. Palla, E.M. Muehl, C.H. Weng, A.T. Iavarone, and M.B. Francis Site-specific protein transamination using N-methylpyridinium-4-carboxaldehyde J. Am. Chem. Soc. 135 2013 17223 17229
79. N.J. Alves, N. Mustafaoglu, and B. Bilgicer Oriented antibody immobilization by site-specific UV photocrosslinking of biotin at the conserved nucleotide binding site for enhanced antigen detection Biosens. Bioelectron. 49 2013 387 393
80. R. Devlin, R.M. Studholme, W.B. Dandliker, E. Fahy, K. Blumeyer, and S.S. Ghosh Homogeneous detection of nucleic acids by transient-state polarized fluorescence Clin. Chem. 39 1993 1939 1943
81. L. Tang, C. Dong, and J. Ren Highly sensitive homogenous immunoassay of cancer biomarker using silver nanoparticles enhanced fluorescence correlation spectroscopy Talanta 81 2010 1560 1567