Ultra Q-bodies: Quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Abe, Ryoji ^a   Jeong, Hee Jin ^b,c   Arakawa, Dai ^b   Dong, Jinhua ^b,c   Ohashi, Hiroyuki ^a,b   Kaigome, Rena ^a   Saiki, Fujio ^a   Yamane, Kyosuke ^a,b   Takagi, Hiroaki ^a   Ueda, Hiroshi ^b,c  

^a USHIO INC   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

5-CARBOXYTETRAMETHYLRHODAMINE SUCCINIMIDYL ESTER; ANTIBODY; ANTIGEN; FLUORESCENT DYE; IMMUNOGLOBULIN F(AB) FRAGMENT; OSTEOCALCIN; RECOMBINANT PROTEIN; RHODAMINE;

BIOSYNTHESIS; CELL LINE; CHEMISTRY; ESCHERICHIA COLI; GENETIC PROCEDURES; GENETICS; HUMAN; IMMUNOLOGY; METABOLISM; PROCEDURES; SPECTROFLUOROMETRY;

ANTIBODIES; ANTIGENS; BIOSENSING TECHNIQUES; CELL LINE; ESCHERICHIA COLI; FLUORESCENT DYES; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; OSTEOCALCIN; RECOMBINANT PROTEINS; RHODAMINES; SPECTROMETRY, FLUORESCENCE;

EID: 84898667396     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04640     Document Type: Article

References (22)

1. Abe, R. et al. "Quenchbodies": quench-based antibody probes that show antigendependent fluorescence. J. Am. Chem. Soc. 133, 17386-17394 (2011).
2. Renard, M. et al. Knowledge-based design of reagentless fluorescent biosensors from recombinant antibodies. J. Mol. Biol. 318, 429-442 (2002). (Pubitemid 34734837)
3. Kummer, L. et al. Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chem Biol 20, 847-856 (2013).
4. Jespers, L., Bonnert, P. T. & Winter, G. Selection of optical biosensors from chemisynthetic antibody libraries. Prot. Eng. Des. Sel. 17, 709-713 (2004). (Pubitemid 40143852)
5. Jager, M. & Pluckthun, A. Domain interactions in antibody Fv and scFv fragments: effects on unfolding kinetics and equilibria. FEBS Letters 462, 307-312(306) (1999).
6. Rothlisberger, D., Honegger, A. & Pluckthun, A. Domain interactions in the Fab fragment: a comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. J. Mol. Biol. 347, 773-789 (2005). (Pubitemid 40357919)
7. Lim, S.-L., Ichinose, H., Shinoda, T. & Ueda, H. Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay. Anal. Chem. 79, 6193-6200 (2007). (Pubitemid 47282330)
8. Niesen, F., Berglund, H. & Vedadi, M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2, 2212-2221 (2007). (Pubitemid 351565860)
9. Ogawa, M., Kosaka, N., Choyke, P. L. & Kobayashi, H. H-Type Dimer Formation of Fluorophores: A Mechanism for Activatable, in Vivo Optical Molecular Imaging. ACS Chem. Biol. 4, 535-546 (2009).
10. Kajihara, D. et al. FRET analysis of protein conformational change through position-specific incorporation of fluorescent amino acids. Nat Methods 3, 923-929 (2006). (Pubitemid 44614728)
11. Corti, D. et al. A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 333, 850-856 (2011).
12. Lerner, U. H. Osteoblasts, Osteoclasts, and Osteocytes: Unveiling Their Intimate-Associated Responses to Applied Orthodontic Forces. Seminars in Orthodontics 18, 237-248 (2012).
13. Lee, A. J., Hodges, S. & Eastell, R. Measurement of osteocalcin. Ann Clin Biochem 37 (Pt 4), 432-446 (2000). (Pubitemid 30426723)
14. Matsugaki, T. et al. N-myc downstream-regulated gene 1/Cap43 expression promotes cell differentiation of human osteosarcoma cells. Oncol. Rep. 24, 721-725 (2010).
15. Hayashi-Takanaka, Y. et al. Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling. Nucleic acids research 39, 6475-6488 (2011).
16. Aburatani, T.,Ueda, H.&Nagamune, T. Importance of a CDR H3 basal residue in VH/VL interaction of human antibodies. J. Biochem. 132, 775-782 (2002). (Pubitemid 35408501)
17. Dillon, P. P.,Manning, B.M., Daly, S. J., Killard, A. J. &O'Kennedy, R. Production of a recombinant anti-morphine-3-glucuronide single-chain variable fragment (scFv) antibody for the development of a "real-time" biosensor-based immunoassay. J Immunol Methods 276, 151-161 (2003). (Pubitemid 36513846)
18. Harvey, B. R. et al. Engineering of recombinant antibody fragments to methamphetamine by anchored periplasmic expression. J ImmunolMethods 308, 43-52 (2006). (Pubitemid 43107953)
19. Pozharski, E. et al. Diversity in hapten recognition: structural study of an anticocaine antibody M82G2. J. Mol. Biol. 349, 570-582 (2005). (Pubitemid 40724567)
20. Abe, R., Shiraga, K., Ebisu, S., Takagi, H. & Hohsaka, T. 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, 32-38 (2010).
21. Taira, H., Matsushita, Y., Kojima, K., Shiraga, K. & Hohsaka, T. Comprehensive screening of amber suppressor tRNAs suitable for incorporation of non-natural amino acids in a cell-free translation system. Biochem. Biophys. Res. Commun. 374, 304-308 (2008).
22. Iijima, I. & Hohsaka, T. Position-Specific Incorporation of Fluorescent Nonnatural Amino Acids into Maltose-Binding Protein for Detection of Ligand Binding by FRET and Fluorescence Quenching. ChemBioChem 10, 999-1006 (2009).