Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation

Bioconjugate Chemistry

Volumn 23, Issue 9, 2012, Pages 1969-1980

  Crisalli, Pete ^a   Hernández, Armando R ^a   Kool, Eric T ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDES; OLIGONUCLEOTIDES; QUENCHING;

AMINOOXY GROUPS; BIO-CONJUGATION; FLUORESCENCE QUENCHERS; HIGHER YIELD; HYDRAZONES; KINETIC STUDY; MODIFIED DNA; OPTIMAL CONDITIONS; PROPERTY; ]+ CATALYST;

HYDRAZINE;

ALDEHYDE DERIVATIVE; DNA; FLUORESCEIN; HYDRAZINE; HYDRAZONE DERIVATIVE; OLIGONUCLEOTIDE; OXIME DERIVATIVE; PHOSPHORAMIDOUS ACID DERIVATIVE;

ARTICLE; CATALYST; CONJUGATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; IN VITRO STUDY; MOLECULAR BEACON; PHOTOCHEMICAL QUENCHING; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84866353959     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc300344b     Document Type: Article

References (49)

1. Kolpashchikov, D. M. (2010) Binary probes for nucleic acid analysis Chem. Rev. 110 (8) 4709-4723
2. Liu, J., Cao, Z., and Lu, Y. (2009) Functional nucleic acid sensors Chem. Rev. 109 (5) 1948-1998
3. Kobayashi, H., Ogawa, K., Alford, R., Choyke, P. L., and Urano, Y. (2010) New strategies for fluorescent probe design in medical diagnostic imaging Chem. Rev. 110 (5) 2620-2640
4. Tyagi, S. and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization Nat. Biotechnol. 14 (3) 303-308
5. Franzini, R. M. and Kool, E. T. (2009) Efficient nucleic acid detection by templated reductive quencher release J. Am. Chem. Soc. 131 (44) 16021-16023
6. Nakayama, S., Yan, L., and Sintim, H.O. (2008) Junction probes - sequence specific detection of nucleic acids via template enhanced hybridization processes J. Am. Chem. Soc. 130 (38) 12560-12561
7. Li, J., Wang, F., Mamon, H., Kulke, M. H., Harris, L., Maher, E., Wang., L., and Makrigiorgos, G. M. (2006) Antiprimer quenching-based real-time PCR and its application to the analysis of clinical cancer samples Clin. Chem. 52 (4) 624-633
8. Peng, X., Chen, H., Draney, D. R., Volcheck, W., Schutz-Geschwender, A., and Olive, D. M. (2009) A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays Anal. Biochem. 388, 220-228
9. Blum, G., Mullins, S. R., Keren, K., Fonovic, M., Jedeszko, C., Rice, M. J., Sloane, B. F., and Bogyo, M. (2005) Dynamic imaging of protease activity with fluorescently quenched activity-based probes Nat. Chem. Biol. 1 (4) 203-209
10. Tung, C. (2004) Fluorescent peptide probes for in vivo diagnostic imaging Pept. Sci. 76 (5) 391-403 (Pubitemid 39540533)
11. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination Nat. Biotechnol. 16, 49-53 (Pubitemid 28035948)
12. Johansson, M. K., Fidder, H., Dick, D., and Cook, R. M. (2002) Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes J. Am. Chem. Soc. 124 (24) 6950-6956 (Pubitemid 34633598)
13. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, Kluwer Academic/Plenum Publishers, New York.
14. Bernacchi, S. and Mely, Y. (2001) Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure Nucleic Acids Res. 29, e62
15. Marras, S. A. E., Kramer, F. R., and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes Nucleic Acids Res. 30, e122
16. Johansson, M. K. (2006) Choosing reporter-quencher pairs for efficient quenching through formation of intramolecular dimers. In Methods of Molecular Biology, Vol 335, Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols, Didenko, V. V., Ed., Humana Press Inc., Totowa, NJ.
17. Cook, R. M., Lyttle, M., and Dick, D. Dark quenchers for donor-acceptor energy transfer. U.S. Patent 7,019,129, March 28, 2006.
18. Haugland, R. P., Singer, V. L., and Yue, S. L. Xanthene dyes and their application as luminescence quenching compounds. U.S. Patent 6,399,392, March 4, 2002.
19. Berry, D. A. and Pearson, W. H. Dark quenchers, probes and other conjugates incorporating the same, and their use. U.S. Patent 7,879,986, February 3, 2006.
20. Kopecky, K., Novakova, V., Miletin, M., Kučera, R., and Zimcik, P. (2010) Solid-phase synthesis of azaphthalocyanine-oligonucleotide conjugates and their evaluation as new dark quenchers of fluorescence Bioconjugate Chem. 21, 1872-1879
21. Kopecky, K., Novakova, V., Miletin, M., Kučera, R., and Zimcik, P. (2011) Synthesis of new azaphthalocyanine dark quencher and evaluation of its quenching efficiency with different fluorophores Tetrahedron 67, 5956-5963
22. Pham, W., Weissleder, R., and Tung., C. H. (2002) An azulene dimer as a near-infrared quencher Angew. Chem., Int. Ed. Engl. 41 (19) 3659-3662 (Pubitemid 35190479)
23. Crisalli, P. and Kool, E. T. (2011) Multi-path quenchers: efficient quenching of common fluorophores Bioconjugate Chem. 22 (11) 2345-2354
24. Dirksen, A., Hackeng, T. M., and Dawson, P. E. (2006) Nucleophilic catalysis of oxime ligation Angew Chem., Int. Ed. 45 (45) 7581-7584 (Pubitemid 44851688)
25. Dirksen, A. and Dawson, P. E. (2008) Rapid oxime and hydrazone ligations with aromatic aldehydes for biomolecular labeling Bioconjugate Chem. 19 (12) 2543-2548
26. Dirksen, A., Yegneswaran, S., and Dawson, P. E. (2010) Bisaryl hydrazones as exchangeable biocompatible linkers Angew. Chem., Int. Ed. 49 (11) 2023-2027
27. Key, J. A., Li, C., and Cairo, C. W. (2012) Detection of cellular sialic acid content using nitrobenzoxadiazole carbonyl-reactive chromophores Bioconjugate Chem. 23 (3) 363-371
28. Dilek, O. and Bane, S. L. (2011) Synthesis and spectroscopic characterization of fluorescent boron dipyrromethane-derived hydrazones J. Fluoresc. 21, 347-354
29. Dilek, O. and Bane, S. L. (2008) Synthesis of boron dipyrromethane fluorescent probes for bioorthogonal labeling Tetrahedron Lett. 49 (8) 1413-1416
30. Mori, Y., Niwa, T., and Toyoshi, K. (1981) Carcinogenic azo dyes XVIII: Synthesis of azo dyes related to 3′-hydroxymethyl-4-(dimethylamino) azobenzene, a new potent hepatocarcinogen Chem. Pharm. Bull. 29 (5) 1439-1442 (Pubitemid 11050213)
31. Muramoto, K., Gotto, R., and Kamiya, H. (1987) Analysis of reducing sugars as their chromophoric hydrazones by high-performance liquid chromatography Anal. Biochem. 162 (2) 435-442 (Pubitemid 17076127)
32. Raddatz, S., Mueller-Ibeler, J., Kluge, J., Wäβ, L., Burdinski, G., Havens, J. R., Onofrey, T. J., Wang, D., and Schweitzer, M. (2002) Hydrazide oligonucleotides: new chemical modification for chip array attachment and conjugation Nucleic Acids Res. 30 (21) 4793-4802 (Pubitemid 35331760)
33. Xu, Y., Suzuki, Y., Lönnberg, T., and Komiyama, M. (2009) Human telomeric DNA sequence-specific cleaving by G-quadruplex formation J. Am. Chem. Soc. 131 (8) 2871-2874
34. Lönnberg, T., Suzuki, Y., and Komiyama, M. (2008) Prompt site-selective DNA hydrolysis by Ce(IV)-EDTA using oligonucleotide multiphosphonate conjugates Org. Biomol. Chem. 6 (19) 3580-3587
35. Kisseljova, K., Tsubrik, O., Sillard, R., Mäeorg, S., and Mäeorg, U. (2006) Addition of arylboronic acids to symmetrical and unsymmetrical azo compounds Org. Lett. 8 (1) 43-45 (Pubitemid 43112833)
36. Blackburn, O. A., Coe, B. J., and Helliwell, M. (2011) Tetrapalladium(II) bisazobenzene and azoazoxybenzene complexes: synthesis, electronic structures, and optical properties Organometallics 30 (18) 4910-4923
37. Li, S., Bowerman, D., Marthandan, N., Klyza, S., Luebke, K. J., Garner, H. R., and Kodadek, T. (2004) Photolithiographic synthesis of peptoides J. Am. Chem. Soc. 126 (13) 4088-4089
38. 99mTc-protein conjugates Bioconjugate Chem. 2, 333-336
39. Mezo, G., Szabó, I., Kertész, I., Hegedüs, R., Orbán, E., Leurs, U., Bösze, S., Halmos, G., and Manea, M. (2011) Efficient synthesis of an (aminooxy) acetylated-somatostatin derivative using (aminooxy)acetic acid as a "carbonyl capture reagent J. Pept. Sci. 17 (1) 39-46
40. Jencks, W. P. (1959) Studies on the mechanism of oxime and semicarbazone formation J. Am. Chem. Soc. 81 (2) 475-481
41. More OFerrall, R. A., OBrien, D. M., and Murphy, D. G. (2000) Rate and equilibrium constants for formation and hydrolysis of 9-formylfluorene oxime: diffusion-controlled trapping of a protonated aldehyde by hydroxylamine Can. J. Chem. 78, 1594-1612 (Pubitemid 32098974)
42. Ray, D. and Bharadwaj, P. K. (2008) A coumarin-derived fluorescence probe selective for magnesium Inorg. Chem. 47, 2252-2254
43. 2+-selective fluorescent chemosensor based on coumarin and its application in bioimaging Dalton Trans. 40, 10815-10817
44. 2 Chem. Commun. 47, 3165-3167
45. Wu, J., Sheng, R., Liu, W., Wang, P., Ma, J., Zhong, H., and Zhuang, J. (2011) Reversible fluorescent probe for highly selective and sensitive detection of mercapto biomolecules Inorg. Chem. 50, 6543-6551
46. Borejdo, J., Muthu, P., Talent, J., Gryczynski, Z., Calander, N., Akopova, I., Shtoyko, T., and Gryczynski, I. (2008) Reduction of photobleaching and photodamage in single molecule detection: observing single actin monomer in skeletal myofibrils J. Biomed. Optics 13 (3) 034021
47. Lepock, J. R., Thompson, J. E., Kruuv, J., and Wallach, D. F. H. (1978) Photoinduced crosslinking of membrane proteins by fluorescein isothiocyanate Biochem. Biophys. Res. Commun. 85, 344-350 (Pubitemid 9062779)
48. Bloom, J. A. and Webb, W. W. (1984) Photodamage to intact erythrocyte membranes at high laser intensities: methods of assay and suppression J. Histochem. Cytochem. 32, 608-616 (Pubitemid 14119124)
49. Wolf, D. E., Edidin, M., and Dragsten, P. R. (1980) Effect of bleaching light on measurements of lateral diffusion in cell membranes by the fluorescence photobleaching recovery method Proc. Natl. Acad. Sci. U.S.A. 77, 2043-2045 (Pubitemid 10089596)