Spectroscopic study and evaluation of red-absorbing fluorescent dyes

Bioconjugate Chemistry

Volumn 14, Issue 1, 2003, Pages 195-204

  Buschmann, Volker ^a   Weston, Kenneth D ^b   Sauer, Markus ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; AMINO ACIDS; BINDING SITES; FLUORESCENCE QUENCHING; FLUORESCENCE SPECTROSCOPY; PROTEINS; SOAPS (DETERGENTS); SPECTROSCOPIC ANALYSIS;

CHARACTERISTIC ABSORPTION; CHARACTERISTIC EMISSION; CHARACTERISTIC FLUORESCENCE; CONDITION; EMISSION LIFETIME; FLUORESCENCE LIFETIMES; RED-ABSORBING FLUORESCENT DYES; SPECTROSCOPIC CHARACTERISTICS; SPECTROSCOPIC EVALUATION; SPECTROSCOPIC STUDIES;

VISCOSITY;

FLUORESCENT DYE; POLYSORBATE 20; STREPTAVIDIN;

ARTICLE; BINDING SITE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CORRELATION ANALYSIS; FLUORESCENCE; HYDROPHOBICITY; MOLECULAR INTERACTION; SPECTROSCOPY; STRUCTURE ANALYSIS; VISCOSITY;

EID: 12244260059     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc025600x     Document Type: Article

References (52)

1. Smith, L. M., Fung, S., Hunkapillar, M. W., and Hood, L. E. (1985) The synthesis of oligonucleotides containing an aliphatic amine group at the 5′-terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis. Nucleic Acids Res. 13, 2328-2410.
2. Waggoner, A. (1995) Covalent labeling of proteins and nucleic acids with fluorophores. In Methods in Enzymology (Abelson, J. N., and Simon, M. I., Eds.) Vol. 246, pp 362-373, Academic Press, San Diego, CA.
3. Daehne, S. (1998) Near-infrared dyes for high technology applications. Kluwer, Dordrecht.
4. Haugland, R. P. (1996) Handbook of fluorescent probes and research chemicals, Sixth Edition, Molecular Probes, Eugene.
5. Hovius, R., Vallotton, P., Wohland, T., and Vogel, H. (2000) Fluorescence techniques: shedding light on ligand acceptor interactions. Trends Pharmacol. Sci. 21, 266-273.
6. Aubin, J. E. (1979) Autofluorescence of viable cultured mammalian cells. J. Histochem. Cytochem. 27, 35-43.
7. Cheng, P. C., and Kriete, A. (1995) Image contrast in confocal light microscopy. In Handbook of biological confocal microscopy (Pawley, J. B., Ed.) 2nd ed., pp 327-346, Plenum Press, New York.
8. Affleck, R. L., Ambrose, W. P., Demas, J. N., Goodwin, P. M., Schecker, J. A., Wu, M., and Keller, R. A. (1996) Reduction of luminescent background in ultrasensitive fluorescence detection by photobleaching. Anal. Chem. 68, 2270-2276.
9. Patonay, G., and Antoine, M. D. (1991) Near-infrared fluorogenic labels: New approach to an old problem. Anal. Chem. 63, 321A-327A.
10. Sauer, M., Han, K. T., Ebert, V., Müller, R., Schulz, A., Seeger, S., Wolfrum, J., Arden-Jacob, J., Deltau, G., Marx, N. J., Zander, C., and Drexhage, K. H. (1995) New fluorescent dyes in the red region for biodiagnostics. J. Fluoresc. 5, 247-261.
11. William, D. C., and Soper, S. A. (1995) Ultrasensitive nearIR fluorescence detection for capillary gel electrophoresis and DNA sequencing applications. Anal. Chem. 67, 3427-3432.
12. Arden-Jacob, J., Marx, N. J., and Drexhage, K. H. (1997) New fluorescent probes for the red spectral region. J. Fluoresc. 7, 91S-93S.
13. Sauer, M., Arden-Jacob, J., Drexhage, K. H., Göbel, F., Lieberwirth, U., Mühlegger, K., Müller, R., Wolfrum, J., and Zander, C. (1998) Time-resolved identification of individual mononucleotide molecules in aqueous solution with pulsed semiconductor lasers. Bioimaging 6, 14-24.
14. Lieberwirth, U., Arden-Jacob, J., Drexhage, K. H., Herten, D. P., Müller, R., Neumann, M., Schulz, A., Siebert, S., Sagner, G., Klingel, S., Sauer, M., and Wolfrum, J. (1998) Multiplex dye DNA sequencing in capillary gel electrophoresis by diode laser-based time-resolved fluorescence detection. Anal. Chem. 70, 4771-4779.
15. Terpetschnig, E., Szmacinski, H., Ozinskas, A., and Lakowicz, J. R. (1994) Synthesis of squaraine-N-hydroxysuccinimide esters and their biological application as long-wavelength fluorescent labels. Anal. Biochem. 217, 197-204.
16. Oswald, B., Patsenker, L., Duschl, J., Szmacinski, H., Wolfbeis, O. S., and Terpetschnig, E. (1999) Synthesis, spectral properties, and detection limits of reactive squaraine dyes, a new class of diode laser compatible fluorescent protein labels. Bioconjugate Chem. 10, 925-931.
17. Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., and Waggoner, A. S. (1989) Cyanine dye labeling reagents containing isothiocyanate groups. Cytometry 10, 11-19.
18. Southwick, P. L., Ernst, L. A., Tauriello, E. V., Parker, S. R., Mujumdar, R. B., Mujumdar, S. R., Clever, H. A., and Waggoner, A. S. (1990) Cyanine dye labeling reagents: carboxymethylinindocyanine esters. Cytometry 11, 418-430.
19. Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., Lewis, C. J., and Waggoner, A. S. (1993) Cyanine dye labeling reagents: Sulfoindocyanine succinimidyl esters. Bioconjugate Chem. 4, 105-111.
20. Flanagan, J. H., Jr., Khan, S. H., Menchen, S., Soper, S. A., and Hammer, R. P. (1997) Functionalized tricarbocyanine dyes as near-infrared fluorescent probes for biomolecules. Bioconjugate Chem. 8, 751-756.
21. Sauer, M., Zander, C., Müller, R., Ullrich, B., Drexhage, K. H., Kaul, S., and Wolfrum, J. (1997) Detection and identification of individual antigen molecules in human serum with pulsed semicoductor lasers. Appl. Phys. B 65, 427-431.
22. Neuweiler, H., Schulz, A., Vaiana, A., Smith, J., Kaul, S., Wolfrum, J., and Sauer, M. (2002) Peptide-based molecular beacons for the detection of p53-autoantibodies in human sera. Angew. Chemie, in press.
23. Terasaki, M., and Dailey, M. E. (1995) Confocal microscopy on living cells. In Handbook of biological confocal microscopy (Pawley, J. B., Ed.) 2nd ed., pp 327-346, Plenum Press, New York.
24. 2+ and protein kinase C signals using novel epifluorescence microscopy: Biophys. J. 82, 1076-1085.
25. Förster, T. (1949) Experimentelle und theoretische Untersuchung des zwischenmolekulares Ubergangs von Elektronenanregungsenergie. Z. Naturforsch. 4a, 321-327.
26. Weiss, S. (1998) Fluorescence spectroscopy of single biomolecules. Science 283, 1676-1683.
27. Gordon, G. W., Berry, G., Liang, X. H., Levine, B., and Herman, B. (1998) Quantitative fluorescence resonance energy transfer measurements using fluorescence microscopy. Biophys. J. 74, 2702-2713.
28. Schwille, P., Meyer-Almes, F. J., and Rigler, R. (1997) Dualcolor fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution. Biophys. J. 72, 1878-1886.
29. Hom, E. F. Y., and Verkman, A. S. (2002) Analysis of coupled bimolecular reaction kinetics and diffusion by two-color fluorescence correlation spectroscopy: Enhanced resolution of kinetics by resonance energy transfer. Biophys. J. 83, 533-546.
30. Seidel, C. A. M., Schulz, A., and Sauer, M. (1996) Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J. Phys. Chem. 100, 5541-5553.
31. Edman, L., Mets, Ü., and Rigler, R. (1996) Conformational transitions monitored for single molecules in solution. Proc. Natl. Acad. Sci. U.S.A. 93, 6710-6715.
32. Eggeling, C., Fries, J. R., Brand, L., Günther, R., and Seidel, C. A. M. (1998) Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 95, 1556-1561.
33. Sauer, M., Drexhage, K. H., Lieberwirth, U., Müller, R., Nord, S., and Zander, C. (1998) Dynamics of the electrontransfer reaction between an oxazine dye and DNA oligonucleotides monitored at the single molecule level. Chem. Phys. Lett. 284, 153-163.
34. Kurata, S., Kanagawa, T., Yamada, K., Torimura, M., Yokomaku, T., Kamagata, Y., and Kurane, R. (2001) Fluorescent quenching-based quantitative detection of specific DNA/RNA using BODIPY FL-labeled probe or primer. Nucleic Acids Res. 29, e34.
35. Wagenknecht, H. A., Stemp, E. D. A., and Barton, J. K. (2000) Evidence of electron transfer from peptides to DNA: Oxidation of DNA-bound tryptophan using the flash-quench technique. J. Am. Chem. Soc. 122, 1-7.
36. Knemeyer, J. P., Marmé, N., and Sauer, M. (2000) Probes for the detection of specific DNA sequences at the singlemolecule level. Anal. Chem. 72, 3717-3724.
37. Czerney, P., Lehmann, F., Wenzel, M., Buschmann, V., Dietrich, A., and Mohr, G. J. (2001) Tailor-made dyes for fluorescence correlation spectroscopy (FCS). Biol. Chem. 382, 495-498.
38. Widengren, J., and Schwille, P. (2000) Characterization of photoinduced isomerization and back-isomerization of the cyanine dye Cy5 by fluorescence correlation spectroscopy. J. Phys. Chem. A 104, 6416-6428.
39. Widengren, J., Schweinberger, E., Berger, S., and Seidel, C. A. M. (2001) Two new concepts to measure fluorescence resonance energy transfer via fluorescence correlation spectroscopy: Theory and experimental realizations. J. Phys. Chem. A 105, 6851-6866.
40. Drexhage, K. H. (1973) Structure and properties of laser dyes. In Dye Lasers (Schäfer, F. P., Ed.), pp 144-193, Springer-Verlag, Berlin.
41. Widengren, J. (2001) Photophysical aspects of FCS. In Fluorescence Correlation Spectroscopy (Rigler, R., and Elson, E. S., Eds.), pp 276-301, Springer-Verlag, Berlin.
42. Weber, P. C., Ohlendorf, D. H., Wendolowski, J. J., and Salemme, F. R. (1989) Structural origins of high-affinity biotin binding to streptavidin. Science 243, 85-88.
43. Chevalier, J., Yi, J., Michel, O., and Ming, T. X. (1997) Biotin and digoxigenin as labels for light and electron microscopy in situ hybridization probes: Where do we stand? J. Histochem. Cytochem. 45, 481-91.
44. Gruber, J. H., Kahn, C. D., Kada, G., Riener, C. K., Harms, G. S., Ahrer, W., Dax, T. G., and Knaus, H. (2000) Anomalous fluorescence enhancement of Cy3 and Cy3.5 versus anomalous fluorescence loss of Cy5 and Cy7 upon covalent linking to IgG and noncovalent binding to avidin. Bioconjugate Chem. 11, 696-704.
45. Emans, N., Biwerski, J., and Verkman, A. S. (1995) Imaging of endosome fusion in BHK fibroblasts based on a novel fluorometric avidin-biotin binding assay. Biophys. J. 69, 716-728.
46. Watt, R. M., and Voss, E. W., Jr. (1977) Mechanism of quenching of fluorescein by antifluorescein IgG antibodies. Immunochemistry 14, 533-541.
47. Magde, D., Elson, E. L., and Webb, W. W. (1972) Thermodynamic fluctuations in a reacting system - Measurement by fluorescence correlation spectroscopy. Phys. Rev. Lett. 29, 705-708.
48. Honig, M. G., and Hume, R. I. (1986) Fluorescent carbocyanine dyes allow living neurons of identified origin to be studied in long-term cultures. J. Cell Biol. 103, 171-187.
49. Weston, K. D., and Goldner, L. (2001) Measuring the orientation and reorientation dynamics of single molecules. J. Phys. Chem. B 105, 3453-3460.
50. Bayliss, N. S. (1950) The effect of electrostatic polarization of the solvent on electronic absorption spectra. J. Chem. Phys. 18, 292-298.
51. Rodriguez, J., Scherlis, D., Estrin, D., Aramendia, P. F., and Negri, R. M. (1997) AM1 study of the ground and excitedstate potential energy surfaces of symmetric carbocyanines. J. Phys. Chem. 101, 6998-7006.
52. Tinnefeld, P., Buschmann, V., Weston, K. D., and Sauer, M. (2002) Direct Observation of Collective Blinking and Energy Transfer in a Bichromophoric System. J. Phys. Chem. A, in press.