Abstract
Fluorescently labeled oligonucleotide probes have been widely used in biotechnology, and fluorescence quenching by the interaction between the dyes and a nucleobase has been pointed out. This quenching causes big problem in analytical methods, but is useful in some other cases. Therefore, it is necessary to estimate the fluorescence quenching intensity under various conditions. We focused on the redox properties of some commercially available fluorescent dyes, and investigated dye-nucleotide interactions between a free dye and a nucleotide in aqueous solution by electrochemical and spectroscopic techniques. Our results suggested that the quenching was accompanied by photoinduced electron transfer between a thermodynamically quenchable excited dye and a specific base. Several kinds of fluorescent dyes labeled to the 5’-end of oligonucleotide C10T6 were prepared, and their quenching ratios compared upon hybridization with the complementary oligonucleotide A6G10. The quenching was completely reversible and their efficiencies depended on the attached fluorophore types. The fluorescence of 5-FAM, BODIPY FL or TAMRA-modified probe was strongly quenched by hybridization.
Similar content being viewed by others
References
J. P. Cooper and P. J. Hagerman, Biochemistry, 1990, 29, 9261.
R. A. Hochstrasser, S.-M. Chen, and D. P. Millar, Biophys. Chem., 1992, 45, 133.
S. P. Lee, D. Porter, J. G. Chirikjian, J. R. Knutson, and M. K. Han, Anal. Biochem., 1994, 220, 377.
L. Edman, Ü. Mets, and R. Rigler, Proc. Natl, Acad. Sci. USA, 1996, 93, 6710.
Y. Jia, A. Sytnik, L. Li, S. Vladimirov, B. S. Cooperman, and R. M. Hochstrasser, Proc. Natl, Acad. Sci. USA, 1997, 94, 7932.
N. G. Walter and J. M. Burke, RNA, 1997, 3, 392.
T. Horn, C.-A. Chang, and M. S. Urdea, Nucleic Acids Res., 1997, 25, 4842.
C. Eggeling, J. R. Fries, L. Brand, R. Gunther, and C. A. M. Seidel, Proc. Natl. Acad. Sci. USA, 1998, 95, 1556.
K. Fukui, K. Tanaka, M. Fujitsuka, A. Watanabe, and O. Ito, J. Photochem. Photobiol. B: Biol, 1999, 50, 18.
A. Draganescu, S. C. Hodawadekar, K. R. Gee, and C. Brenner, J. Biol. Chem., 2000, 275, 4555.
A. Moter and U. B. Göbel, J. Microbiol. Methods, 2000, 41, 85.
C. A. M. Seidel, A. Schulz, and M. H. M. Sauer, J. Phys. Chem., 1996, 100, 5541.
F. D. Lewis, X. Liu, J. Liu, S. E. Miller, R. T. Hayes, and M. R. Wasielewski, Nature, 2000, 406, 51.
F. D. Lewis, T. Wu, X. Liu, R. L. Letsinger, S. E. Miller, R. T. Hayes, and M. R. Wasielewski, J. Am. Chem. Soc, 2000, 122, 2889.
E. Zahavy and M. A. Fox, J. Phys. Chem. B, 1999, 103, 9321.
M. Sauer, K. H. Drexhage, U. Lieberwirth, R. Miiller, S. Nord, and C. Zander, Chem. Phys. Lett, 1998, 284, 153.
M. Sauer, K.-T. Han, R. Miiller, S. Nord, A. Schulz, S. Seeger, J. Wolfrum, J. Arden-Jacob, G. Deltau, N. J. Marx, C. Zander, and K. H. Drexhage, J. Fluoresc, 1995, 5, 247.
S. Nord, M. Sauer, J. Arden-Jacob, K. H. Drexhage, U. Lieberwirth, S. Seeger, and J. Wolfrum, J. Fluoresc, 1997, 7, 79S.
J. Widengren, J. Dapprich, and R. Rigler, Chem. Phys., 1997, 216, 417.
R. Jasuja, D. M. Jameson, C. K. Nishijo, and R. W. Larsen, J. Phys. Chem. B, 1997, 101, 1444.
J.-P. Lecomte, A. K. Mesmaeker, J. M. Kelly, A. B. Tossi, and H. Gorner, Photochem. Photobiol, 1992, 55, 681.
C. Moucheron, A. K. Masmaeker, and J. M. Kelly, Photochem. Photobiol. B: Biol, 1997, 40, 91.
D. A. Dunn, V. H. Lin, and I. E. Kochevar, Photochem. Photobiol, 1991, 53, 47.
S. J. Atherton and A. Harriman, J. Am. Chem. Soc, 1993, 115, 1816.
N. E. Geacintov, R. Zhao, V. A. Kuzmin, S. K. Kim, and L. J. Pecora, Photochem. Photobiol, 1993, 58, 185.
D. O’Connor, V. Y. Shafirovich, and N. E. Geacintov, J. Phys. Chem., 1994, 98, 9831.
V. Y. Shafirovich, P. P. Levin, V. A. Kuzmin, T. E. Thorgersson, D. S. Kliger, and N. E. Geacintov, J. Am. Chem. Soc, 1994, 116, 63.
V. Y. Shafirovich, S. H. Courtney, N. Ya, and N. E. Geacintov, J. Am. Chem. Soc, 1995, 117, 4920.
W. E. Jones and M. A. Fox, J. Phys. Chem., 1994, 98, 5095.
A. Konno, Electrochemistry, 1999, 67, 866.
D. Rehm and A. Weller, Isr. J. Chem., 1970, 8, 259.
A. Z. Weller, Phys. Chem. Neu. Folg., 1982, 133, 93.
J. R. Lakowicz, “Principles of fluorescence spectroscopy, 1989, Plenum Press, New York, 257.
S. Fery-Forgues and B. Delavaux-Nicot, J. Photochem. Photobiol. A: Chem., 2000, 132, 137.
J.-P. Lecomte, A. K.-D. Mesmaeker, J. M. Kelly, A. B. Tossi, and H. Gorner, Photochem. Photobiol, 1992, 55, 681.
S. Kirschstein, S. Winter, D. Turner, and G. Löber, Bioelectrochem. Bioenerg., 1999, 48, 415.
D. G. Norman, R. J. Grainber, D. Uhrin, and D. M. J. Lilley, Biochemistry, 2000, 39, 6317.
J. J. P. Stewart, Int. J. Quant. Chem., 1996, 58, 133.
R. A. Hochstrasser, S.-M. Chen, and D. P. Miller, Biophys. Chem., 1992, 45, 133.
S. M. Gasper and G. B. Schuster, J. Am. Chem. Soc, 1997, 119, 12762.
I. Saito, M. Takayama, H. Sugiyama, and K. Nakatani, J. Am. Chem. Soc, 1995, 117, 6406.
J. Geimer and D. Berkert, Chem. Phys. Lett., 1997, 276, 411.
B. Armitage and G. B. Schuster, Photochem. Photobiol, 1997, 66, 164.
C. Lu, W. Lin, W. Wang, Z. Han, S. Yao, and N. Lin, Phys. Chem. Chem. Phys., 2000, 2, 329.
F. D. Lewis, T. Wu, X. Liu, R. L. Letsinger S. R. Greenfield, S. E. Miller, and M. R. Wasielewski, J. Am. Chem. Soc, 2000, 122, 2889.
C. E. Kerr, C. D. Mitchell, J. Headrick, B. E. Eaton, and T. L. Netzel, J. Phys. Chem. B, 2000, 104, 1637.
C. E. Kerr, C. D. Mitchell, Y.-M. Ying, B. E. Eaton, and T. L. Netzel, J. Phys. Chem. B, 2000, 104, 2166.
B. Önfelt, P. Lincoln, B. Nordén, J. S. Baskin, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 5708.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Torimura, M., Kurata, S., Yamada, K. et al. Fluorescence-Quenching Phenomenon by Photoinduced Electron Transfer between a Fluorescent Dye and a Nucleotide Base. ANAL. SCI. 17, 155–160 (2001). https://doi.org/10.2116/analsci.17.155
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.2116/analsci.17.155