Fluorescence Resonance Energy Transfer in Calf Thymus DNA from a Long-Lifetime Metal-Ligand Complex to Nile Blue

Journal of Biochemistry and Molecular Biology

Volumn 34, Issue 6, 2001, Pages 551-558

  Kang, Jung Sook ^a   Lakowicz, Joseph R ^b  

^a Pusan National University   (South Korea)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

DNA dynamics; Fluorescence resonance energy transfer; Frequency domain fluorometry; Light emitting diode; Long lifetime metal ligand complex

Indexed keywords

EID: 0035643282     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. Allison, S. A. and Schurr, J. M. (1979) Torsion dynamics and depolarization of fluorescence of linear macromolecules. 1. Theory and application to DNA. Chem. Phys. 41, 35-59.
2. Barkley, M. D. and Zimm, B. H. (1979) Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70, 2991-3007.
3. Blumen, A. and Manz, J. (1979) On the concentration and time dependence of the energy transfer to randomly distributed acceptors. J. Chem. Phys. 71, 4694-4702.
4. Cho, Y. S., Chang, S.-G., Choi, K.-D., Shin, H. C., Ahn, B. Y. and Kim, K.-S. (2000) Solution structure of an active miniproinsulin, M2PI: inter-chain flexibility is crucial for insulin activity. J. Biochem. Mol. Biol. 33, 120-125.
5. Clegg, R. M., Murchie, A. I. H. and Lilley, D. M. J. (1994) The solution structures of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis. Biophys. J. 66, 99-109.
6. DeGraff, B. A. and Demas, J. N. (1994) Direct measurement of rotational correlation times of luminescent ruthenium(II) molecular probes by differential polarized phase fluorometry. J. Phys. Chem. 98, 12478-12480.
7. Demas, J. N. and Crosby, G. A. (1971) The measurement of photoluminescence quantum yields. A review. J. Phys. Chem. 75, 991-1024.
8. Eis, P. S. and Millar, D. P. (1993) Conformational distributions of a four-way DNA junction revealed by time-resolved fluorescence energy transfer. Biochemistry 32, 13852-13860.
9. Feddersen, B. A., Piston, D. W. and Gratton, E. (1989) Digital parallel acquisition in frequency domain fluorimetry. Rev. Sci. Instrum. 60, 2929-2936.
10. Förster, Th. (1948) Intermolecular energy migration and fluorescence. Ann. Phys. 2, 55-75. Translated by Knox R. S., Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627.
11. 2+. J. Am. Chem. Soc. 112, 4960-4962.
12. Ghosh, S. S., Eis, P. S., Blumeyer, K., Fearon, K. and Millar, D. P. (1994) Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer. Nucleic Acids Res. 22, 3155-3159.
13. Gohlke, C., Murchie, A. I. H., Lilley, D. M. and Clegg, R. M. (1994) Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 91, 11660-11664.
14. Gratton, E., Lakowicz, J. R., Maliwal, B. P., Cherek, H. and Laczko, G. (1984) Resolution of mixtures of fluorophores using variable-frequency phase and modulation data. Biophys. J. 46, 478-486.
15. Haugen, G. R. and Lytle, F. E. (1981) Quantitation of fluorophores in solution by pulsed laser excitation and time-filtered detection. Anal. Chem. 53, 1554-1559.
16. Hill, J. J. and Royer, C. A. (1997) Fluorescence approaches to study of protein-nucleic acid complexation. Methods Enzymol. 278, 390-416.
17. Hochstrasser, R. A., Chen, S.-M. and Millar, D. P. (1992) Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer. Biophys. Chem. 45, 133-141.
18. + luminescence: dependence on DNA sequences and groove-binding agents. Inorg. Chem., 37, 29-34.
19. Jares-Erijman, E. A. and Jovin, T. M. (1996) Determination of DNA helical handedness by fluorescence resonance energy transfer. J. Mol. Biol. 257, 597-617.
20. Jenkins, Y., Friedman, A. E., Turro, N. J. and Barton, J. K. (1992) Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation. Biochemistry 31, 10809-10816.
21. Jung, J.-W., An, J. H., Kim, Y. S., Bang, E.-J. and Lee, W. (1999) Determination of the solution structure of malonyl-CoA by two-dimensional nuclear magnetic resonance spectroscopy and dynamical simulated annealing calculations. J. Biochem. Mol. Biol. 32, 288-293.
22. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, 2nd ed., pp. 368-374, Kluwer Academic/Plenum Publishers, New York.
23. Lakowicz, J. R., Gratton, E., Laczko, G., Cherek, H. and Limkeman, M. (1984) Analysis of fluorescence decay kinetics from variable-frequency phase shift and modulation data. Biophys. J. 46, 463-477.
24. Lakowicz, J. R., Gryczynski, I., Küsba, J., Wiczk, W., Szmacinski, H. and Johnson, M. L. (1994) Site-to-site diffusion in proteins as observed by energy transfer and frequency domain fluorometry. Photochem. Photobiol. 59, 16-29.
25. Lakowicz, J. R., Gryczynski, I., Piszczek, G., Tolosa, L., Nair, R., Johnson, M. L. and Nowaczyk, K. (2000) Microsecond dynamics of biological macromolecules. Methods Enzymol. 323, 473-509.
26. Lakowicz, J. R., Malak, H. Gryczynski, I., Castellano, F. N. and Meyer, G. J. (1995) DNA dynamics observed with long lifetime metal-ligand complexes. Biospectroscopy 1, 163-168.
27. Lakowicz, J. R. and Maliwal, B. P. (1985) Construction and performance of a variable-frequency phase-modulation fluorometer. Biophys. Chem. 21, 61-78.
28. Lakowicz, J. R., Piszczek, G. and Kang, J. S. (2001) On the possibility of long-wavelength long-lifetime high-quantum yield luminophores. Anal. Biochem. 288, 62-75.
29. Lankiewicz, L., Malicka, J. and Wiczk, W. (1997) Fluorescence resonance energy transfer in studies of interchromophoric distances in biomolecules. Acta Biochim. Pol. 44, 477-489.
30. Lee, J.-H. and Choi, B.-S. (2000) Structure of a DNA duplex containing a site-specific Dewar isomer: structural influence of the 3′-T·G base pair of the Dewar product J. Biochem. Mol. Biol. 33, 268-275.
31. Lilly, D. M. (2000) Structures of helical junctions in nucleic acids. Q. Rev. Biophys. 33, 109-159.
32. Malak, H., Gryczynski, I., Lakowicz, J. R., Meyers, G. J. and Castellano, F. N. (1997) Long-lifetime metal-ligand complexes as luminescent probes for DNA. J. Fluorescence 7, 107-112.
33. Maliwal, B. P., Kúsba, J. and Lakowicz, J. R. (1995) Fluorescence energy transfer in one dimension: frequency-domain fluorescence study of DNA-fluorophore complexes. Biopolymers 35, 245-255.
34. Masuko, M, Ohuchi, S., Sode, K., Ohtani, H. and Shimadzu, A. (2000) Fluorescence resonance energy transfer from pyrene to perylene labels for nucleic acid hybridization assays under homogeneous solution conditions. Nucleic Acids Res. 28, e34 (i-viii).
35. Mergny, J.-L., Garestier, T., Rougée, M., Lebedev, A. V., Chassignol, M., Thuong, N. T. and Hélène, C. (1994) Fluorescence energy transfer between two triple helix-forming oligonucleotides bound to duplex DNA. Biochemistry 33, 15321-15328.
36. Murata, S.-I., Kúsba, J., Piszczek, G., Gryczynski, I. and Lakowicz, J. R. (2000) Donor fluorescence decay analysis for energy transfer in double-helical DNA with various acceptor concentrations. Biopolymers 57, 306-315.
37. Murphy, C. J. and Barton, J. K. (1993) Ruthenium complexes as luminescent reporters of DNA. Methods Enzymol. 226, 576-594.
38. Scaria, P. V., Will, S., Levenson, W. C. and Shafer, R. H. (1995) Physicochemical studies of the d(G3T4G3)*d(G3A4G3).d (C3T4C3) triple helix. J. Biol. Chem. 270, 7295-7303.
39. Sipior, J., Carter, J. M., Lakowicz, J. R. and Rao, G. (1996) Single quantum well light-emitting diodes demonstrated as excitation sources for nanosecond phase modulation fluorescence lifetime measurements. Rev. Sci. Instr. 67, 3795-3798.
40. Small, E. W. and Isenberg, I. (1977) Hydrodynamic properties of a rigid molecule: Rotational and linear diffusion and fluorescence anisotropy. Biopolymers 16, 1907-1928.
41. Steinberg, I. Z. (1971) Long-range nonradiative transfer of electronic excitation energy in proteins and polypeptides. Annu. Rev. Biochem. 40, 83-114.
42. Steinberg, I. Z. and Katchalski, E. (1968) Theoretical analysis of the role of diffusion in chemical reactions, fluorescence quenching, and nonradiative energy transfer. J. Chem. Phys. 48, 2404-2410.
43. Stryer, L. (1978) Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47, 819-846.
44. Stryer, L., Thomas, D. D., and Meares, C. F. (1982) Diffusion-enhanced fluorescence energy transfer. Ann. Rev. Biophys. Bioeng. 11, 203-222.
45. Sung, B. K. and Kim, Y. T. (2000) Structural arrangement for functional requirements of brain recombinant 4-aminobutyrate aminotransferase. J. Biochem. Mol. Biol. 33, 43-48.
46. Terpetschnig, E., Szmacinski, H. and Lakowicz, J. R. (1997) Long-lifetime metal-ligand complexes as probes in biophysics and clinical chemistry. Methods Enzymol. 278, 295-321.
47. Tóth, K., Sauermann, V. and Langowski, J. (1998) DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry 37, 8173-8179.
48. Yang, M. and Millar, D. P. (1996) Conformational flexibility of three-way DNA junctions containing unpaired nucleotides. Biochemistry 35, 7959-7967.