Applications of Fluorescence Anisotropy to the Study of Protein-DNA Interactions

Methods in Cell Biology

Volumn 84, Issue , 2008, Pages 243-262

  LiCata, Vince J ^a   Wowor, Andy J ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA DIRECTED DNA POLYMERASE; EDETIC ACID; PROTEIN; RHODAMINE;

CALIBRATION; DIFFUSION; FLUORESCENCE POLARIZATION; INSTRUMENTATION; KINETICS; METABOLISM; METHODOLOGY; PROTEIN BINDING; REVIEW; ROTATION; TEMPERATURE;

CALIBRATION; DIFFUSION; DNA; DNA-DIRECTED DNA POLYMERASE; EDETIC ACID; FLUORESCENCE POLARIZATION; KINETICS; PROTEIN BINDING; PROTEINS; RHODAMINES; ROTATION; TEMPERATURE;

EID: 35449004399     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(07)84009-X     Document Type: Review

References (37)

1. Bailey M.F., Thompson E.H., and Millar D.P. Probing DNA polymerase fidelity mechanisms using time-resolved fluorescence anisotropy. Methods 25 (2001) 62-77
2. Boyer M., Poujol N., Margeat E., and Royer C.A. Quantitative characterization of the interaction between purified human estrogen receptor alpha and DNA using fluorescence anisotropy. Nucleic Acids Res. 28 (2000) 2492-2502
3. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
4. Brown M.P., and Royer C. Fluorescence spectroscopy as a tool to investigate protein interactions. Curr. Opin. Biotechnol. 8 (1997) 45-49
5. Bujalowski W. Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems. Chem. Rev. 106 (2006) 556-606
6. Burke T.J., Loniello K.R., Beebe J.A., and Ervin K.M. Development and application of fluorescence polarization assays in drug discovery. Comb. Chem. High Throughput Screening 6 (2003) 183-194
7. Cantor C.R., and Schimmel P.R. "Biophysical Chemistry," (1980), W.H. Freeman and Company, San Francisco, CA 454-459
8. Chin J., Langst G., Becker P.B., and Widon J. Fluorescence anisotropy assays for analysis of ISWI-DNA and ISWI-nucleosome interactions. Methods Enzymol. 376 (2004) 3-16
9. Datta K., and LiCata V.J. Salt dependence of DNA binding by Thermus aquaticus and Escherichia coli DNA polymerases. J. Biol. Chem. 278 (2003) 5694-5701
10. Datta K., Wowor A.J., Richard A.J., and LiCata V.J. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys. J. 90 (2006) 1739-1751
11. Eftink M.R. Fluorescence methods for studying equilibrium macromolecule-ligand interactions. Methods Enzymol. 278 (1997) 221-257
12. Fried M., and Crothers D.M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9 (1981) 6505-6525
13. Garner M.M., and Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9 (1981) 3047-3060
14. Guest C.R., Hochstrasser R.A., Dupuy C.G., Allen D.J., Benkovic S.J., and Millar D.P. Interaction of DNA with the Klenow fragment of DNA-polymerase-I studied by time-resolved fluorescence spectroscopy. Biochemistry 30 (1991) 8759-8770
15. Hey T., Lipps G., and Krauss G. Binding of XPA and RPA to damaged DNA investigated by fluorescence anisotropy. Biochemistry 40 (2001) 2901-2910
16. Heyduk T., and Lee J.C. Application of fluorescence energy transfer and polarization to monitor Escherichia coli cAMP receptor protein and lac promoter interaction. Proc. Natl. Acad. Sci. USA 87 (1990) 1744-1748
17. Heyduk T., Ma Y.X., Tang H., and Ebright R.H. Fluorescence anisotropy: Rapid, quantitative assay for protein-DNA and protein-protein interaction. Methods Enzymol. 274 (1996) 492-503
18. Hill J.J., and Royer C.A. Fluorescence approaches to study of protein-nucleic acid complexation. Methods Enzymol. 278 (1997) 390-416
19. Jameson D.M., and Sawyer W.H. Fluorescence anisotropy applied to biomolecular interactions. Methods Enzymol. 246 (1995) 283-300
20. Jezewska M.J., and Bujalowski W. A general method of analysis of ligand binding to competing macromolecules using the spectroscopic signal originating from a reference macromolecule. Application to Escherichia coli replicative helicase DnaB protein-nucleic acid interactions. Biochemistry 35 (1996) 2117-2128
21. Lakowicz J.R. "Principles of Fluorescence Spectroscopy,". 2nd edn (1999), Kluwer Academic/Plenum Publishers, New York
22. Lakowicz J.R., Gryczynski I., Gryczynski Z., and Dattelbaum J.D. Anisotropy-based sensing with reference fluorophores. Anal. Biochem. 267 (1999) 397-405
23. Lohman T.M., and Bujalowski W. Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: Spectroscopic approaches to monitor binding. Methods Enzymol. 208 (1991) 258-290
24. Lundblad J.R., Laurance M., and Goodman R.H. Fluorescence polarization analysis of protein-DNA and protein-protein interactions. Mol. Endocrinol. 10 (1996) 607-612
25. McCauley T.G., Hamaguchi N., and Stanton M. Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Anal. Biochem. 319 (2003) 244-250
26. Millar D.P. Time-resolved fluorescence methods for analysis of DNA-protein interactions. Methods Enzymol. 323 (2000) 442-459
27. Parker G.J., Law T.L., Lenoch F.J., and Bolger R.E. Development of high throughput screening assays using fluorescence polarization: Nuclear receptor-ligand-binding and kinase/phosphatase assays. J. Biomol. Screen. 5 (2000) 77-88
28. Perez-Howard G.M., Weil P.A., and Beehem J.M. Yeast TATA binding protein interaction with DNA: Fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry 34 (1995) 8005-8017
29. Riggs A., Suzuki H., and Bourgeois S. Lac repressor-operator interaction. I. Equilibrium studies. J. Mol. Biol. 48 (1970) 67-83
30. Rishi V., Potter T., Lauderman J., Reinhart R., Silvers T., Selby M., Stevenson T., Krosky P., Stephen A.G., Acharya A., Moll J., Oh W.J., et al. A high-throughput fluorescence-anisotropy screen that identifies small molecule inhibitors of the DNA binding of B-ZIP transcription factors. Anal. Biochem. 340 (2005) 259-271
31. Royer C.A. Quantitative detection of macromolecules with fluorescent nucleotides. (1995) US Patent # 5,445,935
32. Royer C.A. Quantitative detection of macromolecules with fluorescent oligonucleotides (1998) US Patent # 5,756,292
33. Royer C.A. Quantitative detection of macromolecules with fluorescent oligonucleotides. (2001) US Patent # 6,326,142
34. Rusinova E., Tretyachenko-Ladokhina V., Vele O.E., Senear D.F., and Ross J.B.A. Alexa and Oregon Green dyes as fluorescence anisotrophy probes for measuring protein-protein and protein-nucleic acid interactions. Anal. Biochem. 308 (2002) 18-25
35. Waggoner A. Covalent labeling of proteins and nucleic acids with fluorophores. Methods Enzymol. 246 (1995) 362-373
36. Wang S.Y., Ahn B.S., Harris R., Nordeen S.K., and Shapiro D.J. Fluorescence anisotropy microplate assay for analysis of steroid receptor-DNA interactions. Biotechniques 37 (2004) 807-817
37. Zetner A. Principles of competitive binding assays (saturation analyses). I. Equilibrium techniques. Clin. Chem. 19 (1973) 699-705