Exo-Taq-based detection of DNA-binding protein for homogeneous and microarray format

Journal of Biochemistry

Volumn 138, Issue 4, 2005, Pages 473-478

  Fukumori, Takashi ^a,b   Miyachi, Hirotaka ^a   Yokoyama, Kenji ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

DNA binding protein; DNA protein interaction; Exonuclease III stop assay; Fluorescent dye labeled nucleotide; Taq DNA polymerase

Indexed keywords

DEOXYURIDINE TRIPHOSPHATE DERIVATIVE; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; EXODEOXYRIBONUCLEASE III; FLUORESCENT DYE; PROTEIN; TAQ POLYMERASE;

ANALYTIC METHOD; ARTICLE; BACTERIOPHAGE LAMBDA; CRO REPRESSOR GENE; DNA PROBE; ENZYME ACTIVITY; FLUORESCENCE; GEL ELECTROPHORESIS; IMAGE ANALYSIS; PROTEIN DETERMINATION; PROTEIN DNA INTERACTION; REPRESSOR GENE;

BASE SEQUENCE; DNA PROBES; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EXODEOXYRIBONUCLEASES; FLUORESCENT DYES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRESSOR PROTEINS; TAQ POLYMERASE; VIRAL PROTEINS;

BACTERIOPHAGE LAMBDA;

EID: 28244441014     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvi137     Document Type: Article

References (22)

1. Garner, M.M. and Revzin, A. (1981) 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, 3047-3060
2. Jones, O.W. and Leder, P. (1966) Studies on the binding of RNA polymerase to polynucleotides. J. Mol. Biol. 22, 199-209
3. Galas, D.J. and Schmitz, A. (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170
4. Renard, P., Ernest, I., Houbion, A., Art, M., Le Calvez, H., Raes, M., and Remacle, J. (2001) Development of a sensitive multi-well colorimetric assay for active NFkappaB. Nucleic Acids Res. 29, E21
5. Bowen, B., Steinberg, J., Laemmli, U.K., and Weintraub, H. (1980) The detection of DNA-binding proteins by protein blotting. Nucleic Acids Res. 8, 1-20
6. Hanes, S.D. and Brent, R. (1991) Agenetic model for interaction of the homeodomain recognition helix with DNA. Science 251, 426-430
7. Bulyk, M.L., Gentalen, E., Lockhart, D.J., and Church, G.M. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol. 17, 573-577
8. Bulyk, M.L., Huang, X., Choo, Y., and Church, G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163
9. Drobyshev, A.L., Zasedatelev, A.S., Yershov, G.M., and Mirzabekov, A.D. (1999) Massive parallel analysis of DNA-Hoechst 33258 binding specificity with a generic oligodeoxyribonucleotide microchip. Nucleic Acids Res. 27, 4100-4105
10. Krylov, A.S., Zasedateleva, O.A., Prokopenko, D.V., Rouviere-Yaniv, J., and Mirzabekov, A.D. (2001) Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29, 2654-2660
11. Zasedateleva, O.A., Krylov, A.S., Prokopenko, D.V., Skabkin, M.A., Ovchinnikov, L.P., Kolchinsky, A., and Mirzabekov, A.D. (2002) Specificity of mammalian Y-box binding protein p50 in interaction with ss and ds DNA analyzed with generic oligonucleotide microchip. J. Mol. Biol. 324, 73-87
12. Wang, J.K., Li, T.X., Bai, Y.F., and Lu, Z.H. (2003) Evaluating the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray. Anal. Biochem. 316, 192-201
13. Linnell, J., Mott, R., Field, S., Kwiatkowski, D.P., Ragoussis, J., and Udalova, I.A. (2004) Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 32, e44
14. Wu, C. (1985) An exonuclease protection assay reveals heat-shock element and TATA box DNA-binding proteins in crude nuclear extracts. Nature 317, 84-87
15. Han, B., Hamana, H., and Shinozawa, T. (1999) Sensitive detection of the binding of E2F to its promoter by exonuclease III- and BssHII-protection PCR assays. J. Biochem. Biophys. Methods 39, 85-92
16. Wang, J., Li, T., Guo, X., and Lu, Z. (2005) Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins. Nucleic Acids Res. 33, e23
17. Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350-1354
18. Mullis, K.B. and Faloona, F.A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155, 335-350
19. Anderson, W.F., Ohlendorf, D.H., Takeda, Y., and Matthews, B.W. (1981) Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature 290, 754-758
20. Ghosh, S., Gifford, A.M., Riviere, L.R., Tempst, P., Nolan, G.P., and Baltimore, D. (1990) Cloning of the p50 DNA binding subunit of NF-kappa B: homology to rel and dorsal. Cell 62, 1019-1029
21. Baldwin, A.S., Jr. (1996) The NF-kappa B and I kappa B proteins: new discoveries and insights. Annu. Rev. Immunol. 14, 649-683
22. Shen, Z., Peedikayil, J., Olson, G.K., Siebert, P.D., and Fang, Y. (2002) Multiple transcription factor profiling by enzyme-linked immunoassay. Biotechniques 32, 1168, 1170-1162, 1174 passim