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Volumn 34, Issue 6, 2006, Pages

Fast Fenton footprinting: A laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HYDROGEN PEROXIDE; HYDROXYL RADICAL; IRON; LIGAND; NUCLEIC ACID; POLYMER; PROTEIN; RIBOZYME; RNA; EDETIC ACID; FE(II) EDTA; FE(II)-EDTA; FENTON'S REAGENT; FERROUS ION; MAGNESIUM;

EID: 33645819791     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl055     Document Type: Article
Times cited : (85)

References (46)
  • 1
    • 0031013756 scopus 로고    scopus 로고
    • Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches
    • Petri,V. and Brenowitz,M. (1997) Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches. Curr. Opin. Biotechnol., 8, 36-44.
    • (1997) Curr. Opin. Biotechnol. , vol.8 , pp. 36-44
    • Petri, V.1    Brenowitz, M.2
  • 2
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical 'footprinting'
    • Brenowitz,M., Chance,M.R., Dhavan,G. and Takamoto,K. (2002) Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical 'footprinting'. Curr. Opin. Struct. Biol., 12, 648-653.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 648-653
    • Brenowitz, M.1    Chance, M.R.2    Dhavan, G.3    Takamoto, K.4
  • 3
    • 84918833988 scopus 로고
    • Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution
    • Buxton,G.V., Greenstock,C.L., Helman,W.P. and Ross,A.B. (1988) Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution. J. Phys. Chem. Ref. Data., 17, 513-886.
    • (1988) J. Phys. Chem. Ref. Data. , vol.17 , pp. 513-886
    • Buxton, G.V.1    Greenstock, C.L.2    Helman, W.P.3    Ross, A.B.4
  • 4
    • 16244389281 scopus 로고    scopus 로고
    • Mapping nucleic acid structure by hydroxyl radical cleavage
    • Tullius,T.D. and Greenbaum,J.A. (2005) Mapping nucleic acid structure by hydroxyl radical cleavage. Curr. Opin. Chem. Biol., 9, 127-134.
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 127-134
    • Tullius, T.D.1    Greenbaum, J.A.2
  • 5
    • 25144445202 scopus 로고    scopus 로고
    • Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry
    • Guan,J.Q. and Chance,M.R. (2005) Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem. Sci., 30, 583-592.
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 583-592
    • Guan, J.Q.1    Chance, M.R.2
  • 6
    • 0001268975 scopus 로고
    • Hydroxyl radical 'footprinting': High-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein
    • Tullius,T.D. and Dombroski,B.A. (1986) Hydroxyl radical 'footprinting': high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc. Natl Acad. Sci. USA, 83, 5469-5473.
    • (1986) Proc. Natl Acad. Sci. USA , vol.83 , pp. 5469-5473
    • Tullius, T.D.1    Dombroski, B.A.2
  • 7
    • 0022382116 scopus 로고
    • Iron(II) EDTA used to measure the helical twist along any DNA molecule
    • Tullius,T.D. and Dombroski,B.A. (1985) Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science, 230, 679-681.
    • (1985) Science , vol.230 , pp. 679-681
    • Tullius, T.D.1    Dombroski, B.A.2
  • 8
    • 0026680555 scopus 로고
    • A stable solid that generates hydroxyl radical upon dissolution in aqueous solution. Reaction with proteins and nucleic acid
    • King,P.A., Anderson,V.E., Edwards,J.O., Gustafson,G., Plumb,R.C. and Suggs,J.W. (1992) A stable solid that generates hydroxyl radical upon dissolution in aqueous solution. Reaction with proteins and nucleic acid. J. Am. Chem. Soc., 114, 5430-5432.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 5430-5432
    • King, P.A.1    Anderson, V.E.2    Edwards, J.O.3    Gustafson, G.4    Plumb, R.C.5    Suggs, J.W.6
  • 10
    • 0034635167 scopus 로고    scopus 로고
    • Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid
    • Chaulk,S.G. and MacMillan,A.M. (2000) Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid. Biochemistry, 39, 2-8.
    • (2000) Biochemistry , vol.39 , pp. 2-8
    • Chaulk, S.G.1    MacMillan, A.M.2
  • 11
    • 0842283944 scopus 로고    scopus 로고
    • Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry
    • Sharp,J.S., Becker,J.M. and Hettich,R.L. (2004) Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Anal. Chem., 76, 672-683.
    • (2004) Anal. Chem. , vol.76 , pp. 672-683
    • Sharp, J.S.1    Becker, J.M.2    Hettich, R.L.3
  • 12
    • 24944566705 scopus 로고    scopus 로고
    • Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry
    • Aye,T.T., Low,T.Y. and Sze,S.K. (2005) Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry. Anal. Chem., 77, 5814-5822.
    • (2005) Anal. Chem. , vol.77 , pp. 5814-5822
    • Aye, T.T.1    Low, T.Y.2    Sze, S.K.3
  • 13
    • 27844593258 scopus 로고    scopus 로고
    • Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale
    • Hambly,D.M. and Gross,M.L. (2005) Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. J. Am. Soc. Mass Spectrom., 16, 2057-2063.
    • (2005) J. Am. Soc. Mass Spectrom. , vol.16 , pp. 2057-2063
    • Hambly, D.M.1    Gross, M.L.2
  • 14
    • 0033568535 scopus 로고    scopus 로고
    • Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry
    • Maleknia,S.D., Brenowitz,M. and Chance,M.R. (1999) Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry. Anal. Chem., 71, 3965-3973.
    • (1999) Anal. Chem. , vol.71 , pp. 3965-3973
    • Maleknia, S.D.1    Brenowitz, M.2    Chance, M.R.3
  • 15
    • 0025035281 scopus 로고
    • Footprinting protein-DNA complexes with gamma-rays
    • Hayes,J.J., Kam,L. and Tullius,T.D. (1990) Footprinting protein-DNA complexes with gamma-rays. Methods Enzymol., 186, 545-549.
    • (1990) Methods Enzymol. , vol.186 , pp. 545-549
    • Hayes, J.J.1    Kam, L.2    Tullius, T.D.3
  • 16
    • 0034697671 scopus 로고    scopus 로고
    • High-resolution in vivo footprinting of a protein-DNA complex using gamma radiation
    • Ottinger,L.M. and Tullius,T.D. (2000) High-resolution in vivo footprinting of a protein-DNA complex using gamma radiation. J. Am. Chem. Soc., 122, 5901-5902.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 5901-5902
    • Ottinger, L.M.1    Tullius, T.D.2
  • 17
    • 0031566962 scopus 로고    scopus 로고
    • Time-resolved synchrotron X-ray 'footprinting', a new approach to the study of nucleic acid structure and function: Application to protein- DNA interactions and RNA folding
    • Sclavi,B., Woodson,S., Sullivan,M., Chance,M.R. and Brenowitz,M. (1997) Time-resolved synchrotron X-ray 'footprinting', a new approach to the study of nucleic acid structure and function: Application to protein- DNA interactions and RNA folding. J. Mol. Biol., 266, 144-159.
    • (1997) J. Mol. Biol. , vol.266 , pp. 144-159
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.R.4    Brenowitz, M.5
  • 19
    • 0000162325 scopus 로고
    • The catalytic decomposition of hydrogen peroxide by iron salts
    • Haber,F. and Weiss,J. (1934) The catalytic decomposition of hydrogen peroxide by iron salts. Proc. R Soc. Lond. A, 147, 332-351.
    • (1934) Proc. R Soc. Lond. A. , vol.147 , pp. 332-351
    • Haber, F.1    Weiss, J.2
  • 20
    • 0028857011 scopus 로고
    • What Species is Responsible for Strand Scission in the reaction of [FeIIEDTA]2- with H2O2 with DNA?
    • Pogozelski,W.K., McNeese,T.J. and Tullius,T.D. (1995) What Species is Responsible for Strand Scission in the reaction of [FeIIEDTA]2- with H2O2 with DNA? J. Am. Chem. Soc., 117, 11673-11679.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11673-11679
    • Pogozelski, W.K.1    McNeese, T.J.2    Tullius, T.D.3
  • 21
    • 0023623752 scopus 로고
    • Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts
    • Tullius,T.D., Dombroski,B.A., Churchill,M.E. and Kam,L. (1987) Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts. Methods Enzymol., 155, 537-558.
    • (1987) Methods Enzymol. , vol.155 , pp. 537-558
    • Tullius, T.D.1    Dombroski, B.A.2    Churchill, M.E.3    Kam, L.4
  • 23
    • 0034851482 scopus 로고    scopus 로고
    • Time-resolved hydroxyl-radical footprinting of RNA using Fe(II)-EDTA
    • Hampel,K.J. and Burke,J.M. (2001) Time-resolved hydroxyl-radical footprinting of RNA using Fe(II)-EDTA. Methods, 23, 233-239.
    • (2001) Methods , vol.23 , pp. 233-239
    • Hampel, K.J.1    Burke, J.M.2
  • 24
    • 0032809580 scopus 로고    scopus 로고
    • Comments on the mechanism of the 'Fenton-Like' reaction
    • Goldstein,S. and Meyerstein,D. (1999) Comments on the mechanism of the 'Fenton-Like' reaction. Acc. Chem. Res., 32, 547-550.
    • (1999) Acc. Chem. Res. , vol.32 , pp. 547-550
    • Goldstein, S.1    Meyerstein, D.2
  • 25
    • 0034771375 scopus 로고    scopus 로고
    • Investigation of the reaction pathway of OH radicals produced by Fenton oxidation in the conditions of wastewater treatment
    • Yoon,J., Lee,Y. and Kim,S. (2001) Investigation of the reaction pathway of OH radicals produced by Fenton oxidation in the conditions of wastewater treatment. Water Sci. Technol., 44, 15-21.
    • (2001) Water Sci. Technol. , vol.44 , pp. 15-21
    • Yoon, J.1    Lee, Y.2    Kim, S.3
  • 26
    • 0032549780 scopus 로고    scopus 로고
    • RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
    • Sclavi,B., Sullivan,M., Chance,M.R., Brenowitz,M. and Woodson,S.A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 279, 1940-1943.
    • (1998) Science , vol.279 , pp. 1940-1943
    • Sclavi, B.1    Sullivan, M.2    Chance, M.R.3    Brenowitz, M.4    Woodson, S.A.5
  • 28
    • 0024285808 scopus 로고
    • Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes
    • Zaug,A.J., Grosshans,C.A. and Cech,T.R. (1988) Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry, 27, 8924-8931.
    • (1988) Biochemistry , vol.27 , pp. 8924-8931
    • Zaug, A.J.1    Grosshans, C.A.2    Cech, T.R.3
  • 29
    • 0033573008 scopus 로고    scopus 로고
    • TATA element recognition by the TATA box-binding protein has been conserved throughout evolution
    • Patikoglou,G.A., Kim,J.L., Sun,L., Yang,S.H., Kodadek,T. and Burley,S.K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev., 13, 3217-3230.
    • (1999) Genes Dev. , vol.13 , pp. 3217-3230
    • Patikoglou, G.A.1    Kim, J.L.2    Sun, L.3    Yang, S.H.4    Kodadek, T.5    Burley, S.K.6
  • 30
    • 0032506171 scopus 로고    scopus 로고
    • DNA sequence-specific recognition by the Saccharomyces cerevisiae 'TATA' binding protein: Promoter-dependent differences in the thermodynamics and kinetics of binding
    • Petri,V., Hsieh,M., Jamison,E. and Brenowitz,M. (1998) DNA sequence-specific recognition by the Saccharomyces cerevisiae 'TATA' binding protein: Promoter-dependent differences in the thermodynamics and kinetics of binding. Biochemistry, 37, 15842-15849.
    • (1998) Biochemistry , vol.37 , pp. 15842-15849
    • Petri, V.1    Hsieh, M.2    Jamison, E.3    Brenowitz, M.4
  • 31
    • 0037041909 scopus 로고    scopus 로고
    • Novel fluorometric assay for hydroxyl radical prevention capacity using fluorescein as the probe
    • Ou,B., Hampsch-Woodill,M., Flanagan,J., Deemer,E.K., Prior,R.L. and Huang,D. (2002) Novel fluorometric assay for hydroxyl radical prevention capacity using fluorescein as the probe. J. Agri. Food Chem., 50, 2772-2777.
    • (2002) J. Agri. Food Chem. , vol.50 , pp. 2772-2777
    • Ou, B.1    Hampsch-Woodill, M.2    Flanagan, J.3    Deemer, E.K.4    Prior, R.L.5    Huang, D.6
  • 32
    • 0037126447 scopus 로고    scopus 로고
    • Fenton degradation of malachite green catalyzed by aromatic additives
    • Chen,F., Ma,W., He,J. and Zhao,J. (2002) Fenton degradation of malachite green catalyzed by aromatic additives. J. Phys. Chem., 106, 9485-9490.
    • (2002) J. Phys. Chem. , vol.106 , pp. 9485-9490
    • Chen, F.1    Ma, W.2    He, J.3    Zhao, J.4
  • 33
    • 0023297560 scopus 로고
    • The reaction between ferrous polyaminocarboxylate complexes and hydrogen peroxide: An investigation of the reaction intermediates by stopped flow spectrophotometry
    • Rush,J.D. and Koppenol,W.H. (1987) The reaction between ferrous polyaminocarboxylate complexes and hydrogen peroxide: An investigation of the reaction intermediates by stopped flow spectrophotometry. J. Inorg. Biochem., 29, 199-215.
    • (1987) J. Inorg. Biochem. , vol.29 , pp. 199-215
    • Rush, J.D.1    Koppenol, W.H.2
  • 34
    • 0029806242 scopus 로고    scopus 로고
    • Quantitative kinetics footprinting of protein-DNA association reactions
    • Hsieh,M. and Brenowitz,M. (1996) Quantitative kinetics footprinting of protein-DNA association reactions. Methods Enzymol., 274, 478-492.
    • (1996) Methods Enzymol. , vol.274 , pp. 478-492
    • Hsieh, M.1    Brenowitz, M.2
  • 35
    • 0032319210 scopus 로고    scopus 로고
    • Following the folding of RNA with time-resolved synchrotron X-ray footprinting
    • Sclavi,B., Woodson,S., Sullivan,M., Chance,M. and Brenowitz,M. (1998) Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol., 295, 379-402.
    • (1998) Methods Enzymol. , vol.295 , pp. 379-402
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.4    Brenowitz, M.5
  • 36
    • 0022437260 scopus 로고
    • Quantitative DNase footprint titration: A method for studying protein-DNA interactions
    • Brenowitz,M., Senear,D.F., Shea,M.A. and Ackers,G.K. (1986) Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol., 130, 132-181.
    • (1986) Methods Enzymol. , vol.130 , pp. 132-181
    • Brenowitz, M.1    Senear, D.F.2    Shea, M.A.3    Ackers, G.K.4
  • 37
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • Das,R., Laederach,A., Perlman,S.M., Herschlag,D. and Altman,R.B. (2005) SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA, 11, 344-354.
    • (2005) RNA , vol.11 , pp. 344-354
    • Das, R.1    Laederach, A.2    Perlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 38
    • 0036304119 scopus 로고    scopus 로고
    • Concerted binding and bending of DNA by Escherichia coli integration host factor
    • Dhavan,G.M., Crothers,D.M., Chance,M.R. and Brenowitz,M. (2002) Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol., 315, 1027-1037.
    • (2002) J. Mol. Biol. , vol.315 , pp. 1027-1037
    • Dhavan, G.M.1    Crothers, D.M.2    Chance, M.R.3    Brenowitz, M.4
  • 40
    • 0034680558 scopus 로고    scopus 로고
    • A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding
    • Pastor,N., Weinstein,H., Jamison,E. and Brenowitz,M. (2000) A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding. J. Mol. Biol., 304, 55-68.
    • (2000) J. Mol. Biol. , vol.304 , pp. 55-68
    • Pastor, N.1    Weinstein, H.2    Jamison, E.3    Brenowitz, M.4
  • 42
    • 0034141589 scopus 로고    scopus 로고
    • The importance of being r: Greater oxidative stability of RNA compared with DNA
    • Thorp,H.H. (2000) The importance of being r: Greater oxidative stability of RNA compared with DNA. Chem. Biol., 7, R33-36.
    • (2000) Chem. Biol. , vol.7
    • Thorp, H.H.1
  • 43
    • 0037466333 scopus 로고    scopus 로고
    • Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme
    • Uchida,T., Takamoto,K., He,Q., Chance,M.R. and Brenowitz,M. (2003) Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme. J. Mol. Biol., 328, 463-478.
    • (2003) J. Mol. Biol. , vol.328 , pp. 463-478
    • Uchida, T.1    Takamoto, K.2    He, Q.3    Chance, M.R.4    Brenowitz, M.5
  • 44
    • 16344376192 scopus 로고    scopus 로고
    • Real time characterization of intermediates in the pathway to open complex formation by E. coli RNA polymerase at the T7A1 promoter
    • Sclavi,B., Zaychikov,E., Rogozina,A., Walther,F., Buckle,M. and Heumann,H. (2005) Real time characterization of intermediates in the pathway to open complex formation by E. coli RNA polymerase at the T7A1 promoter. Proc. Natl Acad. Sci. USA, 102, 4706-4711.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 4706-4711
    • Sclavi, B.1    Zaychikov, E.2    Rogozina, A.3    Walther, F.4    Buckle, M.5    Heumann, H.6
  • 45
    • 33749103972 scopus 로고
    • Ascorbic acid in aromatic hydroxylation. I. A model system for aromatic hydroxylation
    • Udenfriend,S., Clark,C.T., Axelrod,J. and Brodie,B.B. (1954) Ascorbic acid in aromatic hydroxylation. I. A model system for aromatic hydroxylation. J. Biol. Chem., 208, 731-739.
    • (1954) J. Biol. Chem. , vol.208 , pp. 731-739
    • Udenfriend, S.1    Clark, C.T.2    Axelrod, J.3    Brodie, B.B.4
  • 46
    • 1542789741 scopus 로고
    • Fenton's reagent revisited
    • Walling,C. (1975) Fenton's reagent revisited. Acc. Chem. Res., 8.
    • (1975) Acc. Chem. Res. , pp. 8
    • Walling, C.1


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