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Volumn 90, Issue 9, 2008, Pages 1265-1272

Modern tools for identification of nucleic acid-binding proteins

Author keywords

Affinity chromatography; Multiprotein complexes; Nucleic acid binding protein; Protein library

Indexed keywords

ANTIBIOTIC AGENT; DEOXYRIBONUCLEASE I; DITHIOTHREITOL; MALTOSE; MULTIPROTEIN COMPLEX; MYC PROTEIN; NUCLEIC ACID; NUCLEIC ACID BINDING PROTEIN; RESTRICTION ENDONUCLEASE; STREPTAVIDIN; UNCOUPLING PROTEIN;

EID: 47949099787     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2008.03.012     Document Type: Review
Times cited : (15)

References (62)
  • 1
    • 27144507813 scopus 로고    scopus 로고
    • Regulation of gene expression: probing DNA-protein interactions in vivo and in vitro
    • Vigneault F., and Guérin S.L. Regulation of gene expression: probing DNA-protein interactions in vivo and in vitro. Expert Rev. Proteomics 2 (2005) 705-718
    • (2005) Expert Rev. Proteomics , vol.2 , pp. 705-718
    • Vigneault, F.1    Guérin, S.L.2
  • 3
    • 0034007256 scopus 로고    scopus 로고
    • Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase
    • van Steensel B., and Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat. Biotechnol. 18 (2000) 424-428
    • (2000) Nat. Biotechnol. , vol.18 , pp. 424-428
    • van Steensel, B.1    Henikoff, S.2
  • 4
    • 20044384522 scopus 로고    scopus 로고
    • Mapping of genetic and epigenetic regulatory networks using microarrays
    • van Steensel B. Mapping of genetic and epigenetic regulatory networks using microarrays. Nat. Genet. 37 Suppl. (2005) S18-S24
    • (2005) Nat. Genet. , vol.37 , Issue.SUPPL
    • van Steensel, B.1
  • 6
    • 0033751373 scopus 로고    scopus 로고
    • Protein engineering by expressed protein ligation
    • Blaschke U.K., Silberstein J., and Muir T.W. Protein engineering by expressed protein ligation. Methods Enzymol. 328 (2000) 478-496
    • (2000) Methods Enzymol. , vol.328 , pp. 478-496
    • Blaschke, U.K.1    Silberstein, J.2    Muir, T.W.3
  • 7
    • 34247639968 scopus 로고    scopus 로고
    • Identification of Herpes TATT-binding protein
    • Wyrwicz L.S., and Rychlewski L. Identification of Herpes TATT-binding protein. Antiviral Res. 75 (2007) 167-172
    • (2007) Antiviral Res. , vol.75 , pp. 167-172
    • Wyrwicz, L.S.1    Rychlewski, L.2
  • 8
    • 34748889938 scopus 로고    scopus 로고
    • Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus
    • Fujishima K., Komasa M., Kitamura S., Suzuki H., Tomita M., and Kanai A. Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res. 14 (2007) 91-102
    • (2007) DNA Res. , vol.14 , pp. 91-102
    • Fujishima, K.1    Komasa, M.2    Kitamura, S.3    Suzuki, H.4    Tomita, M.5    Kanai, A.6
  • 9
    • 0036654975 scopus 로고    scopus 로고
    • A genome-wide screen for site-specific DNA-binding proteins
    • Hazbun T.R., and Fields S. A genome-wide screen for site-specific DNA-binding proteins. Mol. Cell. Proteomics 1 (2002) 538-543
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 538-543
    • Hazbun, T.R.1    Fields, S.2
  • 17
    • 33751540859 scopus 로고    scopus 로고
    • Display technologies: application for the discovery of drug and gene delivery agents
    • Sergeeva A., Kolonin M.G., Molldrem J.J., Pasqualini R., and Arap W. Display technologies: application for the discovery of drug and gene delivery agents. Adv. Drug Deliv. Rev. 58 (2006) 1622-1654
    • (2006) Adv. Drug Deliv. Rev. , vol.58 , pp. 1622-1654
    • Sergeeva, A.1    Kolonin, M.G.2    Molldrem, J.J.3    Pasqualini, R.4    Arap, W.5
  • 19
    • 33847630761 scopus 로고    scopus 로고
    • Eukaryotic ribosome display with in situ DNA recovery
    • He M., and Taussig M.J. Eukaryotic ribosome display with in situ DNA recovery. Nat. Methods 4 (2007) 281-288
    • (2007) Nat. Methods , vol.4 , pp. 281-288
    • He, M.1    Taussig, M.J.2
  • 22
    • 34548388477 scopus 로고    scopus 로고
    • Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins
    • Doi N., Takashima H., Wada A., Oishi Y., Nagano T., and Yanagawa H. Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins. J. Biotechnol. 131 (2007) 231-239
    • (2007) J. Biotechnol. , vol.131 , pp. 231-239
    • Doi, N.1    Takashima, H.2    Wada, A.3    Oishi, Y.4    Nagano, T.5    Yanagawa, H.6
  • 24
    • 33748296315 scopus 로고    scopus 로고
    • Proteome chips for whole-organism assays
    • Kung L.A., and Snyder M. Proteome chips for whole-organism assays. Nat. Rev. Mol. Cell Biol. 7 (2006) 617-622
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 617-622
    • Kung, L.A.1    Snyder, M.2
  • 26
    • 34547135225 scopus 로고    scopus 로고
    • Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter
    • Park H.C., Kim M.L., Lee S.M., Bahk J.D., Yun D.J., Lim C.O., Hong J.C., Lee S.Y., Cho M.J., and Chung W.S. Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter. Nucleic Acids Res. 35 (2007) 3612-3623
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3612-3623
    • Park, H.C.1    Kim, M.L.2    Lee, S.M.3    Bahk, J.D.4    Yun, D.J.5    Lim, C.O.6    Hong, J.C.7    Lee, S.Y.8    Cho, M.J.9    Chung, W.S.10
  • 28
    • 0036354598 scopus 로고    scopus 로고
    • Analyzing mRNA-protein complexes using a yeast three-hybrid system
    • Bernstein D.S., Buter N., Stumpf C., and Wickens M. Analyzing mRNA-protein complexes using a yeast three-hybrid system. Methods 26 (2002) 123-141
    • (2002) Methods , vol.26 , pp. 123-141
    • Bernstein, D.S.1    Buter, N.2    Stumpf, C.3    Wickens, M.4
  • 30
    • 0041856095 scopus 로고    scopus 로고
    • Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae
    • Steiner-Mosonyi M., Leslie D.M., Dehghani H., Aitchison J.D., and Mangroo D. Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae. J. Biol. Chem. 278 (2003) 32236-32245
    • (2003) J. Biol. Chem. , vol.278 , pp. 32236-32245
    • Steiner-Mosonyi, M.1    Leslie, D.M.2    Dehghani, H.3    Aitchison, J.D.4    Mangroo, D.5
  • 31
    • 33645466699 scopus 로고    scopus 로고
    • Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system
    • Riley K.J.L., Cassiday L.A., Kumar A., and Maher L.J. Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system. RNA 12 (2006) 620-630
    • (2006) RNA , vol.12 , pp. 620-630
    • Riley, K.J.L.1    Cassiday, L.A.2    Kumar, A.3    Maher, L.J.4
  • 33
    • 0026345777 scopus 로고
    • Phage-enzymes: expression and affinity chromatography of functional alkaline phosphatase on the surface of bacteriophage
    • McCafferty J., Jackson R.H., and Chiswell D.J. Phage-enzymes: expression and affinity chromatography of functional alkaline phosphatase on the surface of bacteriophage. Protein Eng. 4 (1991) 955-961
    • (1991) Protein Eng. , vol.4 , pp. 955-961
    • McCafferty, J.1    Jackson, R.H.2    Chiswell, D.J.3
  • 34
    • 0035369702 scopus 로고    scopus 로고
    • Selection and identification of proteins bound to DNA triple-helical structures by combination of 2D-electrophoresis and MALDI-TOF mass spectrometry
    • Guillonneau F., Guieysse A.L., Caer J.P.L., Rossier J., and Praseuth D. Selection and identification of proteins bound to DNA triple-helical structures by combination of 2D-electrophoresis and MALDI-TOF mass spectrometry. Nucleic Acids Res. 29 (2001) 2427-2436
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2427-2436
    • Guillonneau, F.1    Guieysse, A.L.2    Caer, J.P.L.3    Rossier, J.4    Praseuth, D.5
  • 35
    • 2442450689 scopus 로고    scopus 로고
    • Isolation and characterization of a novel trans-factor for luteinizing hormone receptor mRNA from ovary
    • Nair A.K., and Menon K.M.J. Isolation and characterization of a novel trans-factor for luteinizing hormone receptor mRNA from ovary. J. Biol. Chem. 279 (2004) 14937-14944
    • (2004) J. Biol. Chem. , vol.279 , pp. 14937-14944
    • Nair, A.K.1    Menon, K.M.J.2
  • 36
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 37
    • 0037838969 scopus 로고    scopus 로고
    • Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions
    • Rusconi F., Guillonneau F., and Praseuth D. Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions. Mass Spectrom. Rev. 21 (2002) 305-348
    • (2002) Mass Spectrom. Rev. , vol.21 , pp. 305-348
    • Rusconi, F.1    Guillonneau, F.2    Praseuth, D.3
  • 38
    • 0036615612 scopus 로고    scopus 로고
    • A proteomics approach for the identification of DNA binding activities observed in the electrophoretic mobility shift assay
    • Woo A.J., Dods J.S., Susanto E., Ulgiati D., and Abraham L.J. A proteomics approach for the identification of DNA binding activities observed in the electrophoretic mobility shift assay. Mol. Cell. Proteomics 1 (2002) 472-478
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 472-478
    • Woo, A.J.1    Dods, J.S.2    Susanto, E.3    Ulgiati, D.4    Abraham, L.J.5
  • 39
    • 33749250049 scopus 로고    scopus 로고
    • The identification of nucleic acid-interacting proteins using a simple proteomics-based approach that directly incorporates the electrophoretic mobility shift assay
    • Stead J.A., Keen J.N., and McDowall K.J. The identification of nucleic acid-interacting proteins using a simple proteomics-based approach that directly incorporates the electrophoretic mobility shift assay. Mol. Cell. Proteomics 5 (2006) 1697-1702
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1697-1702
    • Stead, J.A.1    Keen, J.N.2    McDowall, K.J.3
  • 40
    • 0344305798 scopus 로고    scopus 로고
    • Affinity capture of specific DNA-binding proteins for mass spectrometric identification
    • Yaneva M., and Tempst P. Affinity capture of specific DNA-binding proteins for mass spectrometric identification. Anal. Chem. 75 (2003) 6437-6448
    • (2003) Anal. Chem. , vol.75 , pp. 6437-6448
    • Yaneva, M.1    Tempst, P.2
  • 42
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999
    • (1999) Nat. Biotechnol. , vol.17 , pp. 994-999
    • Gygi, S.P.1    Rist, B.2    Gerber, S.A.3    Turecek, F.4    Gelb, M.H.5    Aebersold, R.6
  • 43
    • 1342282907 scopus 로고    scopus 로고
    • Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer
    • Himeda C.L., Ranish J.A., Angello J.C., Maire P., Aebersold R., and Hauschka S.D. Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol. Cell. Biol. 24 (2004) 2132-2143
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 2132-2143
    • Himeda, C.L.1    Ranish, J.A.2    Angello, J.C.3    Maire, P.4    Aebersold, R.5    Hauschka, S.D.6
  • 44
    • 8444246695 scopus 로고    scopus 로고
    • Repression of transcription at the human T-cell receptor Vbeta2.2 segment is mediated by a MAX/MAD/mSin3 complex acting as a scaffold for HDAC activity
    • Font M.P., Cubizolles M., Dombret H., Cazes L., Brenac V., Sigaux F., and Buckle M. Repression of transcription at the human T-cell receptor Vbeta2.2 segment is mediated by a MAX/MAD/mSin3 complex acting as a scaffold for HDAC activity. Biochem. Biophys. Res. Commun. 325 (2004) 1021-1029
    • (2004) Biochem. Biophys. Res. Commun. , vol.325 , pp. 1021-1029
    • Font, M.P.1    Cubizolles, M.2    Dombret, H.3    Cazes, L.4    Brenac, V.5    Sigaux, F.6    Buckle, M.7
  • 46
    • 26644437215 scopus 로고    scopus 로고
    • Identification of mammalian proteins cross-linked to DNA by ionizing radiation
    • Barker S., Weinfeld M., Zheng J., Li L., and Murray D. Identification of mammalian proteins cross-linked to DNA by ionizing radiation. J. Biol. Chem. 280 (2005) 33826-33838
    • (2005) J. Biol. Chem. , vol.280 , pp. 33826-33838
    • Barker, S.1    Weinfeld, M.2    Zheng, J.3    Li, L.4    Murray, D.5
  • 47
    • 0032527924 scopus 로고    scopus 로고
    • In situ cross-linking by cisplatin of nuclear matrix-bound transcription factors to nuclear DNA of human breast cancer cells
    • Samuel S.K., Spencer V.A., Bajno L., Sun J.M., Holth L.T., Oesterreich S., and Davie J.R. In situ cross-linking by cisplatin of nuclear matrix-bound transcription factors to nuclear DNA of human breast cancer cells. Cancer Res. 58 (1998) 3004-3008
    • (1998) Cancer Res. , vol.58 , pp. 3004-3008
    • Samuel, S.K.1    Spencer, V.A.2    Bajno, L.3    Sun, J.M.4    Holth, L.T.5    Oesterreich, S.6    Davie, J.R.7
  • 49
    • 0033636518 scopus 로고    scopus 로고
    • Functional association of U2 snRNP with the ATP-independent spliceosomal complex E
    • Das R., Zhou Z., and Reed R. Functional association of U2 snRNP with the ATP-independent spliceosomal complex E. Mol. Cell 5 (2000) 779-787
    • (2000) Mol. Cell , vol.5 , pp. 779-787
    • Das, R.1    Zhou, Z.2    Reed, R.3
  • 50
    • 34548778175 scopus 로고    scopus 로고
    • The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes
    • Piekna-Przybylska D., Liu B., and Fournier M.J. The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes. Methods Enzymol. 425 (2007) 317-353
    • (2007) Methods Enzymol. , vol.425 , pp. 317-353
    • Piekna-Przybylska, D.1    Liu, B.2    Fournier, M.J.3
  • 51
    • 0037031576 scopus 로고    scopus 로고
    • Single-stranded antisense siRNAs guide target RNA cleavage in RNAi
    • Martinez J., Patkaniowska A., Urlaub H., Lührmann R., and Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110 (2002) 563-574
    • (2002) Cell , vol.110 , pp. 563-574
    • Martinez, J.1    Patkaniowska, A.2    Urlaub, H.3    Lührmann, R.4    Tuschl, T.5
  • 53
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., and Séraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17 (1999) 1030-1032
    • (1999) Nat. Biotechnol. , vol.17 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Séraphin, B.6
  • 54
    • 33644670152 scopus 로고    scopus 로고
    • An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network
    • Guerrero C., Tagwerker C., Kaiser P., and Huang L. An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics 5 (2006) 366-378
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 366-378
    • Guerrero, C.1    Tagwerker, C.2    Kaiser, P.3    Huang, L.4
  • 55
    • 0036463387 scopus 로고    scopus 로고
    • Combinatorial selection of RNA ligands for complex cellular targets: the RNA ligands-based proteomics
    • Tian H. Combinatorial selection of RNA ligands for complex cellular targets: the RNA ligands-based proteomics. Mol. Cell. Proteomics 1 (2002) 99-103
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 99-103
    • Tian, H.1
  • 56
    • 0032758073 scopus 로고    scopus 로고
    • StreptoTag: a novel method for the isolation of RNA-binding proteins
    • Bachler M., Schroeder R., and von Ahsen U. StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA 5 (1999) 1509-1516
    • (1999) RNA , vol.5 , pp. 1509-1516
    • Bachler, M.1    Schroeder, R.2    von Ahsen, U.3
  • 58
    • 0036353344 scopus 로고    scopus 로고
    • RNA affinity tags for purification of RNAs and ribonucleoprotein complexes
    • Srisawat C., and Engelke D.R. RNA affinity tags for purification of RNAs and ribonucleoprotein complexes. Methods 26 (2002) 156-161
    • (2002) Methods , vol.26 , pp. 156-161
    • Srisawat, C.1    Engelke, D.R.2
  • 61
    • 0024291370 scopus 로고
    • An early hierarchic role of U1 small nuclear ribonucleoprotein in spliceosome assembly
    • Ruby S.W., and Abelson J. An early hierarchic role of U1 small nuclear ribonucleoprotein in spliceosome assembly. Science 242 (1988) 1028-1035
    • (1988) Science , vol.242 , pp. 1028-1035
    • Ruby, S.W.1    Abelson, J.2
  • 62
    • 0037047250 scopus 로고    scopus 로고
    • Oligonucleotide trapping method for purification of transcription factors
    • Gadgil H., and Jarrett H.W. Oligonucleotide trapping method for purification of transcription factors. J. Chromatogr. A 966 (2002) 99-110
    • (2002) J. Chromatogr. A , vol.966 , pp. 99-110
    • Gadgil, H.1    Jarrett, H.W.2


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