메뉴 건너뛰기




Volumn 35, Issue 10, 2007, Pages

Sequence specificity of single-stranded DNA-binding proteins: A novel DNA microarray approach

Author keywords

[No Author keywords available]

Indexed keywords

COLD SHOCK PROTEIN; CYTOSINE; GUANINE; PYRIMIDINE; SINGLE STRANDED DNA BINDING PROTEIN; THYMINE; TRANSCRIPTION FACTOR; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; CARBOCYANINE; COLD SHOCK PROTEIN, BACILLUS; CYANINE DYE 5; DNA BINDING PROTEIN; FLUORESCENT DYE; HEAT SHOCK PROTEIN; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

EID: 34250886291     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm040     Document Type: Article
Times cited : (21)

References (32)
  • 2
    • 0037526104 scopus 로고    scopus 로고
    • Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein
    • Kerr,I.D., Wadsworth,R.I., Cubeddu,L., Blankenfeldt,W., Naismith,J.H. and White,M.F. (2003) Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J., 22, 2561-2570.
    • (2003) EMBO J , vol.22 , pp. 2561-2570
    • Kerr, I.D.1    Wadsworth, R.I.2    Cubeddu, L.3    Blankenfeldt, W.4    Naismith, J.H.5    White, M.F.6
  • 3
    • 0037216364 scopus 로고    scopus 로고
    • Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization
    • Zeeb,M. and Balbach,J. (2003) Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization. Protein Sci., 12, 112-123.
    • (2003) Protein Sci , vol.12 , pp. 112-123
    • Zeeb, M.1    Balbach, J.2
  • 4
    • 0031940086 scopus 로고    scopus 로고
    • Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes
    • Swamynathan,S.K., Nambiar,A. and Guntaka,R.V. (1998) Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes. FASEB J., 12, 515-522.
    • (1998) FASEB J , vol.12 , pp. 515-522
    • Swamynathan, S.K.1    Nambiar, A.2    Guntaka, R.V.3
  • 5
    • 0026702105 scopus 로고
    • Role of cytoplasmic mRNP proteins in translation
    • Minich,W.B. and Ovchinnikov,L.P. (1992) Role of cytoplasmic mRNP proteins in translation. Biochimie, 74, 477-483.
    • (1992) Biochimie , vol.74 , pp. 477-483
    • Minich, W.B.1    Ovchinnikov, L.P.2
  • 6
    • 0023654385 scopus 로고
    • Interactions of retroviral structural proteins with single-stranded nucleic acids
    • Karpel,R.L., Henderson,L.E. and Oroszlan,S. (1987) Interactions of retroviral structural proteins with single-stranded nucleic acids. J. Biol. Chem., 262, 4961-4967.
    • (1987) J. Biol. Chem , vol.262 , pp. 4961-4967
    • Karpel, R.L.1    Henderson, L.E.2    Oroszlan, S.3
  • 7
    • 0032169410 scopus 로고    scopus 로고
    • Branch migration during Rad51-promoted strand exchange proceeds in either direction
    • Namsaraev,E.A. and Berg,P. (1998) Branch migration during Rad51-promoted strand exchange proceeds in either direction. Proc. Natl. Acad. Sci. U.S.A., 95, 10477-10481.
    • (1998) Proc. Natl. Acad. Sci. U.S.A , vol.95 , pp. 10477-10481
    • Namsaraev, E.A.1    Berg, P.2
  • 8
    • 0141643216 scopus 로고    scopus 로고
    • Structure/function analysis of mouse Purbeta, a single-stranded DNA-binding repressor of vascular smooth muscle alpha-actin gene transcription
    • Kelm,R.J., Jr, Wang,S.X., Polikandriotis,J.A. and Strauch,A.R. (2003) Structure/function analysis of mouse Purbeta, a single-stranded DNA-binding repressor of vascular smooth muscle alpha-actin gene transcription. J. Biol. Chem., 278, 38749-38757.
    • (2003) J. Biol. Chem , vol.278 , pp. 38749-38757
    • Kelm Jr, R.J.1    Wang, S.X.2    Polikandriotis, J.A.3    Strauch, A.R.4
  • 9
    • 3142736317 scopus 로고    scopus 로고
    • A phage display selection of engrailed homeodomain mutants and the importance of residue Q50
    • Simon,M.D., Sato,K., Weiss,G.A. and Shokat,K.M. (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res., 32, 3623-3631.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3623-3631
    • Simon, M.D.1    Sato, K.2    Weiss, G.A.3    Shokat, K.M.4
  • 10
    • 0030047479 scopus 로고    scopus 로고
    • Mapping of DNA-binding proteins along the yeast genome by UV-induced DNA-protein crosslinking
    • Papatsenko,D.A., Priporova,I.V., Belikov,S.V. and Karpov,V.L. (1996) Mapping of DNA-binding proteins along the yeast genome by UV-induced DNA-protein crosslinking. FEBS Lett., 381, 103-105.
    • (1996) FEBS Lett , vol.381 , pp. 103-105
    • Papatsenko, D.A.1    Priporova, I.V.2    Belikov, S.V.3    Karpov, V.L.4
  • 11
    • 0033134777 scopus 로고    scopus 로고
    • Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA
    • Ding,J., Hayashi,M.K., Zhang,Y., Manche,L., Krainer,A.R. and Xu,R.M. (1999) Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev., 13 1102-1115.
    • (1999) Genes Dev , vol.13 , pp. 1102-1115
    • Ding, J.1    Hayashi, M.K.2    Zhang, Y.3    Manche, L.4    Krainer, A.R.5    Xu, R.M.6
  • 12
    • 0034660450 scopus 로고    scopus 로고
    • Major cold shock proteins, CspA from Escherichia coli and CspB from Bacillus subtilis, interact differently with single-stranded DNA templates
    • Lopez,M.M. and Makhatadze,G.I. (2000) Major cold shock proteins, CspA from Escherichia coli and CspB from Bacillus subtilis, interact differently with single-stranded DNA templates. Biochim. Biophys. Acta, 1479, 196-202.
    • (2000) Biochim. Biophys. Acta , vol.1479 , pp. 196-202
    • Lopez, M.M.1    Makhatadze, G.I.2
  • 13
    • 19744382860 scopus 로고    scopus 로고
    • Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins
    • 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.
    • (2005) Nucleic Acids Res , vol.33
    • Wang, J.1    Li, T.2    Guo, X.3    Lu, Z.4
  • 14
    • 9044248593 scopus 로고    scopus 로고
    • DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein
    • Walker,G.T., Linn,C.P. and Nadeau,J.G. (1996) DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein. Nucleic Acids Res., 24 348-353.
    • (1996) Nucleic Acids Res , vol.24 , pp. 348-353
    • Walker, G.T.1    Linn, C.P.2    Nadeau, J.G.3
  • 15
    • 0028191743 scopus 로고
    • All you wanted to know about SELEX
    • Klug,S.J. and Famulok,M. (1994) All you wanted to know about SELEX. Mol. Biol. Rep., 20, 97-107.
    • (1994) Mol. Biol. Rep , vol.20 , pp. 97-107
    • Klug, S.J.1    Famulok, M.2
  • 16
    • 0026575221 scopus 로고
    • Selection of single-stranded DNA molecules that bind and inhibit human thrombin
    • Bock,L.C., Griffin,L.C., Latham,J.A., Vermaas,E.H. and Toole,J.J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
    • (1992) Nature , vol.355 , pp. 564-566
    • Bock, L.C.1    Griffin, L.C.2    Latham, J.A.3    Vermaas, E.H.4    Toole, J.J.5
  • 17
    • 0011036375 scopus 로고    scopus 로고
    • SELEX Screening and Characterization of Small RNA Molecules That specifically bind the reactive blue dye
    • Wang,C., Xu,F., Jin,Y.X. and Wang,D.B. (1999) SELEX Screening and Characterization of Small RNA Molecules That specifically bind the reactive blue dye. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 31, 504-508.
    • (1999) Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) , vol.31 , pp. 504-508
    • Wang, C.1    Xu, F.2    Jin, Y.X.3    Wang, D.B.4
  • 19
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger,M.F., Philippakis,A.A., Qureshi,A.M., He,F.S., Estep,P.W., 3rd, and Bulyk,M.L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep 3rd, P.W.5    Bulyk, M.L.6
  • 20
    • 25444464374 scopus 로고    scopus 로고
    • The influence of cold shock proteins on transcription and translation studied in cell-free model systems
    • Hofweber,R., Horn,G., Langmann,T., Balbach,J., Kremer,W., Schmitz,G. and Kalbitzer,H.R. (2005) The influence of cold shock proteins on transcription and translation studied in cell-free model systems. FEBS J., 272, 4691-4702.
    • (2005) FEBS J , vol.272 , pp. 4691-4702
    • Hofweber, R.1    Horn, G.2    Langmann, T.3    Balbach, J.4    Kremer, W.5    Schmitz, G.6    Kalbitzer, H.R.7
  • 21
    • 0033584963 scopus 로고    scopus 로고
    • Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition
    • Lopez,M.M., Yutani,K. and Makhatadze,G.I. (1999) Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition. J. Biol. Chem., 274, 33601-33608.
    • (1999) J. Biol. Chem , vol.274 , pp. 33601-33608
    • Lopez, M.M.1    Yutani, K.2    Makhatadze, G.I.3
  • 22
    • 0028012282 scopus 로고
    • The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT sequences in single stranded oligonucleotides
    • Graumann,P. and Marahiel,M.A. (1994) The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT sequences in single stranded oligonucleotides. FEBS Lett., 338 157-160.
    • (1994) FEBS Lett , vol.338 , pp. 157-160
    • Graumann, P.1    Marahiel, M.A.2
  • 23
    • 0035865799 scopus 로고    scopus 로고
    • Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus
    • Wadsworth,R.I. and White,M.F. (2001) Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res., 29, 914-920.
    • (2001) Nucleic Acids Res , vol.29 , pp. 914-920
    • Wadsworth, R.I.1    White, M.F.2
  • 24
    • 0026642589 scopus 로고
    • Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB
    • Schindelin,H., Herrler,M., Willimsky,G., Marahiel,M.A. and Heinemann,U. (1992) Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB. Proteins, 14, 120-124.
    • (1992) Proteins , vol.14 , pp. 120-124
    • Schindelin, H.1    Herrler, M.2    Willimsky, G.3    Marahiel, M.A.4    Heinemann, U.5
  • 25
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • 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. U.S.A., 98, 7158-7163.
    • (2001) Proc. Natl. Acad. Sci. U.S.A , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1    Huang, X.2    Choo, Y.3    Church, G.M.4
  • 26
    • 33745645838 scopus 로고    scopus 로고
    • T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB
    • Max,K.E., Zeeb,M., Bienert,R., Balbach,J. and Heinemann,U. (2006) T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB. J. Mol. Biol., 360, 702-714.
    • (2006) J. Mol. Biol , vol.360 , pp. 702-714
    • Max, K.E.1    Zeeb, M.2    Bienert, R.3    Balbach, J.4    Heinemann, U.5
  • 27
    • 0027296211 scopus 로고
    • Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein
    • Schindelin,H., Marahiel,M.A. and Heinemann,U. (1993) Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature, 364, 164-168.
    • (1993) Nature , vol.364 , pp. 164-168
    • Schindelin, H.1    Marahiel, M.A.2    Heinemann, U.3
  • 28
    • 0035805616 scopus 로고    scopus 로고
    • Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template
    • Lopez,M.M., Yutani,K. and Makhatadze,G.I. (2001) Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template. J. Biol. Chem., 276, 15511-15518.
    • (2001) J. Biol. Chem , vol.276 , pp. 15511-15518
    • Lopez, M.M.1    Yutani, K.2    Makhatadze, G.I.3
  • 29
    • 33750008214 scopus 로고    scopus 로고
    • Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution
    • Zeeb,M., Max,K.E., Weininger,U., Low,C., Sticht,H. and Balbach,J. (2006) Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution. Nucleic Acids Res., 34, 4561-4571.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4561-4571
    • Zeeb, M.1    Max, K.E.2    Weininger, U.3    Low, C.4    Sticht, H.5    Balbach, J.6
  • 30
    • 0025978170 scopus 로고
    • Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements
    • Santoro,I.M., Yi,T.M. and Walsh,K. (1991) Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements. Mol. Cell. Biol., 11, 1944-1953.
    • (1991) Mol. Cell. Biol , vol.11 , pp. 1944-1953
    • Santoro, I.M.1    Yi, T.M.2    Walsh, K.3
  • 31
    • 0027376760 scopus 로고
    • Brn-3.0: A POU-domain protein expressed in the sensory, immune, and endocrine systems that functions on elements distinct from known octamer motifs
    • Gerrero,M.R., McEvilly,R.J., Turner,E., Lin,C.R., O'Connell,S., Jenne,K.J., Hobbs,M.V. and Rosenfeld,M.G. (1993) Brn-3.0: A POU-domain protein expressed in the sensory, immune, and endocrine systems that functions on elements distinct from known octamer motifs. Proc. Natl. Acad. Sci. U.S.A., 90, 10841-10845.
    • (1993) Proc. Natl. Acad. Sci. U.S.A , vol.90 , pp. 10841-10845
    • Gerrero, M.R.1    McEvilly, R.J.2    Turner, E.3    Lin, C.R.4    O'Connell, S.5    Jenne, K.J.6    Hobbs, M.V.7    Rosenfeld, M.G.8
  • 32
    • 0036855530 scopus 로고    scopus 로고
    • Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response
    • Kaan,T., Homuth,G., Mader,U., Bandow,J. and Schweder,T. (2002) Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology, 148, 3441-3455.
    • (2002) Microbiology , vol.148 , pp. 3441-3455
    • Kaan, T.1    Homuth, G.2    Mader, U.3    Bandow, J.4    Schweder, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.