메뉴 건너뛰기




Volumn 48, Issue 5, 2009, Pages 1099-1111

Circular dichroism spectra and electrophoretic mobility shift assays show that human replication protein A binds and melts intramolecular G-quadruplex structures

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITIES; CIRCULAR DICHROISM SPECTRUM; CIRCULAR DICHROISMS; DNA REPLICATIONS; DNA SECONDARY STRUCTURES; DNA STRUCTURES; ELECTROPHORETIC MOBILITY SHIFT ASSAYS; FORMING SEQUENCES; G-QUADRUPLEX; G-QUADRUPLEX STRUCTURES; G-QUADRUPLEXES; GENOMIC INSTABILITIES; HETEROTRIMER; REPLICATION PROTEIN A; SPECTRAL CHANGES; STABLE COMPLEXES;

EID: 61449133312     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801538h     Document Type: Article
Times cited : (29)

References (51)
  • 1
    • 0030908093 scopus 로고    scopus 로고
    • Replication protein A: A heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism
    • Wold, M. S. (1997) Replication protein A: A heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66, 61-92.
    • (1997) Annu. Rev. Biochem , vol.66 , pp. 61-92
    • Wold, M.S.1
  • 3
    • 33749134033 scopus 로고    scopus 로고
    • A dynamic model for replication protein A (RPA) function in DNA processing pathways
    • Fanning, E., Klimovich, V., and Nager, A. R. (2006) A dynamic model for replication protein A (RPA) function in DNA processing pathways. Nucleic Acids Res. 34, 4126-4137.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4126-4137
    • Fanning, E.1    Klimovich, V.2    Nager, A.R.3
  • 4
    • 49649113678 scopus 로고    scopus 로고
    • Cellular functions of human RPA1: Multiple roles of domains in replication, repair, and checkpoints
    • Haring, S. J., Mason, A. C., Binz, S. K., and Wold, M. S. (2008) Cellular functions of human RPA1: Multiple roles of domains in replication, repair, and checkpoints. J. Biol. Chem. 283, 19095-19111.
    • (2008) J. Biol. Chem , vol.283 , pp. 19095-19111
    • Haring, S.J.1    Mason, A.C.2    Binz, S.K.3    Wold, M.S.4
  • 5
    • 0027479161 scopus 로고
    • OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for nonhomologous sequences
    • Murzin, A. G. (1993) OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for nonhomologous sequences. EMBO J. 12, 861-867.
    • (1993) EMBO J , vol.12 , pp. 861-867
    • Murzin, A.G.1
  • 6
    • 0033887437 scopus 로고    scopus 로고
    • Structure of the DNA binding domain of E. coli SSB bound to ssDNA
    • Raghunathan, S., Kozlov, A. G., Lohman, T. M., and Waksman, G. (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol. 7, 648-652.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 648-652
    • Raghunathan, S.1    Kozlov, A.G.2    Lohman, T.M.3    Waksman, G.4
  • 8
    • 0035253862 scopus 로고    scopus 로고
    • Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding
    • Bochkareva, E., Belegu, V., Korolev, S., and Bochkarev, A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J. 20, 612-618.
    • (2001) EMBO J , vol.20 , pp. 612-618
    • Bochkareva, E.1    Belegu, V.2    Korolev, S.3    Bochkarev, A.4
  • 9
    • 0033230182 scopus 로고    scopus 로고
    • RPA subunit arrangement near the 3'-end of the primer is modulated by the length of the template strand and cooperative protein interactions
    • Lavrik, O. I., Kolpashchikov, D. M., Weisshart, K., Nasheuer, H. P., Khodyreva, S. N., and Favre, A. (1999) RPA subunit arrangement near the 3'-end of the primer is modulated by the length of the template strand and cooperative protein interactions. Nucleic Acids Res. 27, 4235-4240.
    • (1999) Nucleic Acids Res , vol.27 , pp. 4235-4240
    • Lavrik, O.I.1    Kolpashchikov, D.M.2    Weisshart, K.3    Nasheuer, H.P.4    Khodyreva, S.N.5    Favre, A.6
  • 10
    • 0035965188 scopus 로고    scopus 로고
    • Functional analysis of the four DNA binding domains of replication protein A. The role of RPA2 in ssDNA binding
    • Bastin-Shanower, S. A., and Brill, S. J. (2001) Functional analysis of the four DNA binding domains of replication protein A. The role of RPA2 in ssDNA binding. J. Biol. Chem. 276, 36446-36453.
    • (2001) J. Biol. Chem , vol.276 , pp. 36446-36453
    • Bastin-Shanower, S.A.1    Brill, S.J.2
  • 11
    • 0028333942 scopus 로고
    • Human replication protein A binds single-stranded DNA in two distinct complexes
    • Blackwell, L. J., and Borowiec, J. A. (1994) Human replication protein A binds single-stranded DNA in two distinct complexes. Mol. Cell. Biol. 14, 3993-4001.
    • (1994) Mol. Cell. Biol , vol.14 , pp. 3993-4001
    • Blackwell, L.J.1    Borowiec, J.A.2
  • 12
    • 37549060645 scopus 로고    scopus 로고
    • Replication protein A prevents accumulation of single-stranded telomeric DNA in cells that use alternative lengthening of telomeres
    • Grudic, A., Jul-Larsen, Å., Haring, S. J., Wold, M. S., Lønning, P. E., Bjerkvij, R., and Bøe, S. O. (2007) Replication protein A prevents accumulation of single-stranded telomeric DNA in cells that use alternative lengthening of telomeres. Nucleic Acids Res. 35, 7267-7278.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7267-7278
    • Grudic, A.1    Jul-Larsen, A.2    Haring, S.J.3    Wold, M.S.4    Lønning, P.E.5    Bjerkvij, R.6    Bøe, S.O.7
  • 13
    • 0033951868 scopus 로고    scopus 로고
    • Characterization of genetic interactions with RFA1: The role of RPA in DNA replication and telomere maintenance
    • Smith, J., Zou, H., and Rothstein, R. (2000) Characterization of genetic interactions with RFA1: The role of RPA in DNA replication and telomere maintenance. Biochimie 82, 71-78.
    • (2000) Biochimie , vol.82 , pp. 71-78
    • Smith, J.1    Zou, H.2    Rothstein, R.3
  • 15
    • 33747751221 scopus 로고    scopus 로고
    • Themes in ssDNA recognition by telomere-end protection proteins
    • Croy, J. E., and Wuttke, D. S. (2006) Themes in ssDNA recognition by telomere-end protection proteins. Trends Biochem. Sci. 31, 516-525.
    • (2006) Trends Biochem. Sci , vol.31 , pp. 516-525
    • Croy, J.E.1    Wuttke, D.S.2
  • 18
    • 41149125565 scopus 로고    scopus 로고
    • Probing the mechanism of recognition of ssDNA by the Cdc13-DBD
    • Eldridge, A. M., and Wuttke, D. S. (2008) Probing the mechanism of recognition of ssDNA by the Cdc13-DBD. Nucleic Acids Res. 36, 1624-1633.
    • (2008) Nucleic Acids Res , vol.36 , pp. 1624-1633
    • Eldridge, A.M.1    Wuttke, D.S.2
  • 21
    • 42949179012 scopus 로고    scopus 로고
    • Human replication protein A melts a DNA triple helix structure in a potent and specific manner
    • Wu, Y., Rawtani, N., Thazhathveetil, A. K., Kenny, M. K., Seidman, M. M., and Brosh, R. M., Jr. (2008) Human replication protein A melts a DNA triple helix structure in a potent and specific manner. Biochemistry 47, 5068-5077.
    • (2008) Biochemistry , vol.47 , pp. 5068-5077
    • Wu, Y.1    Rawtani, N.2    Thazhathveetil, A.K.3    Kenny, M.K.4    Seidman, M.M.5    Brosh Jr., R.M.6
  • 22
    • 3042829478 scopus 로고    scopus 로고
    • Human replication protein A (RPA) binds a primer-template junction in the absence of its major ssDNA-binding domains
    • Pestryakov, P. E., Khlimankov, D. Y., Bochkareva, E., Bochkarev, A., and Lavrik, O. I. (2004) Human replication protein A (RPA) binds a primer-template junction in the absence of its major ssDNA-binding domains. Nucleic Acids Res. 32, 1894-1903.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1894-1903
    • Pestryakov, P.E.1    Khlimankov, D.Y.2    Bochkareva, E.3    Bochkarev, A.4    Lavrik, O.I.5
  • 23
    • 0037167620 scopus 로고    scopus 로고
    • The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex
    • Wen, J. D., and Gray, D. M. (2002) The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry 41, 11438-11448.
    • (2002) Biochemistry , vol.41 , pp. 11438-11448
    • Wen, J.D.1    Gray, D.M.2
  • 24
    • 39749116244 scopus 로고    scopus 로고
    • Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities
    • Gray, D. M., Wen, J. D., Gray, C. W., Repges, R., Repges, C., Raabe, G., and Fleischhauer, J. (2008) Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality 20, 431-440.
    • (2008) Chirality , vol.20 , pp. 431-440
    • Gray, D.M.1    Wen, J.D.2    Gray, C.W.3    Repges, R.4    Repges, C.5    Raabe, G.6    Fleischhauer, J.7
  • 25
    • 0035822710 scopus 로고    scopus 로고
    • SELEX selection of high-affinity oligonucleotides for bacteriophage ff gene 5 protein
    • Wen, J. D., Gray, C. W., and Gray, D. M. (2001) SELEX selection of high-affinity oligonucleotides for bacteriophage ff gene 5 protein. Biochemistry 40, 9300-9310.
    • (2001) Biochemistry , vol.40 , pp. 9300-9310
    • Wen, J.D.1    Gray, C.W.2    Gray, D.M.3
  • 26
    • 0028945546 scopus 로고
    • Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes
    • Gray, D. M., Hung, S.-H., and Johnson, K. H. (1995) Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 246, 19-34.
    • (1995) Methods Enzymol , vol.246 , pp. 19-34
    • Gray, D.M.1    Hung, S.-H.2    Johnson, K.H.3
  • 27
    • 0032512745 scopus 로고    scopus 로고
    • The RPA32 subunit of human replication protein A contains a single-stranded DNA-binding domain
    • Bochkareva, E., Frappier, L., Edwards, A. M., and Bochkarev, A. (1998) The RPA32 subunit of human replication protein A contains a single-stranded DNA-binding domain. J. Biol. Chem. 273, 3932-3936.
    • (1998) J. Biol. Chem , vol.273 , pp. 3932-3936
    • Bochkareva, E.1    Frappier, L.2    Edwards, A.M.3    Bochkarev, A.4
  • 28
    • 0031014993 scopus 로고    scopus 로고
    • Replication protein A. Characterization and crystallization of the DNA binding domain
    • Pfuetzner, R. A., Bochkarev, A., Frappier, L., and Edwards, A. M. (1997) Replication protein A. Characterization and crystallization of the DNA binding domain. J. Biol. Chem. 272, 430-434.
    • (1997) J. Biol. Chem , vol.272 , pp. 430-434
    • Pfuetzner, R.A.1    Bochkarev, A.2    Frappier, L.3    Edwards, A.M.4
  • 29
    • 0014690791 scopus 로고
    • The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresis
    • Weber, K., and Osborn, M. (1969) The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresis. J. Biol. Chem. 244, 4406-4412.
    • (1969) J. Biol. Chem , vol.244 , pp. 4406-4412
    • Weber, K.1    Osborn, M.2
  • 30
    • 0028871804 scopus 로고
    • How to measure and predict the molar absorption coefficient of a protein
    • Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423.
    • (1995) Protein Sci , vol.4 , pp. 2411-2423
    • Pace, C.N.1    Vajdos, F.2    Fee, L.3    Grimsley, G.4    Gray, T.5
  • 31
    • 0042553279 scopus 로고
    • Smoothing and Differentiation of Data by Simplified Least Squares Procedures
    • Savitzky, A., and Golay, M. J. E. (1964) Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Anal. Chem. 36, 1627-1639.
    • (1964) Anal. Chem , vol.36 , pp. 1627-1639
    • Savitzky, A.1    Golay, M.J.E.2
  • 32
    • 0034672122 scopus 로고    scopus 로고
    • Estimation of protein secondary structure from circular dichroism spectra: Inclusion of denatured proteins with native proteins in the analysis
    • Sreerama, N., Venyaminov, S. Y., and Woody, R. W. (2000) Estimation of protein secondary structure from circular dichroism spectra: Inclusion of denatured proteins with native proteins in the analysis. Anal. Biochem. 287, 243-251.
    • (2000) Anal. Biochem , vol.287 , pp. 243-251
    • Sreerama, N.1    Venyaminov, S.Y.2    Woody, R.W.3
  • 33
    • 0034672325 scopus 로고    scopus 로고
    • Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set
    • Sreerama, N., and Woody, R. W. (2000) Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem. 287, 252-260.
    • (2000) Anal. Biochem , vol.287 , pp. 252-260
    • Sreerama, N.1    Woody, R.W.2
  • 34
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 35
    • 0035253862 scopus 로고    scopus 로고
    • Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding
    • Bochkareva, E., Belegu, V., Korolev, S., and Bochkarev, A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J. 20, 612-618.
    • (2001) EMBO J , vol.20 , pp. 612-618
    • Bochkareva, E.1    Belegu, V.2    Korolev, S.3    Bochkarev, A.4
  • 36
    • 0037007223 scopus 로고    scopus 로고
    • Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA
    • Bochkareva, E., Korolev, S., Lees-Miller, S. P., and Bochkarev, A. (2002) Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J. 21, 1855-1863.
    • (2002) EMBO J , vol.21 , pp. 1855-1863
    • Bochkareva, E.1    Korolev, S.2    Lees-Miller, S.P.3    Bochkarev, A.4
  • 38
    • 1942473144 scopus 로고    scopus 로고
    • Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activity
    • Nuss, J. E., and Alter, G. M. (2004) Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activity. Protein Sci. 13, 1365-1378.
    • (2004) Protein Sci , vol.13 , pp. 1365-1378
    • Nuss, J.E.1    Alter, G.M.2
  • 39
    • 0242507460 scopus 로고    scopus 로고
    • Replication protein A interactions with DNA: Differential binding of the core domains and analysis of the DNA interaction surface
    • Wyka, I. M., Dhar, K., Binz, S. K., and Wold, M. S. (2003) Replication protein A interactions with DNA: Differential binding of the core domains and analysis of the DNA interaction surface. Biochemistry 42, 12909-12918.
    • (2003) Biochemistry , vol.42 , pp. 12909-12918
    • Wyka, I.M.1    Dhar, K.2    Binz, S.K.3    Wold, M.S.4
  • 40
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C., and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 41
    • 0029165745 scopus 로고
    • High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus
    • Schneider, D. J., Feigon, J., Hostomsky, Z., and Gold, L. (1995) High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 34, 9599-9610.
    • (1995) Biochemistry , vol.34 , pp. 9599-9610
    • Schneider, D.J.1    Feigon, J.2    Hostomsky, Z.3    Gold, L.4
  • 43
    • 0032437740 scopus 로고    scopus 로고
    • The use of CD spectroscopy for the study of the self-assembly of guanine derivatives
    • Gottarelli, G., Masiero, S., and Spada, G. P. (1998) The use of CD spectroscopy for the study of the self-assembly of guanine derivatives. Enantiomer 3, 429-498.
    • (1998) Enantiomer , vol.3 , pp. 429-498
    • Gottarelli, G.1    Masiero, S.2    Spada, G.P.3
  • 44
    • 0037489470 scopus 로고    scopus 로고
    • CD of Protein-Nucleic Acid Interactions
    • Berova, N, Nakanishi, K, and Woody, R. W, Eds, 2nd ed, pp, John Wiley & Sons, New York
    • Gray, D. M. (2000) CD of Protein-Nucleic Acid Interactions. In Circular Dichroism: Principles and Applications (Berova, N., Nakanishi, K., and Woody, R. W., Eds.) 2nd ed., pp 769-796, John Wiley & Sons, New York.
    • (2000) Circular Dichroism: Principles and Applications , pp. 769-796
    • Gray, D.M.1
  • 45
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292.
    • (2004) Proc. Natl. Acad. Sci. U.S.A , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 46
    • 0033056434 scopus 로고    scopus 로고
    • The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate
    • Mou, T.-C., Gray, C. W., and Gray, D. M. (1999) The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate. Biophys. J. 76, 1637-1551.
    • (1999) Biophys. J , vol.76 , pp. 1637-1551
    • Mou, T.-C.1    Gray, C.W.2    Gray, D.M.3
  • 47
    • 0034282879 scopus 로고    scopus 로고
    • The role for zinc in replication protein A
    • Bochkareva, E., Korolev, S., and Bochkarev, A. (2000) The role for zinc in replication protein A. J. Biol. Chem. 275, 27332-27338.
    • (2000) J. Biol. Chem , vol.275 , pp. 27332-27338
    • Bochkareva, E.1    Korolev, S.2    Bochkarev, A.3
  • 48
    • 0027939024 scopus 로고
    • Interactions of human replication protein A with oligonucleotides
    • Kim, C., Paulus, B. F., and Wold, M. S. (1994) Interactions of human replication protein A with oligonucleotides. Biochemistry 33, 14197-14206.
    • (1994) Biochemistry , vol.33 , pp. 14197-14206
    • Kim, C.1    Paulus, B.F.2    Wold, M.S.3
  • 49
    • 33749354956 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes
    • Kumaran, S., Kozlov, A., and Lohman, T. M. (2006) Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes. Biochemistry 45, 11958-11973.
    • (2006) Biochemistry , vol.45 , pp. 11958-11973
    • Kumaran, S.1    Kozlov, A.2    Lohman, T.M.3
  • 50
    • 47849105417 scopus 로고    scopus 로고
    • Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions
    • Qin, Y., and Hurley, L. H. (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 90, 1149-1171.
    • (2008) Biochimie , vol.90 , pp. 1149-1171
    • Qin, Y.1    Hurley, L.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.