메뉴 건너뛰기




Volumn 53, Issue 41, 2014, Pages 6430-6438

Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; PROTEINS; TEMPERATURE;

EID: 84908215709     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500344j     Document Type: Article
Times cited : (75)

References (69)
  • 1
    • 77957240284 scopus 로고    scopus 로고
    • DNA curvature and flexibility in vitro and in vivo
    • Peters, J. P., III and Maher, L. J. (2010) DNA curvature and flexibility in vitro and in vivo Q. Rev. Biophys. 43, 23-63
    • (2010) Q. Rev. Biophys. , vol.43 , pp. 23-63
    • Peters, J.P.1    Maher, L.J.2
  • 4
    • 57749209893 scopus 로고    scopus 로고
    • The major architects of chromatin: Architectural proteins in bacteria, archaea and eukaryotes
    • Luijsterburg, M. S., White, M. F., van Driel, R., and Dame, R. T. (2008) The major architects of chromatin: Architectural proteins in bacteria, archaea and eukaryotes Crit. Rev. Biochem. Mol. Biol. 43, 393-418
    • (2008) Crit. Rev. Biochem. Mol. Biol. , vol.43 , pp. 393-418
    • Luijsterburg, M.S.1    White, M.F.2    Van Driel, R.3    Dame, R.T.4
  • 5
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389, 251-260
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 8
    • 23244443772 scopus 로고    scopus 로고
    • Dual binding modes for an HMG domain from human HMGB2 on DNA
    • McCauley, M., Hardwidge, P. R., Maher, L. J., III, and Williams, M. C. (2005) Dual binding modes for an HMG domain from human HMGB2 on DNA Biophys. J. 89, 353-364
    • (2005) Biophys. J. , vol.89 , pp. 353-364
    • McCauley, M.1    Hardwidge, P.R.2    Maher, L.J.3    Williams, M.C.4
  • 9
    • 18444369954 scopus 로고    scopus 로고
    • The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin
    • Dame, R. T. (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin Mol. Microbiol. 56, 858-870
    • (2005) Mol. Microbiol. , vol.56 , pp. 858-870
    • Dame, R.T.1
  • 10
    • 33750527566 scopus 로고    scopus 로고
    • The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
    • Luijsterburg, M. S., Noom, M. C., Wuite, G. J., and Dame, R. T. (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective J. Struct. Biol. 156, 262-272
    • (2006) J. Struct. Biol. , vol.156 , pp. 262-272
    • Luijsterburg, M.S.1    Noom, M.C.2    Wuite, G.J.3    Dame, R.T.4
  • 12
    • 0028298256 scopus 로고
    • Promoters responsive to DNA bending: A common theme in prokaryotic gene expression
    • Perez-Martin, J., Rojo, F., and de Lorenzo, V. (1994) Promoters responsive to DNA bending: A common theme in prokaryotic gene expression Microbiol. Rev. 58, 268-290
    • (1994) Microbiol. Rev. , vol.58 , pp. 268-290
    • Perez-Martin, J.1    Rojo, F.2    De Lorenzo, V.3
  • 13
    • 33744807717 scopus 로고    scopus 로고
    • DNA looping: The consequences and its control
    • Saiz, L. and Vilar, J. M. (2006) DNA looping: The consequences and its control Curr. Opin. Struct. Biol. 16, 344-350
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 344-350
    • Saiz, L.1    Vilar, J.M.2
  • 14
    • 19444387811 scopus 로고    scopus 로고
    • Bacterial repression loops require enhanced DNA flexibility
    • Becker, N. A., Kahn, J. D., and Maher, L. J., III (2005) Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 349, 716-730
    • (2005) J. Mol. Biol. , vol.349 , pp. 716-730
    • Becker, N.A.1    Kahn, J.D.2    Maher, L.J.3
  • 15
    • 34547642985 scopus 로고    scopus 로고
    • Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
    • Becker, N. A., Kahn, J. D., and Maher, L. J., III (2007) Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli Nucleic Acids Res. 35, 3988-4000
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3988-4000
    • Becker, N.A.1    Kahn, J.D.2    Maher, L.J.3
  • 16
    • 79955907601 scopus 로고    scopus 로고
    • Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins
    • Czapla, L., Peters, J. P., Rueter, E. M., Olson, W. K., and Maher, L. J., III (2011) Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins J. Mol. Biol. 409, 278-289
    • (2011) J. Mol. Biol. , vol.409 , pp. 278-289
    • Czapla, L.1    Peters, J.P.2    Rueter, E.M.3    Olson, W.K.4    Maher, L.J.5
  • 17
    • 34547852967 scopus 로고    scopus 로고
    • Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    • Zhang, Y., McEwen, A. E., Crothers, D. M., and Levene, S. D. (2006) Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping PLoS One 1, e136
    • (2006) PLoS One , vol.1 , pp. 136
    • Zhang, Y.1    McEwen, A.E.2    Crothers, D.M.3    Levene, S.D.4
  • 19
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier, T. E. and Widom, J. (2004) Spontaneous sharp bending of double-stranded DNA Mol. Cell 14, 355-362
    • (2004) Mol. Cell , vol.14 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 20
    • 84865546608 scopus 로고    scopus 로고
    • Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
    • Vafabakhsh, R. and Ha, T. (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization Science 337, 1097-1101
    • (2012) Science , vol.337 , pp. 1097-1101
    • Vafabakhsh, R.1    Ha, T.2
  • 21
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • Yan, J. and Marko, J. F. (2004) Localized single-stranded bubble mechanism for cyclization of short double helix DNA Phys. Rev. Lett. 93, 108108
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 108108
    • Yan, J.1    Marko, J.F.2
  • 26
    • 14844342574 scopus 로고    scopus 로고
    • DNA twisting flexibility and the formation of sharply looped protein-DNA complexes
    • Cloutier, T. E. and Widom, J. (2005) DNA twisting flexibility and the formation of sharply looped protein-DNA complexes Proc. Natl. Acad. Sci. U.S.A. 102, 3645-3650
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 3645-3650
    • Cloutier, T.E.1    Widom, J.2
  • 27
    • 79952326786 scopus 로고    scopus 로고
    • Temperature dependence of DNA persistence length
    • Geggier, S., Kotlyar, A., and Vologodskii, A. (2011) Temperature dependence of DNA persistence length Nucleic Acids Res. 39, 1419-1426
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1419-1426
    • Geggier, S.1    Kotlyar, A.2    Vologodskii, A.3
  • 28
    • 20144381079 scopus 로고    scopus 로고
    • Transcriptional response of Escherichia coli to temperature shift
    • Gadgil, M., Kapur, V., and Hu, W. S. (2005) Transcriptional response of Escherichia coli to temperature shift Biotechnol. Prog. 21, 689-699
    • (2005) Biotechnol. Prog. , vol.21 , pp. 689-699
    • Gadgil, M.1    Kapur, V.2    Hu, W.S.3
  • 29
    • 33745008644 scopus 로고    scopus 로고
    • Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus
    • Tachdjian, S. and Kelly, R. M. (2006) Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus J. Bacteriol. 188, 4553-4559
    • (2006) J. Bacteriol. , vol.188 , pp. 4553-4559
    • Tachdjian, S.1    Kelly, R.M.2
  • 30
    • 80053226878 scopus 로고    scopus 로고
    • The RpoS-mediated general stress response in Escherichia coli
    • Battesti, A., Majdalani, N., and Gottesman, S. (2011) The RpoS-mediated general stress response in Escherichia coli Annu. Rev. Microbiol. 65, 189-213
    • (2011) Annu. Rev. Microbiol. , vol.65 , pp. 189-213
    • Battesti, A.1    Majdalani, N.2    Gottesman, S.3
  • 32
    • 0028066920 scopus 로고
    • Helicase motifs v and VI of the Escherichia coli UvrB protein of the UvrABC endonuclease are essential for the formation of the preincision complex
    • Moolenaar, G. F., Visse, R., Ortiz-Buysse, M., Goosen, N., and van de Putte, P. (1994) Helicase motifs V and VI of the Escherichia coli UvrB protein of the UvrABC endonuclease are essential for the formation of the preincision complex J. Mol. Biol. 240, 294-307
    • (1994) J. Mol. Biol. , vol.240 , pp. 294-307
    • Moolenaar, G.F.1    Visse, R.2    Ortiz-Buysse, M.3    Goosen, N.4    Van De Putte, P.5
  • 34
    • 4444320606 scopus 로고    scopus 로고
    • A high-copy T7 Escherichia coli expression vector for the production of recombinant proteins with a minimal N-terminal His-tagged fusion peptide
    • Ramos, C. R., Abreu, P. A., Nascimento, A. L., and Ho, P. L. (2004) A high-copy T7 Escherichia coli expression vector for the production of recombinant proteins with a minimal N-terminal His-tagged fusion peptide Braz. J. Med. Biol. Res. 37, 1103-1109
    • (2004) Braz. J. Med. Biol. Res. , vol.37 , pp. 1103-1109
    • Ramos, C.R.1    Abreu, P.A.2    Nascimento, A.L.3    Ho, P.L.4
  • 39
    • 34147198324 scopus 로고    scopus 로고
    • Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers
    • Schaffer, E., Norrelykke, S. F., and Howard, J. (2007) Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers Langmuir 23, 3654-3665
    • (2007) Langmuir , vol.23 , pp. 3654-3665
    • Schaffer, E.1    Norrelykke, S.F.2    Howard, J.3
  • 40
    • 37349067907 scopus 로고    scopus 로고
    • Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6-7 μm
    • Seol, Y., Li, J., Nelson, P. C., Perkins, T. T., and Betterton, M. D. (2007) Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6-7 μm Biophys. J. 93, 4360-4373
    • (2007) Biophys. J. , vol.93 , pp. 4360-4373
    • Seol, Y.1    Li, J.2    Nelson, P.C.3    Perkins, T.T.4    Betterton, M.D.5
  • 42
  • 46
    • 84893195831 scopus 로고    scopus 로고
    • Force-dependent melting of supercoiled DNA at thermophilic temperatures
    • Galburt, E. A., Tomko, E. J., Stump, W. T., and Ruiz Manzano, A. (2014) Force-dependent melting of supercoiled DNA at thermophilic temperatures Biophys. Chem. 187-188C, 23-28
    • (2014) Biophys. Chem. , vol.187-188 , pp. 23-28
    • Galburt, E.A.1    Tomko, E.J.2    Stump, W.T.3    Ruiz Manzano, A.4
  • 47
    • 79551483682 scopus 로고    scopus 로고
    • Nucleoid-associated proteins in Crenarchaea
    • Driessen, R. P. C. and Dame, R. T. (2011) Nucleoid-associated proteins in Crenarchaea Biochem. Soc. Trans. 39, 116-121
    • (2011) Biochem. Soc. Trans. , vol.39 , pp. 116-121
    • Driessen, R.P.C.1    Dame, R.T.2
  • 48
    • 84873161522 scopus 로고    scopus 로고
    • Structure and dynamics of the crenarchaeal nucleoid
    • Driessen, R. P. C. and Dame, R. T. (2013) Structure and dynamics of the crenarchaeal nucleoid Biochem. Soc. Trans. 41, 321-325
    • (2013) Biochem. Soc. Trans. , vol.41 , pp. 321-325
    • Driessen, R.P.C.1    Dame, R.T.2
  • 49
    • 0015275944 scopus 로고
    • Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature
    • Brock, T. D., Brock, K. M., Belly, R. T., and Weiss, R. L. (1972) Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature Arch. Mikrobiol, 84, 54-68
    • (1972) Arch. Mikrobiol , vol.84 , pp. 54-68
    • Brock, T.D.1    Brock, K.M.2    Belly, R.T.3    Weiss, R.L.4
  • 50
    • 77952731659 scopus 로고    scopus 로고
    • Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex
    • Feng, Y., Yao, H., and Wang, J. (2010) Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex Protein Sci. 19, 1253-1257
    • (2010) Protein Sci. , vol.19 , pp. 1253-1257
    • Feng, Y.1    Yao, H.2    Wang, J.3
  • 51
    • 77951565302 scopus 로고    scopus 로고
    • Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA
    • Zhang, Z., Gong, Y., Guo, L., Jiang, T., and Huang, L. (2010) Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA Mol. Microbiol. 76, 749-759
    • (2010) Mol. Microbiol. , vol.76 , pp. 749-759
    • Zhang, Z.1    Gong, Y.2    Guo, L.3    Jiang, T.4    Huang, L.5
  • 53
    • 0028533719 scopus 로고
    • Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus
    • Baumann, H., Knapp, S., Lundbäck, T., Ladenstein, R., and Härd, T. (1994) Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus Nat. Struct. Biol. 1, 808-819
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 808-819
    • Baumann, H.1    Knapp, S.2    Lundbäck, T.3    Ladenstein, R.4    Härd, T.5
  • 54
    • 40249110035 scopus 로고    scopus 로고
    • Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea
    • Guo, L., Feng, Y., Zhang, Z., Yao, H., Luo, Y., Wang, J., and Huang, L. (2008) Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea Nucleic Acids Res. 36, 1129-1137
    • (2008) Nucleic Acids Res. , vol.36 , pp. 1129-1137
    • Guo, L.1    Feng, Y.2    Zhang, Z.3    Yao, H.4    Luo, Y.5    Wang, J.6    Huang, L.7
  • 56
    • 0016175370 scopus 로고
    • Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice
    • McGhee, J. D. and von Hippel, P. H. (1974) Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice J. Mol. Biol. 86, 469-489
    • (1974) J. Mol. Biol. , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 57
    • 0031851758 scopus 로고    scopus 로고
    • Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex
    • Agback, P., Baumann, H., Knapp, S., Ladenstein, R., and Hard, T. (1998) Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex Nat. Struct. Biol. 5, 579-584
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 579-584
    • Agback, P.1    Baumann, H.2    Knapp, S.3    Ladenstein, R.4    Hard, T.5
  • 58
    • 7244245362 scopus 로고    scopus 로고
    • Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes
    • Skoko, D., Wong, B., Johnson, R. C., and Marko, J. F. (2004) Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes Biochemistry 43, 13867-13874
    • (2004) Biochemistry , vol.43 , pp. 13867-13874
    • Skoko, D.1    Wong, B.2    Johnson, R.C.3    Marko, J.F.4
  • 60
    • 84885435342 scopus 로고    scopus 로고
    • Single-Molecule Unzipping Force Analysis of HU-DNA Complexes
    • Dame, R. T., Hall, M. A., and Wang, M. D. (2013) Single-Molecule Unzipping Force Analysis of HU-DNA Complexes ChemBioChem 14, 1954-1957
    • (2013) ChemBioChem , vol.14 , pp. 1954-1957
    • Dame, R.T.1    Hall, M.A.2    Wang, M.D.3
  • 61
    • 32644434270 scopus 로고    scopus 로고
    • Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
    • Yakovchuk, P., Protozanova, E., and Frank-Kamenetskii, M. D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Nucleic Acids Res. 34, 564-574
    • (2006) Nucleic Acids Res. , vol.34 , pp. 564-574
    • Yakovchuk, P.1    Protozanova, E.2    Frank-Kamenetskii, M.D.3
  • 63
    • 84886052484 scopus 로고    scopus 로고
    • Temperature dependence of the DNA double helix at the nanoscale: Structure, elasticity, and fluctuations
    • Meyer, S., Jost, D., Theodorakopoulos, N., Peyrard, M., Lavery, R., and Everaers, R. (2013) Temperature dependence of the DNA double helix at the nanoscale: Structure, elasticity, and fluctuations Biophys. J. 105, 1904-1914
    • (2013) Biophys. J. , vol.105 , pp. 1904-1914
    • Meyer, S.1    Jost, D.2    Theodorakopoulos, N.3    Peyrard, M.4    Lavery, R.5    Everaers, R.6
  • 64
    • 4644342209 scopus 로고    scopus 로고
    • Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d
    • Peters, W. B., Edmondson, S. P., and Shriver, J. W. (2004) Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d J. Mol. Biol. 343, 339-360
    • (2004) J. Mol. Biol. , vol.343 , pp. 339-360
    • Peters, W.B.1    Edmondson, S.P.2    Shriver, J.W.3
  • 65
    • 0000162429 scopus 로고    scopus 로고
    • Salt Dependence of the Free Energy, Enthalpy, and Entropy of Nonsequence Specific DNA Binding
    • Lundbäck, T. and Härd, T. (1996) Salt Dependence of the Free Energy, Enthalpy, and Entropy of Nonsequence Specific DNA Binding J. Phys. Chem. 100, 17690-17695
    • (1996) J. Phys. Chem. , vol.100 , pp. 17690-17695
    • Lundbäck, T.1    Härd, T.2
  • 66
    • 84867648701 scopus 로고    scopus 로고
    • Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: Insights from molecular dynamics simulation and free energy analysis
    • Chen, L., Zhang, J. L., Yu, L. Y., Zheng, Q. C., Chu, W. T., Xue, Q., Zhang, H. X., and Sun, C. C. (2012) Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: Insights from molecular dynamics simulation and free energy analysis J. Phys. Chem. B 116, 12415-12425
    • (2012) J. Phys. Chem. B , vol.116 , pp. 12415-12425
    • Chen, L.1    Zhang, J.L.2    Yu, L.Y.3    Zheng, Q.C.4    Chu, W.T.5    Xue, Q.6    Zhang, H.X.7    Sun, C.C.8
  • 67
    • 0041312645 scopus 로고    scopus 로고
    • Flexible DNA bending in HU-DNA cocrystal structures
    • Swinger, K. K., Lemberg, K. M., Zhang, Y., and Rice, P. A. (2003) Flexible DNA bending in HU-DNA cocrystal structures EMBO J. 22, 3749-3760
    • (2003) EMBO J. , vol.22 , pp. 3749-3760
    • Swinger, K.K.1    Lemberg, K.M.2    Zhang, Y.3    Rice, P.A.4
  • 68
    • 84887910248 scopus 로고    scopus 로고
    • Dynamic DNA underpins chromosome dynamics
    • Travers, A. (2013) Dynamic DNA underpins chromosome dynamics Biophys. J. 105, 2235-2237
    • (2013) Biophys. J. , vol.105 , pp. 2235-2237
    • Travers, A.1
  • 69
    • 0036953237 scopus 로고    scopus 로고
    • DNA topology-mediated control of global gene expression in Escherichia coli
    • Hatfield, G. W. and Benham, C. J. (2002) DNA topology-mediated control of global gene expression in Escherichia coli Annu. Rev. Genet. 36, 175-203
    • (2002) Annu. Rev. Genet. , vol.36 , pp. 175-203
    • Hatfield, G.W.1    Benham, C.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.