메뉴 건너뛰기




Volumn 50, Issue 37, 2011, Pages 7901-7908

Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy

Author keywords

[No Author keywords available]

Indexed keywords

AFM; DNA SUBSTRATES; HIGH-SPEED; MONONUCLEOSOMES; NUCLEOSOMES; SINGLE-MOLECULE; STATIC SYSTEMS; TEMPORAL RESOLUTION; TIME-SCALES;

EID: 80052704421     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200946z     Document Type: Article
Times cited : (105)

References (43)
  • 1
    • 0031260520 scopus 로고    scopus 로고
    • Chromatin: The nucleosome unwrapped
    • Widom, J. (1997) Chromatin: The nucleosome unwrapped Curr. Biol. 7, R653-R655
    • (1997) Curr. Biol. , vol.7
    • Widom, J.1
  • 2
    • 33745790132 scopus 로고    scopus 로고
    • Chromatin remodelling: The industrial revolution of DNA around histones
    • DOI 10.1038/nrm1945, PII NRM1945
    • Saha, A., Wittmeyer, J., and Cairns, B. R. (2006) Chromatin remodelling: The industrial revolution of DNA around histones Nat. Rev. Mol. Cell Biol. 7, 437-447 (Pubitemid 44050097)
    • (2006) Nature Reviews Molecular Cell Biology , vol.7 , Issue.6 , pp. 437-447
    • Saha, A.1    Wittmeyer, J.2    Cairns, B.R.3
  • 3
    • 3542998667 scopus 로고    scopus 로고
    • Nucleosomes facilitate their own invasion
    • DOI 10.1038/nsmb801
    • Li, G. and Widom, J. (2004) Nucleosomes facilitate their own invasion Nat. Struct. Mol. Biol. 11, 763-769 (Pubitemid 39014502)
    • (2004) Nature Structural and Molecular Biology , vol.11 , Issue.8 , pp. 763-769
    • Li, G.1    Widom, J.2
  • 4
    • 18144366598 scopus 로고    scopus 로고
    • A fluorescence resonance energy transfer-based probe to monitor nucleosome structure
    • DOI 10.1016/j.ab.2005.03.022
    • Lovullo, D., Daniel, D., Yodh, J., Lohr, D., and Woodbury, N. W. (2005) A fluorescence resonance energy transfer-based probe to monitor nucleosome structure Anal. Biochem. 341, 165-172 (Pubitemid 40615733)
    • (2005) Analytical Biochemistry , vol.341 , Issue.1 , pp. 165-172
    • Lovullo, D.1    Daniel, D.2    Yodh, J.3    Lohr, D.4    Woodbury, N.W.5
  • 5
    • 43149091474 scopus 로고    scopus 로고
    • Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time
    • DOI 10.1007/s10577-008-1235-5
    • Leuba, S. H., Anand, S. P., Harp, J. M., and Khan, S. A. (2008) Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time Chromosome Res. 16, 451-467 (Pubitemid 351644866)
    • (2008) Chromosome Research , vol.16 , Issue.3 , pp. 451-467
    • Leuba, S.H.1    Anand, S.P.2    Harp, J.M.3    Khan, S.A.4
  • 6
    • 72949099668 scopus 로고    scopus 로고
    • Dynamics of nucleosome remodelling by individual ACF complexes
    • Blosser, T. R., Yang, J. G., Stone, M. D., Narlikar, G. J., and Zhuang, X. (2009) Dynamics of nucleosome remodelling by individual ACF complexes Nature 462, 1022-1027
    • (2009) Nature , vol.462 , pp. 1022-1027
    • Blosser, T.R.1    Yang, J.G.2    Stone, M.D.3    Narlikar, G.J.4    Zhuang, X.5
  • 7
    • 70350437772 scopus 로고    scopus 로고
    • Single-molecule fluorescence studies of nucleosome dynamics
    • Gurunathan, K. and Levitus, M. (2009) Single-molecule fluorescence studies of nucleosome dynamics Curr. Pharm. Biotechnol. 10, 559-568
    • (2009) Curr. Pharm. Biotechnol. , vol.10 , pp. 559-568
    • Gurunathan, K.1    Levitus, M.2
  • 8
    • 35948933368 scopus 로고    scopus 로고
    • Single-pair FRET microscopy reveals mononucleosome dynamics
    • DOI 10.1007/s10895-007-0218-9
    • Koopmans, W. J., Brehm, A., Logie, C., Schmidt, T., and van Noort, J. (2007) Single-pair FRET microscopy reveals mononucleosome dynamics J. Fluoresc. 17, 785-795 (Pubitemid 350075697)
    • (2007) Journal of Fluorescence , vol.17 , Issue.6 , pp. 785-795
    • Koopmans, W.J.A.1    Brehm, A.2    Logie, C.3    Schmidt, T.4    Van Noort, J.5
  • 9
    • 37749035092 scopus 로고    scopus 로고
    • Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes
    • Kelbauskas, L., Chan, N., Bash, R., DeBartolo, P., Sun, J., Woodbury, N., and Lohr, D. (2008) Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes Biophys. J. 94, 147-158
    • (2008) Biophys. J. , vol.94 , pp. 147-158
    • Kelbauskas, L.1    Chan, N.2    Bash, R.3    Debartolo, P.4    Sun, J.5    Woodbury, N.6    Lohr, D.7
  • 10
    • 68949085807 scopus 로고    scopus 로고
    • SpFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes
    • Koopmans, W. J., Buning, R., Schmidt, T., and van Noort, J. (2009) spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes Biophys. J. 97, 195-204
    • (2009) Biophys. J. , vol.97 , pp. 195-204
    • Koopmans, W.J.1    Buning, R.2    Schmidt, T.3    Van Noort, J.4
  • 11
    • 0037823505 scopus 로고    scopus 로고
    • Chromatin fibers, one-at-a-time
    • DOI 10.1016/S0022-2836(03)00691-0
    • Zlatanova, J. and Leuba, S. H. (2003) Chromatin fibers, one-at-a-time J. Mol. Biol. 331, 1-19 (Pubitemid 36870772)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.1 , pp. 1-19
    • Zlatanova, J.1    Leuba, S.H.2
  • 13
    • 10044241878 scopus 로고    scopus 로고
    • DNA-loop formation on nucleosomes shown by in situ scanning force microscopy of supercoiled DNA
    • DOI 10.1016/j.jmb.2004.11.016, PII S002228360401455X
    • Bussiek, M., Toth, K., Brun, N., and Langowski, J. (2005) DNA-loop formation on nucleosomes shown by in situ scanning force microscopy of supercoiled DNA J. Mol. Biol. 345, 695-706 (Pubitemid 39600927)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.4 , pp. 695-706
    • Bussiek, M.1    Toth, K.2    Brun, N.3    Langowski, J.4
  • 14
    • 44149119036 scopus 로고    scopus 로고
    • Spontaneous access to DNA target sites in folded chromatin fibers
    • Poirier, M. G., Bussiek, M., Langowski, J., and Widom, J. (2008) Spontaneous access to DNA target sites in folded chromatin fibers J. Mol. Biol. 379, 772-786
    • (2008) J. Mol. Biol. , vol.379 , pp. 772-786
    • Poirier, M.G.1    Bussiek, M.2    Langowski, J.3    Widom, J.4
  • 15
    • 36348960704 scopus 로고    scopus 로고
    • Organisation of nucleosomal arrays reconstituted with repetitive African green monkey α-satellite DNA as analysed by atomic force microscopy
    • DOI 10.1007/s00249-007-0166-y
    • Bussiek, M., Muller, G., Waldeck, W., Diekmann, S., and Langowski, J. (2007) Organisation of nucleosomal arrays reconstituted with repetitive African green monkey α-satellite DNA as analysed by atomic force microscopy Eur. Biophys. J. 37, 81-93 (Pubitemid 350159852)
    • (2007) European Biophysics Journal , vol.37 , Issue.1 , pp. 81-93
    • Bussiek, M.1    Muller, G.2    Waldeck, W.3    Diekmann, S.4    Langowski, J.5
  • 16
    • 68949136888 scopus 로고    scopus 로고
    • The dynamics of individual nucleosomes controls the chromatin condensation pathway: Direct atomic force microscopy visualization of variant chromatin
    • Montel, F., Menoni, H., Castelnovo, M., Bednar, J., Dimitrov, S., Angelov, D., and Faivre-Moskalenko, C. (2009) The dynamics of individual nucleosomes controls the chromatin condensation pathway: Direct atomic force microscopy visualization of variant chromatin Biophys. J. 97, 544-553
    • (2009) Biophys. J. , vol.97 , pp. 544-553
    • Montel, F.1    Menoni, H.2    Castelnovo, M.3    Bednar, J.4    Dimitrov, S.5    Angelov, D.6    Faivre-Moskalenko, C.7
  • 17
    • 0036786970 scopus 로고    scopus 로고
    • Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation
    • Anderson, J. D., Thastrom, A., and Widom, J. (2002) Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation Mol. Cell. Biol. 22, 7147-7157
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 7147-7157
    • Anderson, J.D.1    Thastrom, A.2    Widom, J.3
  • 18
    • 0036849262 scopus 로고    scopus 로고
    • Epigenetic consequences of nucleosome dynamics
    • DOI 10.1016/S0092-8674(02)01081-4
    • Ahmad, K. and Henikoff, S. (2002) Epigenetic consequences of nucleosome dynamics Cell 111, 281-284 (Pubitemid 35341384)
    • (2002) Cell , vol.111 , Issue.3 , pp. 281-284
    • Ahmad, K.1    Henikoff, S.2
  • 20
    • 33746322063 scopus 로고    scopus 로고
    • Rapid accessibility of nucleosomal DNA in yeast on a second time scale
    • DOI 10.1038/sj.emboj.7601196, PII 7601196
    • Bucceri, A., Kapitza, K., and Thoma, F. (2006) Rapid accessibility of nucleosomal DNA in yeast on a second time scale EMBO J. 25, 3123-3132 (Pubitemid 44106763)
    • (2006) EMBO Journal , vol.25 , Issue.13 , pp. 3123-3132
    • Bucceri, A.1    Kapitza, K.2    Thoma, F.3
  • 21
    • 0031806540 scopus 로고    scopus 로고
    • Contributions of linker histones and histone H3 to chromatin structure: Scanning force microscopy studies on trypsinized fibers
    • Leuba, S. H., Bustamante, C., Zlatanova, J., and van Holde, K. (1998) Contributions of linker histones and histone H3 to chromatin structure: Scanning force microscopy studies on trypsinized fibers Biophys. J. 74, 2823-2829 (Pubitemid 28268106)
    • (1998) Biophysical Journal , vol.74 , Issue.6 , pp. 2823-2829
    • Leuba, S.H.1    Bustamante, C.2    Zlatanova, J.3    Van Holde, K.4
  • 22
    • 0033619736 scopus 로고    scopus 로고
    • Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM
    • Yodh, J. G., Lyubchenko, Y. L., Shlyakhtenko, L. S., Woodbury, N., and Lohr, D. (1999) Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM Biochemistry 38, 15756-15763 (Pubitemid 129520468)
    • (1999) Biochemistry , vol.38 , Issue.48 , pp. 15756-15763
    • Yodh, J.G.1    Lyubchenko, Y.L.2    Shlyakhtenko, L.S.3    Woodbury, N.4    Lohr, D.5
  • 23
    • 0037133515 scopus 로고    scopus 로고
    • Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation
    • DOI 10.1021/bi011612e
    • Yodh, J. G., Woodbury, N., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Lohr, D. (2002) Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation Biochemistry 41, 3565-3574 (Pubitemid 34224668)
    • (2002) Biochemistry , vol.41 , Issue.11 , pp. 3565-3574
    • Yodh, J.G.1    Woodbury, N.2    Shlyakhtenko, L.S.3    Lyubchenko, Y.L.4    Lohr, D.5
  • 24
    • 10044275571 scopus 로고    scopus 로고
    • Unexpected binding motifs for subnucleosomal particles revealed by atomic force microscopy
    • DOI 10.1529/biophysj.104.048983
    • Nikova, D. N., Pope, L. H., Bennink, M. L., van Leijenhorst-Groener, K. A., van der Werf, K., and Greve, J. (2004) Unexpected binding motifs for subnucleosomal particles revealed by atomic force microscopy Biophys. J. 87, 4135-4145 (Pubitemid 39602917)
    • (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 4135-4145
    • Nikova, D.N.1    Pope, L.H.2    Bennink, M.L.3    Van Leijenhorst-Groener, K.A.4    Van Der Werf, K.5    Greve, J.6
  • 25
    • 67649099651 scopus 로고    scopus 로고
    • Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: Silatrane surface chemistry
    • Lyubchenko, Y. L., Shlyakhtenko, L. S., and Gall, A. A. (2009) Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: Silatrane surface chemistry Methods Mol. Biol. 543, 337-351
    • (2009) Methods Mol. Biol. , vol.543 , pp. 337-351
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2    Gall, A.A.3
  • 26
    • 69049097259 scopus 로고    scopus 로고
    • Dynamics of nucleosomes revealed by time-lapse atomic force microscopy
    • Shlyakhtenko, L. S., Lushnikov, A. Y., and Lyubchenko, Y. L. (2009) Dynamics of nucleosomes revealed by time-lapse atomic force microscopy Biochemistry 48, 7842-7848
    • (2009) Biochemistry , vol.48 , pp. 7842-7848
    • Shlyakhtenko, L.S.1    Lushnikov, A.Y.2    Lyubchenko, Y.L.3
  • 30
    • 70449416758 scopus 로고    scopus 로고
    • Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy
    • Gilmore, J. L., Suzuki, Y., Tamulaitis, G., Siksnys, V., Takeyasu, K., and Lyubchenko, Y. L. (2009) Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy Biochemistry 48, 10492-10498
    • (2009) Biochemistry , vol.48 , pp. 10492-10498
    • Gilmore, J.L.1    Suzuki, Y.2    Tamulaitis, G.3    Siksnys, V.4    Takeyasu, K.5    Lyubchenko, Y.L.6
  • 31
    • 77953541934 scopus 로고    scopus 로고
    • Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy
    • Suzuki, Y., Higuchi, Y., Hizume, K., Yokokawa, M., Yoshimura, S. H., Yoshikawa, K., and Takeyasu, K. (2010) Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy Ultramicroscopy 110, 682-688
    • (2010) Ultramicroscopy , vol.110 , pp. 682-688
    • Suzuki, Y.1    Higuchi, Y.2    Hizume, K.3    Yokokawa, M.4    Yoshimura, S.H.5    Yoshikawa, K.6    Takeyasu, K.7
  • 32
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • DOI 10.1006/jmbi.1997.1494
    • Lowary, P. T. and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning J. Mol. Biol. 276, 19-42 (Pubitemid 28085408)
    • (1998) Journal of Molecular Biology , vol.276 , Issue.1 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 34
    • 0033039285 scopus 로고    scopus 로고
    • Preparation of nucleosome core particle from recombinant histones
    • DOI 10.1016/S0076-6879(99)04003-3
    • Luger, K., Rechsteiner, T. J., Richmond, T. J., Wassarman, Paul M., and A., P. W. (1999) Preparation of nucleosome core particle from recombinant histones Methods Enzymol. 304, 3-19 (Pubitemid 29268874)
    • (1999) Methods in Enzymology , vol.304 , pp. 3-19
    • Luger, K.1    Rechsteiner, T.J.2    Richmond, T.J.3
  • 35
    • 0037841390 scopus 로고    scopus 로고
    • Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials
    • DOI 10.1016/S0304-3991(03)00053-6
    • Shlyakhtenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A., and Lyubchenko, Y. L. (2003) Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials Ultramicroscopy 97, 279-287 (Pubitemid 36686737)
    • (2003) Ultramicroscopy , vol.97 , Issue.1-4 , pp. 279-287
    • Shlyakhtenko, L.S.1    Gall, A.A.2    Filonov, A.3    Cerovac, Z.4    Lushnikov, A.5    Lyubchenko, Y.L.6
  • 36
    • 59749090938 scopus 로고    scopus 로고
    • AFM for analysis of structure and dynamics of DNA and protein-DNA complexes
    • Lyubchenko, Y. L. and Shlyakhtenko, L. S. (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes Methods 47, 206-213
    • (2009) Methods , vol.47 , pp. 206-213
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2
  • 37
    • 78649867694 scopus 로고    scopus 로고
    • Preparation of DNA and nucleoprotein samples for AFM imaging
    • Lyubchenko, Y. L. (2011) Preparation of DNA and nucleoprotein samples for AFM imaging Micron 42, 196-206
    • (2011) Micron , vol.42 , pp. 196-206
    • Lyubchenko, Y.L.1
  • 38
    • 79958754967 scopus 로고    scopus 로고
    • Imaging of nucleic acids with atomic force microscopy
    • Lyubchenko, Y. L., Shlyakhtenko, L. S., and Ando, T. (2011) Imaging of nucleic acids with atomic force microscopy Methods 54, 274-283
    • (2011) Methods , vol.54 , pp. 274-283
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2    Ando, T.3
  • 39
    • 80052720714 scopus 로고    scopus 로고
    • High-speed atomic force microscopy and biomolecular processes
    • Uchihashi, T. and Ando, T. (2011) High-speed atomic force microscopy and biomolecular processes Methods Mol. Biol. 736, 285-300
    • (2011) Methods Mol. Biol. , vol.736 , pp. 285-300
    • Uchihashi, T.1    Ando, T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.