메뉴 건너뛰기




Volumn 13, Issue 3, 1997, Pages 271-279

A brownian dynamics model for the chromatin fiber

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA;

EID: 0030916931     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.3.271     Document Type: Article
Times cited : (31)

References (31)
  • 1
    • 0000598304 scopus 로고
    • Bending and twisting dynamics of short linear DNA. Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation
    • Allison, S., Austin, R. and Hogan.M. (1989) Bending and twisting dynamics of short linear DNA. Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation. J. Chem. Phys., 90, 3843-3854.
    • (1989) J. Chem. Phys. , vol.90 , pp. 3843-3854
    • Allison, S.1    Austin, R.2    Hogan, M.3
  • 2
    • 0029583420 scopus 로고
    • Chromatin conformation and salt-induced compaction: Three-dimensional information from cryoelectron microscopy
    • pp
    • Bednar.J., Horowitz.R.A., Dubochet.J. and Woodock.C.L. (1995) Chromatin conformation and salt-induced compaction: Three-dimensional information from cryoelectron microscopy. J. Cell Biol. 131, pp. 1365-1376.
    • (1995) J. Cell Biol. , vol.131 , pp. 1365-1376
    • Bednar, J.1    Horowitz, R.A.2    Dubochet, J.3    Woodock, C.L.4
  • 3
    • 0002121327 scopus 로고
    • Stochastic problem in physics and astronomy
    • Chandrasekhar.S. (1943) Stochastic problem in physics and astronomy. Rev. Modern Phys., 14, 1-87.
    • (1943) Rev. Modern Phys. , vol.14 , pp. 1-87
    • Chandrasekhar, S.1
  • 4
    • 0028184699 scopus 로고
    • Kinetics of DNA supercoiling studied by Brownian dynamics simulation
    • Chirico.G. and Langowski.J. (1994) Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers, 34, 415-433.
    • (1994) Biopolymers , vol.34 , pp. 415-433
    • Chirico, G.1    Langowski, J.2
  • 5
    • 0025327471 scopus 로고
    • Electrostatic mechanism of chromatin folding
    • Clark.D. and Kimura.T. (1990) Electrostatic mechanism of chromatin folding. J. Mol. Biol., 211, 883-896.
    • (1990) J. Mol. Biol. , vol.211 , pp. 883-896
    • Clark, D.1    Kimura, T.2
  • 7
    • 85071214068 scopus 로고
    • Brownian dynamics and hydrodynamic interaction
    • Ermak.D.L. and McCammon.J.A. (1978) Brownian dynamics and hydrodynamic interaction. J. Chem. Phys., 69, 1325-1360.
    • (1978) J. Chem. Phys. , vol.69 , pp. 1325-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 8
    • 0025366778 scopus 로고
    • Dependence of the torsion rigidity of DNA on base composition
    • Fujimoto.B.S. and SchurrJ.M. (1990) Dependence of the torsion rigidity of DNA on base composition. Nature, 344, 175-178.
    • (1990) Nature , vol.344 , pp. 175-178
    • Fujimoto, B.S.1    Schurrj, M.2
  • 11
    • 0019526265 scopus 로고
    • Hydrodynamic properties of complex rigid biological macromolecules: Theory and applications
    • Garcia de la Torre.J. and Bloomfield.V.A. (1981) Hydrodynamic properties of complex rigid biological macromolecules: Theory and applications. Q. Rev. Biophys., 14,81-139.
    • (1981) Q. Rev. Biophys. , vol.14 , pp. 81-139
    • Garcia de la Torre, J.1    Bloomfield, V.A.2
  • 14
    • 0028221098 scopus 로고
    • The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon
    • Horowitz, R.A., Agard.D.A., Sedat.J.W. and Woodcock.C.L. (1994) The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon./ Cell Biol., 125, 1-10.
    • (1994) J Cell Biol , vol.125 , pp. 1-10
    • Horowitz, R.A.1    Agard, D.A.2    Sedat, J.W.3    Woodcock, C.L.4
  • 16
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interactions on polymers
    • Rotne.J. and Prager.S. (1969) Variational treatment of hydrodynamic interactions on polymers. J. Chem. Phys., 50, 4831-4837.
    • (1969) J. Chem. Phys. , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 17
    • 0000166387 scopus 로고
    • Fluorescence studies of nucleic acids: Dynamics, rigidities and structures
    • LakowiczJ.R (ed.), Plenum Press, New York, Vol., pp
    • Schurr.J.M., Fujimoto.B.S., Wu, P. and Song, L. (1992) Fluorescence studies of nucleic acids: dynamics, rigidities and structures. In LakowiczJ.R (ed.), Topics in Fluorescence Spectroscopy. Plenum Press, New York, Vol. 3, pp. 137-229.
    • (1992) Topics in Fluorescence Spectroscopy , vol.3 , pp. 137-229
    • Schurr, J.M.1    Fujimoto, B.S.2    Wu, P.3    Song, L.4
  • 18
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
    • Smith.S., Cui.Y. and Bustamante, C. (1996) Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
    • (1996) Science , vol.271 , pp. 795-799
    • Smith, S.1    Cui, Y.2    Bustamante, C.3
  • 19
    • 0017389770 scopus 로고
    • Interactions of highly charged colloidal cylinders with application to double-stranded DNA
    • Stigter.D. (1977) Interactions of highly charged colloidal cylinders with application to double-stranded DNA. Biopolymers, 16, 1435-1448.
    • (1977) Biopolymers , vol.16 , pp. 1435-1448
    • Stigter, D.1
  • 22
    • 0022541447 scopus 로고
    • Salt-induced folding of sea urchin sperm chromatin
    • Thomas, J., Rees.C. and Butler.P. (1986) Salt-induced folding of sea urchin sperm chromatin. Eur. J. Biochem., 154, 343-348.
    • (1986) Eur. J. Biochem. , vol.154 , pp. 343-348
    • Thomas, J.1    Rees, C.2    Butler, P.3
  • 24
  • 25
    • 0028935863 scopus 로고
    • Chromatin Higher order structure: Chasing a mirage?
    • van Holde.K. and Zlatanova.J. (1995) Chromatin Higher order structure: Chasing a mirage? J. Biol. Chem., 270, 8373-8376.
    • (1995) J. Biol. Chem. , vol.270 , pp. 8373-8376
    • van Holde, K.1    Zlatanova, J.2
  • 27
    • 0028207905 scopus 로고
    • Chromatin fibers observed in situ frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length
    • Woodcock.C.L. (1994) Chromatin fibers observed in situ frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J. Cell Biol., 125, 11-19.
    • (1994) J. Cell Biol. , vol.125 , pp. 11-19
    • Woodcock, C.L.1
  • 29
    • 0027517831 scopus 로고
    • A chromatin folding model that incorporates linker variability generates fibers resembling the native structures
    • Woodcock.C.L., Grigoryev.S.A., Horowitz.R.A. and Whitaker.N. (1993) A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc. Natl Acad. Sci. USA, 90, 9021-9025.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 9021-9025
    • Woodcock, C.L.1    Grigoryev, S.A.2    Horowitz, R.A.3    Whitaker, N.4
  • 31
    • 0025009844 scopus 로고
    • Direct detection of linker DNA bending in defined-length oligomers of chromatin
    • Yao, Y., Lowary, P. and Widom, J. (1990) Direct detection of linker DNA bending in defined-length oligomers of chromatin. Proc. Natl Acad. Sci. USA., 87, 7603-7607.
    • (1990) Proc. Natl Acad. Sci. USA. , vol.87 , pp. 7603-7607
    • Yao, Y.1    Lowary, P.2    Widom, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.