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Volumn 10, Issue 1, 2013, Pages 41-67

Sequence-dependent collective properties of DNAs and their role in biological systems

Author keywords

DNA dynamic curvature; DNA recognition; DNA static curvature; Gel electrophoretic retardation; Nucleosome mapping; Nucleosome stability

Indexed keywords

COLLECTIVE PROPERTIES; DNA DYNAMICS; DNA RECOGNITION; GEL ELECTROPHORESIS; HELICAL PERIODICITY; INORGANIC CRYSTALS; NUCLEOSOMES; SELECTIVE INTERACTION;

EID: 84876329805     PISSN: 15710645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plrev.2013.01.004     Document Type: Review
Times cited : (14)

References (125)
  • 3
    • 0025078851 scopus 로고
    • Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature
    • De Santis P., Palleschi A., Savino M., Scipioni A. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry 1990, 29:9269-9273.
    • (1990) Biochemistry , vol.29 , pp. 9269-9273
    • De Santis, P.1    Palleschi, A.2    Savino, M.3    Scipioni, A.4
  • 4
    • 33751014843 scopus 로고    scopus 로고
    • Recognition on the nanoscale of a DNA sequence by an inorganic crystal surface
    • Scipioni A., Pisano S., Bergia A., Savino M., Samorì B., De Santis P. Recognition on the nanoscale of a DNA sequence by an inorganic crystal surface. ChemBioChem 2006, 7:1645-1648.
    • (2006) ChemBioChem , vol.7 , pp. 1645-1648
    • Scipioni, A.1    Pisano, S.2    Bergia, A.3    Savino, M.4    Samorì, B.5    De Santis, P.6
  • 5
    • 0001415964 scopus 로고
    • The pitch of chromatin DNA is reflected in its nucleotide sequence
    • Trifonov E.N., Sussman J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci USA 1980, 77:3816-3820.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 3816-3820
    • Trifonov, E.N.1    Sussman, J.L.2
  • 6
    • 0019322507 scopus 로고
    • Sequence-dependent deformational anisotropy of chromatin DNA
    • Trifonov E.N. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res 1980, 8:4041-4053.
    • (1980) Nucleic Acids Res , vol.8 , pp. 4041-4053
    • Trifonov, E.N.1
  • 7
    • 0021100990 scopus 로고
    • Nucleotide sequence-directed mapping nucleosomes
    • Mengeritsky G., Trifonov E.N. Nucleotide sequence-directed mapping nucleosomes. Nucleic Acids Res 1983, 11:3833-3851.
    • (1983) Nucleic Acids Res , vol.11 , pp. 3833-3851
    • Mengeritsky, G.1    Trifonov, E.N.2
  • 8
    • 0022418377 scopus 로고
    • Sequence dependence of the curvature of DNA: a test of the phasing hypothesis
    • Hagerman P.J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry 1985, 24:7033-7036.
    • (1985) Biochemistry , vol.24 , pp. 7033-7036
    • Hagerman, P.J.1
  • 9
    • 0022477409 scopus 로고
    • DNA bending at adenine-thymine tracts
    • Koo H.S., Wu H.M., Crothers D.M. DNA bending at adenine-thymine tracts. Nature 1986, 320:501-506.
    • (1986) Nature , vol.320 , pp. 501-506
    • Koo, H.S.1    Wu, H.M.2    Crothers, D.M.3
  • 10
    • 0022527052 scopus 로고
    • Sequence-directed curvature of DNA
    • Hagerman P.J. Sequence-directed curvature of DNA. Nature 1986, 321:449-450.
    • (1986) Nature , vol.321 , pp. 449-450
    • Hagerman, P.J.1
  • 12
    • 0028931709 scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Gorin A.A., Zhurkin V.B., Olson W.K. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. J Mol Biol 1995, 247:34-48.
    • (1995) J Mol Biol , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 13
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W.K., Gorin A.A., Lu X.-J., Hock L.M., Zhurkin V.B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 95:11163-11168.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.-J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 15
    • 0030572367 scopus 로고    scopus 로고
    • Sequence dependent circularization of DNAs: a physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending
    • De Santis P., Fuà M., Savino M., Anselmi C., Bocchinfuso G. Sequence dependent circularization of DNAs: a physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending. J Phys Chem 1996, 100:9968-9976.
    • (1996) J Phys Chem , vol.100 , pp. 9968-9976
    • De Santis, P.1    Fuà, M.2    Savino, M.3    Anselmi, C.4    Bocchinfuso, G.5
  • 16
    • 0001448835 scopus 로고    scopus 로고
    • Statistical thermodynamic approach for evaluating the writhe transformations in circular DNAs
    • Anselmi C., Bocchinfuso G., De Santis P., Fuà M., Scipioni A., Savino M. Statistical thermodynamic approach for evaluating the writhe transformations in circular DNAs. J Phys Chem B 1998, 102:5704-5714.
    • (1998) J Phys Chem B , vol.102 , pp. 5704-5714
    • Anselmi, C.1    Bocchinfuso, G.2    De Santis, P.3    Fuà, M.4    Scipioni, A.5    Savino, M.6
  • 17
    • 0033548524 scopus 로고    scopus 로고
    • Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability
    • Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol 1999, 286:1293-1301.
    • (1999) J Mol Biol , vol.286 , pp. 1293-1301
    • Anselmi, C.1    Bocchinfuso, G.2    De Santis, P.3    Savino, M.4    Scipioni, A.5
  • 18
    • 0033869101 scopus 로고    scopus 로고
    • A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability
    • Anselmi C., Bocchinfuso G., De Santis P., Savino M., Scipioni A. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys J 2000, 79:601-613.
    • (2000) Biophys J , vol.79 , pp. 601-613
    • Anselmi, C.1    Bocchinfuso, G.2    De Santis, P.3    Savino, M.4    Scipioni, A.5
  • 19
    • 1042267433 scopus 로고    scopus 로고
    • Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract
    • Scipioni A., Pisano S., Anselmi C., Savino M., De Santis P. Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract. Biophys Chem 2004, 107:7-17.
    • (2004) Biophys Chem , vol.107 , pp. 7-17
    • Scipioni, A.1    Pisano, S.2    Anselmi, C.3    Savino, M.4    De Santis, P.5
  • 20
    • 71749089641 scopus 로고    scopus 로고
    • A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes
    • Scipioni A., Morosetti S., De Santis P. A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes. Biopolymers 2009, 91:1143-1153.
    • (2009) Biopolymers , vol.91 , pp. 1143-1153
    • Scipioni, A.1    Morosetti, S.2    De Santis, P.3
  • 21
    • 0037108749 scopus 로고    scopus 로고
    • Recognition of the DNA sequence by an inorganic crystal surface
    • Sampaolese B., Bergia A., Scipioni A., et al. Recognition of the DNA sequence by an inorganic crystal surface. Proc Natl Acad Sci USA 2002, 99:13566-13570.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 13566-13570
    • Sampaolese, B.1    Bergia, A.2    Scipioni, A.3
  • 24
    • 0034614487 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: tetranucleotide conformational maps
    • Packer M.J., Dauncey M.P., Hunter C.A. Sequence-dependent DNA structure: tetranucleotide conformational maps. J Mol Biol 2000, 295:85-103.
    • (2000) J Mol Biol , vol.295 , pp. 85-103
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 26
    • 0021268779 scopus 로고
    • The locus of sequence-directed and protein-induced DNA bending
    • Wu H.-M., Crothers D.H. The locus of sequence-directed and protein-induced DNA bending. Nature 1984, 308:509-513.
    • (1984) Nature , vol.308 , pp. 509-513
    • Wu, H.-M.1    Crothers, D.H.2
  • 28
    • 35148860246 scopus 로고
    • Reptation of a polymer chain in the presence of fixed obstacles
    • De Gennes P.G. Reptation of a polymer chain in the presence of fixed obstacles. J Chem Phys 1971, 55:572-579.
    • (1971) J Chem Phys , vol.55 , pp. 572-579
    • De Gennes, P.G.1
  • 29
    • 0021878850 scopus 로고
    • Theory of gel electrophoresis of DNA
    • Lumpkin O.J., Dejardin P., Zimm B.H. Theory of gel electrophoresis of DNA. Biopolymers 1985, 24:1573-1593.
    • (1985) Biopolymers , vol.24 , pp. 1573-1593
    • Lumpkin, O.J.1    Dejardin, P.2    Zimm, B.H.3
  • 30
    • 0023661366 scopus 로고
    • DNA methylation can enhance or induce DNA curvature
    • Diekmann S. DNA methylation can enhance or induce DNA curvature. EMBO J 1987, 6:4213-4217.
    • (1987) EMBO J , vol.6 , pp. 4213-4217
    • Diekmann, S.1
  • 31
    • 0025195894 scopus 로고
    • Saturation mutagenesis of a DNA region of bend. Base steps other than ApA influence the bend
    • Milton D.L., Casper M.L., Gesteland R.F. Saturation mutagenesis of a DNA region of bend. Base steps other than ApA influence the bend. J Mol Biol 1990, 213:135-140.
    • (1990) J Mol Biol , vol.213 , pp. 135-140
    • Milton, D.L.1    Casper, M.L.2    Gesteland, R.F.3
  • 32
    • 0028846524 scopus 로고
    • Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes
    • Chastain P.D., Eichler E.E., Kang S., Nelson D.L., Levene S.D., Sinden R.R. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry 1995, 34:16125-16131.
    • (1995) Biochemistry , vol.34 , pp. 16125-16131
    • Chastain, P.D.1    Eichler, E.E.2    Kang, S.3    Nelson, D.L.4    Levene, S.D.5    Sinden, R.R.6
  • 33
    • 0032559372 scopus 로고    scopus 로고
    • CTG repeats associated with human genetic disease are inherently flexible
    • Chastain P.D., Sinden R.R. CTG repeats associated with human genetic disease are inherently flexible. J Mol Biol 1998, 275:405-411.
    • (1998) J Mol Biol , vol.275 , pp. 405-411
    • Chastain, P.D.1    Sinden, R.R.2
  • 35
    • 0030596081 scopus 로고    scopus 로고
    • Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis
    • Rivetti C., Guthold M., Bustamante C. Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol 1996, 264:919-932.
    • (1996) J Mol Biol , vol.264 , pp. 919-932
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 36
    • 0032479186 scopus 로고    scopus 로고
    • Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
    • Rivetti C., Walker C., Bustamante C. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol 1998, 280:41-59.
    • (1998) J Mol Biol , vol.280 , pp. 41-59
    • Rivetti, C.1    Walker, C.2    Bustamante, C.3
  • 38
    • 0036840332 scopus 로고    scopus 로고
    • Sequence-dependent DNA curvature and flexibility from scanning force microscopy images
    • Scipioni A., Anselmi C., Zuccheri G., Samorì B., De Santis P. Sequence-dependent DNA curvature and flexibility from scanning force microscopy images. Biophys J 2002, 83:2408-2418.
    • (2002) Biophys J , vol.83 , pp. 2408-2418
    • Scipioni, A.1    Anselmi, C.2    Zuccheri, G.3    Samorì, B.4    De Santis, P.5
  • 39
    • 12244267728 scopus 로고    scopus 로고
    • Sequence-dependent DNA dynamics by scanning force microscopy time-resolved imaging
    • Scipioni A., Zuccheri G., Anselmi C., Bergia A., Samorì B., De Santis P. Sequence-dependent DNA dynamics by scanning force microscopy time-resolved imaging. Chem Biol 2002, 9:1315-1321.
    • (2002) Chem Biol , vol.9 , pp. 1315-1321
    • Scipioni, A.1    Zuccheri, G.2    Anselmi, C.3    Bergia, A.4    Samorì, B.5    De Santis, P.6
  • 40
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Sponer J., Leszczynski J., Hobza P. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 2002, 61:3-31.
    • (2002) Biopolymers , vol.61 , pp. 3-31
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 41
    • 0023058994 scopus 로고
    • Visualization of the bent helix in kinetoplast DNA by electron microscopy
    • Griffith J., Bleyman M., Rauch C.A., Kitchin P.A., Englund P.T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell 1986, 46:717-724.
    • (1986) Cell , vol.46 , pp. 717-724
    • Griffith, J.1    Bleyman, M.2    Rauch, C.A.3    Kitchin, P.A.4    Englund, P.T.5
  • 42
    • 0019488496 scopus 로고
    • Sequence-dependent helical periodicity of DNA
    • Rhodes D., Klug A. Sequence-dependent helical periodicity of DNA. Nature 1981, 292:378-380.
    • (1981) Nature , vol.292 , pp. 378-380
    • Rhodes, D.1    Klug, A.2
  • 43
    • 5444254359 scopus 로고
    • Liss, New York, H.O. Halvorson, K.E. van Holde (Eds.)
    • van Holde K.E. The origin of life and evolution 1980, 31-46. Liss, New York. H.O. Halvorson, K.E. van Holde (Eds.).
    • (1980) The origin of life and evolution , pp. 31-46
    • van Holde, K.E.1
  • 44
    • 23644442092 scopus 로고    scopus 로고
    • Synthesis and degradation of nucleic acid components by formamide and cosmic dust analogues
    • Saladino R., Crestini C., Neri V., Brucato J.R., Colangeli L., Ciciriello F., et al. Synthesis and degradation of nucleic acid components by formamide and cosmic dust analogues. ChemBioChem 2005, 6:1368-1374.
    • (2005) ChemBioChem , vol.6 , pp. 1368-1374
    • Saladino, R.1    Crestini, C.2    Neri, V.3    Brucato, J.R.4    Colangeli, L.5    Ciciriello, F.6
  • 47
    • 84888836518 scopus 로고
    • Structure of the nucleosome core particle at 7 Å resolution
    • Richmond T.J., Finch J.T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 Å resolution. Nature 1984, 269:29-36.
    • (1984) Nature , vol.269 , pp. 29-36
    • Richmond, T.J.1    Finch, J.T.2    Rushton, B.3    Rhodes, D.4    Klug, A.5
  • 48
    • 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., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997, 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
  • 49
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution
    • Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol 2002, 319:1097-1113.
    • (2002) J Mol Biol , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 50
    • 17044365726 scopus 로고    scopus 로고
    • Nucleosome and chromatin fiber dynamics
    • Luger K., Hansen J.C. Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol 2005, 15:188-196.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 188-196
    • Luger, K.1    Hansen, J.C.2
  • 51
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S., Drew H.R., Travers A.A. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 1986, 191:659-675.
    • (1986) J Mol Biol , vol.191 , pp. 659-675
    • Satchwell, S.1    Drew, H.R.2    Travers, A.A.3
  • 52
    • 0001079085 scopus 로고
    • Artificial nucleosome positioning sequences
    • Shrader T.E., Crothers D.M. Artificial nucleosome positioning sequences. Proc Natl Acad Sci USA 1989, 86:7418-7422.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 7418-7422
    • Shrader, T.E.1    Crothers, D.M.2
  • 53
    • 0025144957 scopus 로고
    • Effects of DNA sequences and histone-histone interactions on nucleosome placement
    • Shrader T.E., Crothers D.M. Effects of DNA sequences and histone-histone interactions on nucleosome placement. J Mol Biol 1990, 216:69-84.
    • (1990) J Mol Biol , vol.216 , pp. 69-84
    • Shrader, T.E.1    Crothers, D.M.2
  • 54
    • 0031030691 scopus 로고    scopus 로고
    • Nucleosome packaging and nucleosome positioning of genomic DNA
    • Lowary P.T., Widom J. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc Natl Acad Sci USA 1997, 94:1183-1188.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1183-1188
    • Lowary, P.T.1    Widom, J.2
  • 55
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence directed nucleosome positioning
    • Lowary P.T., Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence directed nucleosome positioning. J Mol Biol 1998, 276:19-42.
    • (1998) J Mol Biol , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 56
    • 51049119256 scopus 로고    scopus 로고
    • Geometry of the nucleosomal DNA superhelix
    • Bishop T.J. Geometry of the nucleosomal DNA superhelix. Biophys J 2008, 95:1007-1017.
    • (2008) Biophys J , vol.95 , pp. 1007-1017
    • Bishop, T.J.1
  • 57
    • 84856806926 scopus 로고    scopus 로고
    • Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner
    • Moshkin Y.M., Chalkley G.E., Kan T.W., Reddy B.A., Ozgur Z., van Ijcken W.F.J., et al. Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Mol Cell Biol 2012, 32:675-688.
    • (2012) Mol Cell Biol , vol.32 , pp. 675-688
    • Moshkin, Y.M.1    Chalkley, G.E.2    Kan, T.W.3    Reddy, B.A.4    Ozgur, Z.5    van Ijcken, W.F.J.6
  • 58
    • 27444439375 scopus 로고    scopus 로고
    • Relative affinities of DNA sequences for the histone octamer depend strongly upon both the temperature and octamer concentration
    • Wu C., Travers A.A. Relative affinities of DNA sequences for the histone octamer depend strongly upon both the temperature and octamer concentration. Biochemistry 2005, 44:14329-14334.
    • (2005) Biochemistry , vol.44 , pp. 14329-14334
    • Wu, C.1    Travers, A.A.2
  • 59
    • 17544367055 scopus 로고    scopus 로고
    • Nucleosome assembly on CTG triplet repeats
    • Godde S., Wolffe A.P. Nucleosome assembly on CTG triplet repeats. J Biol Chem 1996, 271:15222-15229.
    • (1996) J Biol Chem , vol.271 , pp. 15222-15229
    • Godde, S.1    Wolffe, A.P.2
  • 60
    • 0029744342 scopus 로고    scopus 로고
    • Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter
    • Godde S., Kass S.U., Hirst M.C., Wolffe A.P. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J Biol Chem 1996, 271:24325-24328.
    • (1996) J Biol Chem , vol.271 , pp. 24325-24328
    • Godde, S.1    Kass, S.U.2    Hirst, M.C.3    Wolffe, A.P.4
  • 61
    • 0030575839 scopus 로고    scopus 로고
    • Long CCG triplet repeat blocks exclude nucleosomes: a possible mechanism for the nature of fragile sites in chromosomes
    • Wang Y., Gellibolian R., Shimizu M., Wells R.D., Griffith J. Long CCG triplet repeat blocks exclude nucleosomes: a possible mechanism for the nature of fragile sites in chromosomes. J Mol Biol 1996, 263:511-516.
    • (1996) J Mol Biol , vol.263 , pp. 511-516
    • Wang, Y.1    Gellibolian, R.2    Shimizu, M.3    Wells, R.D.4    Griffith, J.5
  • 63
    • 0031031106 scopus 로고    scopus 로고
    • In vitro low propensity to form nucleosomes of four telomeric sequences
    • Cacchione S., Cerone A.M., Savino M. In vitro low propensity to form nucleosomes of four telomeric sequences. FEBS Lett 1997, 400:37-41.
    • (1997) FEBS Lett , vol.400 , pp. 37-41
    • Cacchione, S.1    Cerone, A.M.2    Savino, M.3
  • 65
    • 0032503961 scopus 로고    scopus 로고
    • DNA superstructural features and nucleosomal organization on the two centromers of Kluyveromyces lactis chromosome 1 and Saccharomyces cerevisiae chromosome 6
    • Del Cornò M., De Santis P., Sampaolese B., Savino M. DNA superstructural features and nucleosomal organization on the two centromers of Kluyveromyces lactis chromosome 1 and Saccharomyces cerevisiae chromosome 6. FEBS Lett 1998, 431:66-70.
    • (1998) FEBS Lett , vol.431 , pp. 66-70
    • Del Cornò, M.1    De Santis, P.2    Sampaolese, B.3    Savino, M.4
  • 67
    • 0032103910 scopus 로고    scopus 로고
    • Unique translational positioning of nucleosomes on synthetic DNAs
    • Fitzgerald D.J., Anderson J.N. Unique translational positioning of nucleosomes on synthetic DNAs. Nucleic Acids Res 1998, 26:2526-2535.
    • (1998) Nucleic Acids Res , vol.26 , pp. 2526-2535
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 68
    • 0032760667 scopus 로고    scopus 로고
    • DNA distortion as a factor in nucleosome positioning
    • Fitzgerald D.J., Anderson J.N. DNA distortion as a factor in nucleosome positioning. J Mol Biol 1999, 293:477-491.
    • (1999) J Mol Biol , vol.293 , pp. 477-491
    • Fitzgerald, D.J.1    Anderson, J.N.2
  • 69
    • 0033988692 scopus 로고    scopus 로고
    • The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs
    • Filesi, Cacchione S., De Santis P., Rossetti L., Savino M. The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs. Biophys Chem 1999, 83:223-237.
    • (1999) Biophys Chem , vol.83 , pp. 223-237
    • Filesi1    Cacchione, S.2    De Santis, P.3    Rossetti, L.4    Savino, M.5
  • 70
    • 0037134772 scopus 로고    scopus 로고
    • Nucleosome organization on Kluyveromyces lactis centromeric DNAs
    • Mattei S., Sampaolese B., De Santis P., Savino M. Nucleosome organization on Kluyveromyces lactis centromeric DNAs. Biophys Chem 2002, 97:173-187.
    • (2002) Biophys Chem , vol.97 , pp. 173-187
    • Mattei, S.1    Sampaolese, B.2    De Santis, P.3    Savino, M.4
  • 73
    • 0004032961 scopus 로고
    • McGraw-Hill Book Company, New York
    • Spiegel M.R. Fourier analysis 1974, McGraw-Hill Book Company, New York.
    • (1974) Fourier analysis
    • Spiegel, M.R.1
  • 74
    • 34447644439 scopus 로고    scopus 로고
    • A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning
    • Tolstorukov M.Y., Colasanti A.V., Mccandlish D.M., Olson W.K., Zhurkin V.B. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol 2007, 371:725-738.
    • (2007) J Mol Biol , vol.371 , pp. 725-738
    • Tolstorukov, M.Y.1    Colasanti, A.V.2    Mccandlish, D.M.3    Olson, W.K.4    Zhurkin, V.B.5
  • 75
    • 84985667623 scopus 로고
    • Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles
    • Gotoh O., Tagashira Y. Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 1981, 20:1033-1042.
    • (1981) Biopolymers , vol.20 , pp. 1033-1042
    • Gotoh, O.1    Tagashira, Y.2
  • 76
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998, 95:1460-1465.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 1460-1465
    • SantaLucia, J.1
  • 78
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • Drew H.R., Dickerson R.E. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol 1981, 151:535-556.
    • (1981) J Mol Biol , vol.151 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 79
    • 0027058824 scopus 로고
    • NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution
    • Liepnish E., Otting G., Wuthrich K. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res 1992, 20:4549-4553.
    • (1992) Nucleic Acids Res , vol.20 , pp. 4549-4553
    • Liepnish, E.1    Otting, G.2    Wuthrich, K.3
  • 80
    • 0028241354 scopus 로고
    • Hydration of DNA: take 2
    • Berman H.M. Hydration of DNA: take 2. Curr Opin Struct Biol 1994, 4:345-350.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 345-350
    • Berman, H.M.1
  • 81
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shui X., McFail-Isom L., VanDerveer D., William L.D. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 1998, 37:8341-8355.
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shui, X.1    McFail-Isom, L.2    VanDerveer, D.3    William, L.D.4
  • 82
    • 0032387836 scopus 로고    scopus 로고
    • Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
    • Shui X., Sines C.C., McFail-Isom L., VanDerveer D., William L.D. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 1998, 37:16877-16887.
    • (1998) Biochemistry , vol.37 , pp. 16877-16887
    • Shui, X.1    Sines, C.C.2    McFail-Isom, L.3    VanDerveer, D.4    William, L.D.5
  • 84
    • 0033605083 scopus 로고    scopus 로고
    • Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
    • Hud N.V., Sklenar V., Feigon J. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J Mol Biol 1999, 286:651-660.
    • (1999) J Mol Biol , vol.286 , pp. 651-660
    • Hud, N.V.1    Sklenar, V.2    Feigon, J.3
  • 86
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • Lee C.K., Shibata Y., Rao B., Strahl B.D., Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 2004, 36:900-905.
    • (2004) Nat Genet , vol.36 , pp. 900-905
    • Lee, C.K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5
  • 87
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • Yuan G.C., Liu Y.J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005, 309:626-630.
    • (2005) Science , vol.309 , pp. 626-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5    Altschuler, S.J.6
  • 88
    • 20444403749 scopus 로고    scopus 로고
    • Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
    • Sekinger E.A., Moqtaderi Z., Struhl K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 2005, 18:735-748.
    • (2005) Mol Cell , vol.18 , pp. 735-748
    • Sekinger, E.A.1    Moqtaderi, Z.2    Struhl, K.3
  • 89
  • 90
    • 46449112319 scopus 로고    scopus 로고
    • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    • Mavrich T.N., Ioshikhes I.P., Venters B.J., Jiang C., Tomsho L.P., Qi J., et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008, 18:1073-1083.
    • (2008) Genome Res , vol.18 , pp. 1073-1083
    • Mavrich, T.N.1    Ioshikhes, I.P.2    Venters, B.J.3    Jiang, C.4    Tomsho, L.P.5    Qi, J.6
  • 93
    • 75349098018 scopus 로고    scopus 로고
    • A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
    • Jiang C., Pugh B.F. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 2009, 10:R109.
    • (2009) Genome Biol , vol.10
    • Jiang, C.1    Pugh, B.F.2
  • 94
  • 95
    • 77956034122 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosomes in yeast
    • Rando O.J. Genome-wide mapping of nucleosomes in yeast. Methods Enzymol 2010, 470:105-118.
    • (2010) Methods Enzymol , vol.470 , pp. 105-118
    • Rando, O.J.1
  • 96
    • 77950361329 scopus 로고    scopus 로고
    • Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?
    • Stein A., Takasuka T.E., Collings C.K. Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?. Nucleic Acids Res 2009, 38:709-719.
    • (2009) Nucleic Acids Res , vol.38 , pp. 709-719
    • Stein, A.1    Takasuka, T.E.2    Collings, C.K.3
  • 99
    • 77955388311 scopus 로고    scopus 로고
    • A preoccupied position on nucleosomes
    • Pugh B.F. A preoccupied position on nucleosomes. Nat Struct Mol Biol 2010, 17:923.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 923
    • Pugh, B.F.1
  • 100
    • 0026074664 scopus 로고
    • The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning
    • Boffelli D., De Santis P., Palleschi A., Savino M. The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning. Biophys Chem 1991, 39:127-136.
    • (1991) Biophys Chem , vol.39 , pp. 127-136
    • Boffelli, D.1    De Santis, P.2    Palleschi, A.3    Savino, M.4
  • 101
    • 0027512862 scopus 로고
    • Relationship between intrinsic and induced curvature in DNAs: theoretical prediction of nucleosome positioning
    • De Santis P., Fuà M., Palleschi A., Savino M. Relationship between intrinsic and induced curvature in DNAs: theoretical prediction of nucleosome positioning. Biophys Chem 1993, 46:193-204.
    • (1993) Biophys Chem , vol.46 , pp. 193-204
    • De Santis, P.1    Fuà, M.2    Palleschi, A.3    Savino, M.4
  • 102
    • 0030595138 scopus 로고    scopus 로고
    • Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences
    • Ioshikhes I.P., Bolshoy A., Derenshteyn K., Borodovsky M., Trifonov E.N. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J Mol Biol 1996, 262:129-139.
    • (1996) J Mol Biol , vol.262 , pp. 129-139
    • Ioshikhes, I.P.1    Bolshoy, A.2    Derenshteyn, K.3    Borodovsky, M.4    Trifonov, E.N.5
  • 103
    • 0021100990 scopus 로고
    • Nucleotide sequence-directed mapping of the nucleosomes
    • Mengeritsky G., Trifonov E.N. Nucleotide sequence-directed mapping of the nucleosomes. Nucleic Acids Res 1983, 11:3833-3851.
    • (1983) Nucleic Acids Res , vol.11 , pp. 3833-3851
    • Mengeritsky, G.1    Trifonov, E.N.2
  • 104
    • 57749182426 scopus 로고    scopus 로고
    • Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans
    • Salih F., Salih B., Trifonov E.N. Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans. J Biomol Struct Dyn 2008, 26:273-282.
    • (2008) J Biomol Struct Dyn , vol.26 , pp. 273-282
    • Salih, F.1    Salih, B.2    Trifonov, E.N.3
  • 106
    • 77956510995 scopus 로고    scopus 로고
    • Single-base resolution nucleosome mapping on DNA sequences
    • Gabdank I., Barash D., Trifonov E.N. Single-base resolution nucleosome mapping on DNA sequences. J Biomol Struct Dyn 2010, 28:107-122.
    • (2010) J Biomol Struct Dyn , vol.28 , pp. 107-122
    • Gabdank, I.1    Barash, D.2    Trifonov, E.N.3
  • 108
    • 79957660882 scopus 로고    scopus 로고
    • Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes
    • Bettecken T., Frenkel Z.M., Trifonov E.N. Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes. BMC Genomics 2011, 31:273.
    • (2011) BMC Genomics , vol.31 , pp. 273
    • Bettecken, T.1    Frenkel, Z.M.2    Trifonov, E.N.3
  • 109
    • 78650937771 scopus 로고    scopus 로고
    • Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences
    • Rapoport A.E., Frenkel Z.M., Trifonov E.N. Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Struct Dyn 2011, 28:567-574.
    • (2011) J Biomol Struct Dyn , vol.28 , pp. 567-574
    • Rapoport, A.E.1    Frenkel, Z.M.2    Trifonov, E.N.3
  • 113
    • 77953314889 scopus 로고    scopus 로고
    • Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches
    • Scipioni A., Morosetti S., De Santis P. Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches. J Biomol Struct Dyn 2010, 27:747-764.
    • (2010) J Biomol Struct Dyn , vol.27 , pp. 747-764
    • Scipioni, A.1    Morosetti, S.2    De Santis, P.3
  • 114
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V., Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 1995, 14:2570-2579.
    • (1995) EMBO J , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 116
    • 36349006915 scopus 로고    scopus 로고
    • Experiments confirm the influence of genome long-range correlations on nucleosome positioning
    • Vaillant C., Audit B., Arneodo A. Experiments confirm the influence of genome long-range correlations on nucleosome positioning. Phys Rev Lett 2007, 99:218103.
    • (2007) Phys Rev Lett , vol.99 , pp. 218103
    • Vaillant, C.1    Audit, B.2    Arneodo, A.3
  • 117
    • 84861805229 scopus 로고    scopus 로고
    • Structure-based identification of new high-affinity nucleosome binding sequences
    • Battistini F., Hunter C.A., Moore I.K., Widom J. Structure-based identification of new high-affinity nucleosome binding sequences. J Mol Biol 2012, 420:8-16.
    • (2012) J Mol Biol , vol.420 , pp. 8-16
    • Battistini, F.1    Hunter, C.A.2    Moore, I.K.3    Widom, J.4
  • 118
    • 84866536073 scopus 로고    scopus 로고
    • Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy
    • van der Heijden T., van Vugt J.J.F.A., Logie C., van Noort J. Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy. Proc Natl Acad Sci USA 2012, 109:E2514-2522.
    • (2012) Proc Natl Acad Sci USA , vol.109
    • van der Heijden, T.1    van Vugt, J.J.F.A.2    Logie, C.3    van Noort, J.4
  • 120
    • 33745221438 scopus 로고    scopus 로고
    • Analysis of nucleosome repositioning by yeast |SW| and Chd1 chromatin remodeling complexes
    • Stockdale C., Flaus A., Ferreira H., Owen-Hughes T. Analysis of nucleosome repositioning by yeast |SW| and Chd1 chromatin remodeling complexes. J Biol Chem 2006, 281:16279-16288.
    • (2006) J Biol Chem , vol.281 , pp. 16279-16288
    • Stockdale, C.1    Flaus, A.2    Ferreira, H.3    Owen-Hughes, T.4
  • 121
    • 0029862602 scopus 로고    scopus 로고
    • Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation
    • Verdone L., Camilloni G., Di Mauro E., Caserta M. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol Cell Biol 1996, 16:1978-1988.
    • (1996) Mol Cell Biol , vol.16 , pp. 1978-1988
    • Verdone, L.1    Camilloni, G.2    Di Mauro, E.3    Caserta, M.4
  • 122
    • 83755224395 scopus 로고    scopus 로고
    • Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes
    • Cole H.A., Howard B.H., Clark D.J. Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic Acids Res 2011, 39(22):9521-9535.
    • (2011) Nucleic Acids Res , vol.39 , Issue.22 , pp. 9521-9535
    • Cole, H.A.1    Howard, B.H.2    Clark, D.J.3
  • 123
    • 0026517738 scopus 로고
    • A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells
    • Widom J. A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc Natl Acad Sci USA 1992, 89:1095-1099.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 1095-1099
    • Widom, J.1
  • 124
    • 77951978209 scopus 로고    scopus 로고
    • Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin
    • Scipioni A., Turchetti G., Morosetti S., De Santis P. Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin. Biophys Chem 2010, 148:56-67.
    • (2010) Biophys Chem , vol.148 , pp. 56-67
    • Scipioni, A.1    Turchetti, G.2    Morosetti, S.3    De Santis, P.4
  • 125
    • 84862979650 scopus 로고    scopus 로고
    • A map of nucleosome positions in yeast at base-pair resolution
    • Brogaard K., Xi L., Wang J.-P., Widom J. A map of nucleosome positions in yeast at base-pair resolution. Nature 2012, 486:496-501.
    • (2012) Nature , vol.486 , pp. 496-501
    • Brogaard, K.1    Xi, L.2    Wang, J.-P.3    Widom, J.4


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