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Volumn 332, Issue 5, 2003, Pages 1025-1035

Sequence-dependent DNA Structure: A database of octamer structural parameters

Author keywords

A form; DNA bentness; DNA flexibility; Octamers; Sequence dependent structure

Indexed keywords

ALANYLALANINE; AMINO ACID; CURVED DNA; DNA; GLYCYLCYSTEINYLCYSTEINE; GLYCYLGLYCYLCYSTEINE; TETRAMER; UNCLASSIFIED DRUG;

EID: 0042386600     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.08.006     Document Type: Article
Times cited : (55)

References (38)
  • 1
    • 0024373679 scopus 로고
    • DNA conformation and protein-binding
    • Travers A.A. DNA conformation and protein-binding. Annu. Rev. Biochem. 58:1989;427-452.
    • (1989) Annu. Rev. Biochem. , vol.58 , pp. 427-452
    • Travers, A.A.1
  • 2
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Ångstrom 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 Ångstrom resolution. J. Mol. Biol. 319:2002;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
  • 3
    • 0030908093 scopus 로고    scopus 로고
    • Replication protein A: A heterotrimeric, singlestranded DNA-binding protein required for eukaryotic DNA metabolism
    • Wold M.S. Replication protein A: a heterotrimeric, singlestranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66:1997;61-92.
    • (1997) Annu. Rev. Biochem. , vol.66 , pp. 61-92
    • Wold, M.S.1
  • 4
    • 0020012345 scopus 로고
    • Interactions between functional-groups in protein-nucleic acid associations
    • Helene C., Lancelot G. Interactions between functional-groups in protein-nucleic acid associations. Prog. Biophys. Mol. Biol. 39:1982;1-68.
    • (1982) Prog. Biophys. Mol. Biol. , vol.39 , pp. 1-68
    • Helene, C.1    Lancelot, G.2
  • 5
    • 0036569686 scopus 로고    scopus 로고
    • Bending of DNA by asymmetric charge neutralization: All-atom energy simulations
    • Kosikov K.M., Gorin A.A., Lu X.J., Olson W.K., Manning G.S. Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J. Am. Chem. Soc. 124:2002;4838-4847.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4838-4847
    • Kosikov, K.M.1    Gorin, A.A.2    Lu, X.J.3    Olson, W.K.4    Manning, G.S.5
  • 6
    • 0033613915 scopus 로고    scopus 로고
    • Molecular dynamics studies of axis bending in d(G(5)-(GA(4)T(4)C)(2)-C-5) and d(G(5)-(GT(4)A(4)C)(2)-C-5): Effects of sequence polarity on DNA curvature
    • Sprous D., Young M.A., Beveridge D.L. Molecular dynamics studies of axis bending in d(G(5)-(GA(4)T(4)C)(2)-C-5) and d(G(5)-(GT(4)A(4)C)(2)-C-5): effects of sequence polarity on DNA curvature. J. Mol. Biol. 285:1999;1623-1632.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1623-1632
    • Sprous, D.1    Young, M.A.2    Beveridge, D.L.3
  • 7
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized born solvation model
    • Tsui V., Case D.A. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. J. Am. Chem. Soc. 122:2000;2489-2498.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 8
    • 0020385863 scopus 로고
    • Mechanics of sequence-dependent stacking of bases in B-DNA
    • Calladine C.R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161:1982;343-352.
    • (1982) J. Mol. Biol. , vol.161 , pp. 343-352
    • Calladine, C.R.1
  • 9
    • 0021770861 scopus 로고
    • A base-centered explanation of the B-to-A transition in DNA
    • Calladine C.R., Drew H.R. A base-centered explanation of the B-to-A transition in DNA. J. Mol. Biol. 178:1984;773-781.
    • (1984) J. Mol. Biol. , vol.178 , pp. 773-781
    • Calladine, C.R.1    Drew, H.R.2
  • 10
    • 0027318463 scopus 로고
    • Sequence-dependent DNA-structure: The role of base stacking interactions
    • Hunter C.A. Sequence-dependent DNA-structure: the role of base stacking interactions. J. Mol. Biol. 230:1993;1025-1054.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 12
    • 0033371146 scopus 로고    scopus 로고
    • Sequence-dependent modeling of local DNA bending phenomena: Curvature prediction and vibrational analysis
    • Vlahovicek K., Munteanu M.G., Pongor S. Sequence-dependent modeling of local DNA bending phenomena: curvature prediction and vibrational analysis. Genetica. 106:1999;63-73.
    • (1999) Genetica , vol.106 , pp. 63-73
    • Vlahovicek, K.1    Munteanu, M.G.2    Pongor, S.3
  • 13
    • 0028826669 scopus 로고
    • Trinucleotide models for dna bending propensity - Comparison of models based on DNAseI digestion and nucleosome packaging data
    • Brukner I., Sanchez R., Suck D., Pongor S. Trinucleotide models for dna bending propensity - comparison of models based on DNAseI digestion and nucleosome packaging data. J. Biomol. Struct. Dyn. 13:1995;309-317.
    • (1995) J. Biomol. Struct. Dyn. , vol.13 , pp. 309-317
    • Brukner, I.1    Sanchez, R.2    Suck, D.3    Pongor, S.4
  • 14
    • 0032417682 scopus 로고    scopus 로고
    • DNA curvature and deformation in protein-DNA complexes: A step in the right direction
    • Crothers D.M. DNA curvature and deformation in protein-DNA complexes: a step in the right direction. Proc. Natl Acad. Sci. USA. 95:1998;15163-15165.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 15163-15165
    • Crothers, D.M.1
  • 15
    • 0030919777 scopus 로고    scopus 로고
    • Construction of double-helical DNA structures based on dinucleotide building blocks
    • Hunter C.A., Lu X.J. Construction of double-helical DNA structures based on dinucleotide building blocks. J. Biomol. Struct. Dynam. 14:1997;747-756.
    • (1997) J. Biomol. Struct. Dynam. , vol.14 , pp. 747-756
    • Hunter, C.A.1    Lu, X.J.2
  • 16
    • 0031556948 scopus 로고    scopus 로고
    • DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures
    • Hunter C.A., Lu X.J. DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265:1997;603-619.
    • (1997) J. Mol. Biol. , vol.265 , pp. 603-619
    • Hunter, C.A.1    Lu, X.J.2
  • 17
    • 0032540859 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: The role of the sugar-phosphate backbone
    • Packer M.J., Hunter C.A. Sequence-dependent DNA structure: the role of the sugar-phosphate backbone. J. Mol. Biol. 280:1998;407-420.
    • (1998) J. Mol. Biol. , vol.280 , pp. 407-420
    • Packer, M.J.1    Hunter, C.A.2
  • 18
    • 0034614483 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: Dinucleotide conformational maps
    • Packer M.J., Dauncey M.P., Hunter C.A. Sequence-dependent DNA structure: dinucleotide conformational maps. J. Mol. Biol. 295:2000;71-83.
    • (2000) J. Mol. Biol. , vol.295 , pp. 71-83
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 19
    • 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. 295:2000;85-103.
    • (2000) J. Mol. Biol. , vol.295 , pp. 85-103
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 20
    • 0024974308 scopus 로고
    • Definitions and nomenclature of nucleic acid structure parameters
    • Diekmann S. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205:1989;787-791.
    • (1989) J. Mol. Biol. , vol.205 , pp. 787-791
    • Diekmann, S.1
  • 21
    • 0034823069 scopus 로고    scopus 로고
    • Sequence-structure relationships in DNA oligomers: A computational approach
    • Packer M.J., Hunter C.A. Sequence-structure relationships in DNA oligomers: a computational approach. J. Am. Chem. Soc. 123:2001;7399-7406.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 7399-7406
    • Packer, M.J.1    Hunter, C.A.2
  • 22
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu X.J., Shakked Z., Olson W.K. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300:2000;819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.J.1    Shakked, Z.2    Olson, W.K.3
  • 23
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behavior of dinucleotide steps
    • ElHassan M.A., Calladine C.R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behavior of dinucleotide steps. Phil. Trans. ser. A. 355:1997;43-100.
    • (1997) Phil. Trans. ser. A , vol.355 , pp. 43-100
    • ElHassan, M.A.1    Calladine, C.R.2
  • 24
    • 0035704707 scopus 로고    scopus 로고
    • Role of DNA sequence in nucleosome stability and dynamics
    • Widom J. Role of DNA sequence in nucleosome stability and dynamics. Quart. Rev. Biophys. 34:2001;269-324.
    • (2001) Quart. Rev. Biophys. , vol.34 , pp. 269-324
    • Widom, J.1
  • 25
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin A.A., Zhurkin V.B., Olson W.K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 26
    • 6744266061 scopus 로고
    • A helical polymer with a cooperative response to chiral information
    • Green M.M., Peterson N.C., Sato T., Teramoto A., Cook R., Lifson S. A helical polymer with a cooperative response to chiral information. Science. 268:1995;1860-1866.
    • (1995) Science , vol.268 , pp. 1860-1866
    • Green, M.M.1    Peterson, N.C.2    Sato, T.3    Teramoto, A.4    Cook, R.5    Lifson, S.6
  • 27
    • 0025966606 scopus 로고
    • Analysis of local helix geometry in three B-DNA decamers and eight dodecamers
    • Yanagi K., Prive G.G., Dickerson R.E. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217:1991;201-214.
    • (1991) J. Mol. Biol. , vol.217 , pp. 201-214
    • Yanagi, K.1    Prive, G.G.2    Dickerson, R.E.3
  • 28
    • 0000789168 scopus 로고
    • Free energy increments for hydrogen bonds in nucleic acid base pairs
    • Turner D.H., Sugimoto N., Kierzek R., Dreiker S.D. Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc. 109:1987;3783-3785.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 3783-3785
    • Turner, D.H.1    Sugimoto, N.2    Kierzek, R.3    Dreiker, S.D.4
  • 30
    • 0023657337 scopus 로고
    • The bending of DNA in nucleosomes and its wider implications
    • Travers A.A., Klug A. The bending of DNA in nucleosomes and its wider implications. Phil. Trans. R. Soc. Lond. B. 317:1987;537-561.
    • (1987) Phil. Trans. R. Soc. Lond. B , vol.317 , pp. 537-561
    • Travers, A.A.1    Klug, A.2
  • 31
    • 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. 95:1998;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
  • 33
    • 0018460380 scopus 로고
    • Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence
    • Simpson R.T., Kunzler P. Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucl. Acids Res. 6:1979;1387-1415.
    • (1979) Nucl. Acids Res. , vol.6 , pp. 1387-1415
    • Simpson, R.T.1    Kunzler, P.2
  • 34
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S.C., Drew D.R., Travers A.A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:1986;659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, D.R.2    Travers, A.A.3
  • 35
    • 0022422660 scopus 로고
    • Nomenclature for incompletely specified bases in nucleic-acid sequences - Recommendations 1984
    • Cornishbowden A. Nomenclature for incompletely specified bases in nucleic-acid sequences - recommendations 1984. Nucl. Acids Res. 13:1985;3021-3030.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 3021-3030
    • Cornishbowden, A.1
  • 36
    • 0029027735 scopus 로고
    • An A-DNA triplet code - Thermodynamic rules for predicting A-dna and B-dna
    • Basham B., Schroth G.P., Ho P.S. An A-DNA triplet code - thermodynamic rules for predicting A-dna and B-dna. Proc. Natl Acad. Sci. USA. 92:1995;6464-6468.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 6464-6468
    • Basham, B.1    Schroth, G.P.2    Ho, P.S.3
  • 37
    • 0023990696 scopus 로고
    • Some rules for predicting the base-sequence dependence of DNA conformation
    • Peticolas W.L., Wang Y., Thomas G.A. Some rules for predicting the base-sequence dependence of DNA conformation. Proc. Natl Acad. Sci. USA. 85:1988;2579-2583.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2579-2583
    • Peticolas, W.L.1    Wang, Y.2    Thomas, G.A.3
  • 38
    • 0035193091 scopus 로고    scopus 로고
    • Sequence-dependent B↔A transition in DNA evaluated with dimeric and trimeric scales
    • Tolstorukov M.Y., Ivanov V.I., Malenkov G.G., Jernigan R.L., Zhurkin V.B. Sequence-dependent B↔A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 81:2001;3409-3421.
    • (2001) Biophys. J. , vol.81 , pp. 3409-3421
    • Tolstorukov, M.Y.1    Ivanov, V.I.2    Malenkov, G.G.3    Jernigan, R.L.4    Zhurkin, V.B.5


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