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Volumn 295, Issue 1, 2000, Pages 85-103

Sequence-dependent DNA structure: Tetranucleotide conformational maps

Author keywords

Base stacking interactions; Force field energy calculations; Sequence context; Sequence dependent structure; Tetranucleotides

Indexed keywords

CURVED DNA; DINUCLEOTIDE; DNA A; DNA B; DOUBLE STRANDED DNA; SUGAR;

EID: 0034614487     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3237     Document Type: Article
Times cited : (176)

References (40)
  • 1
    • 0016299918 scopus 로고
    • Structural details of a double-helix observed for DNA containing alternating purine-pyrimidine sequences
    • Arnott S., Chandrasekaran R., Hukins D. W. L., Smith P. J. C., Watts L. Structural details of a double-helix observed for DNA containing alternating purine-pyrimidine sequences. J. Mol. Biol. 88:1974;523-533.
    • (1974) J. Mol. Biol. , vol.88 , pp. 523-533
    • Arnott, S.1    Chandrasekaran, R.2    Hukins, D.W.L.3    Smith, P.J.C.4    Watts, L.5
  • 2
    • 0001425230 scopus 로고    scopus 로고
    • Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids
    • Beckers M. L. M., Buydens L. M. C. Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids. J. Comp. Chem. 19:1998;695-715.
    • (1998) J. Comp. Chem. , vol.19 , pp. 695-715
    • Beckers, M.L.M.1    Buydens, L.M.C.2
  • 3
    • 0032029586 scopus 로고    scopus 로고
    • Flexibility of the B-DNA backbone: Effects of loal and neighbouring sequences on pyrimidine-purine steps
    • Bertrand H. O., Haduong T., Fermandjian S., Hartmann B. Flexibility of the B-DNA backbone: effects of loal and neighbouring sequences on pyrimidine-purine steps. Nucl. Acids Res. 26:1998;1261-1267.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 1261-1267
    • Bertrand, H.O.1    Haduong, T.2    Fermandjian, S.3    Hartmann, B.4
  • 4
    • 0029039118 scopus 로고
    • Sequence-dependent bending propensity of DNA as revealed by DNAse-I-parameters for trinucleotides
    • Brukner I., Sanchez R., Suck D., Pongor S. Sequence-dependent bending propensity of DNA as revealed by DNAse-I-parameters for trinucleotides. EMBO J. 14:1995;1812-1818.
    • (1995) EMBO J. , vol.14 , pp. 1812-1818
    • Brukner, I.1    Sanchez, R.2    Suck, D.3    Pongor, S.4
  • 5
    • 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
  • 7
    • 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
  • 8
    • 0026702486 scopus 로고
    • DNA structure from A to Z
    • Dickerson R. E. DNA structure from A to Z. Methods Enzymol. 211:1992;67-111.
    • (1992) Methods Enzymol. , vol.211 , pp. 67-111
    • Dickerson, R.E.1
  • 9
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • Dickerson R. E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucl. Acids Res. 26:1998;1906-1926.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 1906-1926
    • Dickerson, R.E.1
  • 10
    • 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
  • 11
    • 0032530597 scopus 로고    scopus 로고
    • Unconventional helical phasing of repetitive DNA motifs reveals their relative beding contributions
    • Dlakic M., Harrington R. E. Unconventional helical phasing of repetitive DNA motifs reveals their relative beding contributions. Nucl. Acids Res. 26:1998;4274-4279.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 4274-4279
    • Dlakic, M.1    Harrington, R.E.2
  • 12
    • 0029126044 scopus 로고
    • The assessment of the geometry of dinucleotide steps in double-helical DNA-a new local calculation scheme
    • El Hassan M. A., Calladine C. R. The assessment of the geometry of dinucleotide steps in double-helical DNA-a new local calculation scheme. J. Mol. Biol. 251:1995;648-664.
    • (1995) J. Mol. Biol. , vol.251 , pp. 648-664
    • El Hassan, M.A.1    Calladine, C.R.2
  • 13
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
    • El Hassan M. A., Calladine G. R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. ser. A. 355:1997a;43-100.
    • (1997) Phil. Trans. Ser. a , vol.355 , pp. 43-100
    • El Hassan, M.A.1    Calladine, G.R.2
  • 14
    • 33645088570 scopus 로고    scopus 로고
    • Curvature and torsion of infinitely repeating DNA sequences: A geometric investigation
    • El Hassan M. A., Calladine C. R. Curvature and torsion of infinitely repeating DNA sequences: a geometric investigation. Proc. Roy. Soc. Lond. ser. A. 453:1997b.
    • (1997) Proc. Roy. Soc. Lond. Ser. a , vol.453
    • El Hassan, M.A.1    Calladine, C.R.2
  • 15
    • 0032544507 scopus 로고    scopus 로고
    • Two distinct modes of protein-induced bending in DNA
    • El Hassan M. A., Calladine C. R. Two distinct modes of protein-induced bending in DNA. J. Mol. Biol. 282:1998;331-343.
    • (1998) J. Mol. Biol. , vol.282 , pp. 331-343
    • El Hassan, M.A.1    Calladine, C.R.2
  • 16
    • 0017587485 scopus 로고
    • Theory of DNA melting curves
    • Fixman M., Friere J. J. Theory of DNA melting curves. Biopolymers. 16:1977;2693-2704.
    • (1977) Biopolymers , vol.16 , pp. 2693-2704
    • Fixman, M.1    Friere, J.J.2
  • 17
    • 0030576959 scopus 로고    scopus 로고
    • Distribution of bending propensity in DNA sequences
    • Gabrielian A., Simoncsits A., Pongor S. Distribution of bending propensity in DNA sequences. FEBS Letters. 393:1996;124-130.
    • (1996) FEBS Letters , vol.393 , pp. 124-130
    • Gabrielian, A.1    Simoncsits, A.2    Pongor, S.3
  • 18
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • Goodsell D. S., Dickerson R. E. Bending and curvature calculations in B-DNA. Nucl. Acids Res. 22:1994;5497-5503.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.S.1    Dickerson, R.E.2
  • 19
    • 0027536101 scopus 로고
    • Crystal-structure of CATGGCCATG and its implications for A-tract bending models
    • Goodsell D. S., Kopka M. L., Cascio D., Dickerson R. E. Crystal-structure of CATGGCCATG and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA. 90:1993;2930-2934.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 2930-2934
    • Goodsell, D.S.1    Kopka, M.L.2    Cascio, D.3    Dickerson, R.E.4
  • 20
    • 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. 20:1981;1033-1042.
    • (1981) Biopolymers , vol.20 , pp. 1033-1042
    • Gotoh, O.1    Tagashira, Y.2
  • 21
    • 0027318463 scopus 로고
    • Sequence-dependent DNA structure - The role of base stacking interaction
    • Hunter C. A. Sequence-dependent DNA structure - the role of base stacking interaction. J. Mol. Biol. 230:1993;1025-1054.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 22
    • 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. 14:1997a;747-756.
    • (1997) J. Biomol. Struct. Dynam. , vol.14 , pp. 747-756
    • Hunter, C.A.1    Lu, X.J.2
  • 23
    • 0031556948 scopus 로고    scopus 로고
    • DNA base stacking interactions - A comparison of theoretical calculations with oligonucleotide crystal structures
    • Hunter C. A., Lu X. J. DNA base stacking interactions - a comparison of theoretical calculations with oligonucleotide crystal structures. J. Mol. Biol. 265:1997b;603-619.
    • (1997) J. Mol. Biol. , vol.265 , pp. 603-619
    • Hunter, C.A.1    Lu, X.J.2
  • 26
    • 0031592942 scopus 로고    scopus 로고
    • Structure and conformation of helical nucleic acids: Analysis program (SCHNAAP)
    • Lu X. J., El Hassan M. A., Hunter C. A. Structure and conformation of helical nucleic acids: analysis program (SCHNAAP). J. Mol. Biol. 273:1997;668-680.
    • (1997) J. Mol. Biol. , vol.273 , pp. 668-680
    • Lu, X.J.1    El Hassan, M.A.2    Hunter, C.A.3
  • 27
    • 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. 389:1997;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
  • 28
    • 0021099136 scopus 로고
    • Conformational transitions in oriented fibers of the synthetic polynucleotide poly[d(AT)] poly[d(AT)] double helix
    • Mahendrasingam A., Rhodes N. J., Goodwin D. C., Nave C., Pigram W. J., Fuller W., Brahms J., Vergne J. Conformational transitions in oriented fibers of the synthetic polynucleotide poly[d(AT)] poly[d(AT)] double helix. Nature. 301:1983;535-537.
    • (1983) Nature , vol.301 , pp. 535-537
    • Mahendrasingam, A.1    Rhodes, N.J.2    Goodwin, D.C.3    Nave, C.4    Pigram, W.J.5    Fuller, W.6    Brahms, J.7    Vergne, J.8
  • 30
    • 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
  • 31
    • 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
  • 32
    • 0034614487 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. 295:1999;55-70.
    • (1999) J. Mol. Biol. , vol.295 , pp. 55-70
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 33
    • 0017276138 scopus 로고
    • Polymorphism of a synthetic DNA in solution
    • Pohl F. M. Polymorphism of a synthetic DNA in solution. Nature. 260:1976;365-366.
    • (1976) Nature , vol.260 , pp. 365-366
    • Pohl, F.M.1
  • 34
    • 0015527119 scopus 로고
    • Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-C)
    • Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-C). J. Mol. Biol. 67:1972;375-396.
    • (1972) J. Mol. Biol. , vol.67 , pp. 375-396
    • Pohl, F.M.1    Jovin, T.M.2
  • 37
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S. C., Drew H. 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, H.R.2    Travers, A.A.3
  • 40
    • 0025966606 scopus 로고
    • Analysis of local helix geometry in 3 B-DNA decamers and 8 dodecamers
    • Yanagi K., Privé G. G., Dickerson R. E. Analysis of local helix geometry in 3 B-DNA decamers and 8 dodecamers. J. Mol. Biol. 217:1991;201-214.
    • (1991) J. Mol. Biol. , vol.217 , pp. 201-214
    • Yanagi, K.1    Privé, G.G.2    Dickerson, R.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.