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Volumn 288, Issue 5, 1999, Pages 953-963

The mechanics of minor groove width variation in DNA, and its implications for the accommodation of ligands

Author keywords

DNA; Drug DNA interactions; Minor groove; Molecular modelling; Molecular recognition

Indexed keywords

DOUBLE STRANDED DNA; SUGAR PHOSPHATE; TATA BINDING PROTEIN;

EID: 0033591320     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2733     Document Type: Article
Times cited : (26)

References (49)
  • 2
    • 0029059536 scopus 로고
    • DNA-sequence preferences of several AT-selective minor-groove binding ligands
    • Abudaya A., Brown P. M., Fox K. R. DNA-sequence preferences of several AT-selective minor-groove binding ligands. Nucl. Acids Res. 23:1995;3385-3392.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 3385-3392
    • Abudaya, A.1    Brown, P.M.2    Fox, K.R.3
  • 3
    • 0030907883 scopus 로고    scopus 로고
    • Sequence-selective binding to DNA of bis(amidinophenoxy)alkanes related to propamidine and pentamidine
    • Bailly C., Perrine D., Lancelot J. C., Saturnino C., Robba M., Waring M. J. Sequence-selective binding to DNA of bis(amidinophenoxy)alkanes related to propamidine and pentamidine. Biochem. J. 323:1997;23-31.
    • (1997) Biochem. J. , vol.323 , pp. 23-31
    • Bailly, C.1    Perrine, D.2    Lancelot, J.C.3    Saturnino, C.4    Robba, M.5    Waring, M.J.6
  • 4
    • 0026698647 scopus 로고
    • Groove width and depth of B -DNA structures depend on local variation in slide
    • Bhattacharyya D., Bansal M. Groove width and depth of B -DNA structures depend on local variation in slide. J. Biomol. Struct. Dynam. 10:1992;213-226.
    • (1992) J. Biomol. Struct. Dynam. , vol.10 , pp. 213-226
    • Bhattacharyya, D.1    Bansal, M.2
  • 5
    • 0025272657 scopus 로고
    • Crystal structure of a berenil-dodecanucleotide complex: The role of water in sequence-specific ligand binding
    • Brown D. G., Sanderson M. R., Skelly J. V., Jenkins T. C., Brown T., Garman E., Stuart D. I., Neidle S. Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding. EMBO J. 9:1990;1329-1334.
    • (1990) EMBO J. , vol.9 , pp. 1329-1334
    • Brown, D.G.1    Sanderson, M.R.2    Skelly, J.V.3    Jenkins, T.C.4    Brown, T.5    Garman, E.6    Stuart, D.I.7    Neidle, S.8
  • 6
    • 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
  • 8
    • 0024599312 scopus 로고
    • Definitions and nomenclature of nucleic acid structure components
    • Dickerson R. E. Definitions and nomenclature of nucleic acid structure components. Nucl. Acids Res. 17:1989;1797-1803.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 1797-1803
    • Dickerson, R.E.1
  • 11
    • 0026707681 scopus 로고
    • Crystal structure of a pentamidine-oligonucleotide complex: Implications for DNA-binding properties
    • Edwards K. J., Jenkins T. C., Neidle S. Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties. Biochemistry. 31:1992;7104-7109.
    • (1992) Biochemistry , vol.31 , pp. 7104-7109
    • Edwards, K.J.1    Jenkins, T.C.2    Neidle, S.3
  • 12
    • 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 C. R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. Roy. Soc. London. 355:1997;43-100.
    • (1997) Phil. Trans. Roy. Soc. London , vol.355 , pp. 43-100
    • El Hassan, M.A.1    Calladine, C.R.2
  • 14
    • 0029565563 scopus 로고
    • Structure of a dicationic monoimidazole lexitropsin bound to DNA
    • Goodsell D. S., Ng H. L., Kopka M. L., Lown J. W., Dickerson R. E. Structure of a dicationic monoimidazole lexitropsin bound to DNA. Biochemistry. 34:1995;16654-16661.
    • (1995) Biochemistry , vol.34 , pp. 16654-16661
    • Goodsell, D.S.1    Ng, H.L.2    Kopka, M.L.3    Lown, J.W.4    Dickerson, R.E.5
  • 15
    • 0028931709 scopus 로고
    • B -DNA twisting correlates with base pair morphology
    • Gorin A. A., Zhurkin V. E., 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.E.2    Olson, W.K.3
  • 17
    • 84977299328 scopus 로고
    • Anisotropic thermal-parameter refinement of the DNA dodecamer CGCGAATTCGCG by the segmented rigid-body method
    • Holbrook S. R., Dickerson R. E., Kim S. H. Anisotropic thermal-parameter refinement of the DNA dodecamer CGCGAATTCGCG by the segmented rigid-body method. Acta Crystallog. sect. B. 41:1985;255-262.
    • (1985) Acta Crystallog. Sect. B , vol.41 , pp. 255-262
    • Holbrook, S.R.1    Dickerson, R.E.2    Kim, S.H.3
  • 19
    • 0027974851 scopus 로고
    • 1.9 Å resolution structure of TBP recognizing the minor groove of the TATA-box
    • Kim J. L., Burley S. K. 1.9 Å resolution structure of TBP recognizing the minor groove of the TATA-box. Nature Struct. Biol. 1:1994;638-645.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 638-645
    • Kim, J.L.1    Burley, S.K.2
  • 22
    • 0027122080 scopus 로고
    • Minor-groove width and accessibility in B -DNA drug and protein complexes
    • Neidle S. Minor-groove width and accessibility in B -DNA drug and protein complexes. FEBS Letters. 298:1992;97-99.
    • (1992) FEBS Letters , vol.298 , pp. 97-99
    • Neidle, S.1
  • 23
    • 0031424230 scopus 로고    scopus 로고
    • Crystallographic insights into DNA minor groove recognition by drugs
    • Neidle S. Crystallographic insights into DNA minor groove recognition by drugs. Biopolymers. 44:1997;105-121.
    • (1997) Biopolymers , vol.44 , pp. 105-121
    • Neidle, S.1
  • 24
    • 0028241531 scopus 로고
    • Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes
    • Nekludova L., Pabo C. O. Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. Proc. Natl Acad. Sci. USA. 91:1994;6948-6951.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 6948-6951
    • Nekludova, L.1    Pabo, C.O.2
  • 25
    • 0023513912 scopus 로고
    • The structure of an oligo(dA).oligo(dT) tract and its biological implications
    • Nelson H. C. M., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 330:1987;221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 26
    • 0027772178 scopus 로고
    • Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine
    • Nunn C. M., Jenkins T. C., Neidle S. Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine. Biochemistry. 32:1993;13838-13843.
    • (1993) Biochemistry , vol.32 , pp. 13838-13843
    • Nunn, C.M.1    Jenkins, T.C.2    Neidle, S.3
  • 27
    • 0028670449 scopus 로고
    • 2- The effects of drug structural-change on DNA minor-groove recognition
    • 2- the effects of drug structural-change on DNA minor-groove recognition. Eur. J. Biochem. 226:1994;953-961.
    • (1994) Eur. J. Biochem. , vol.226 , pp. 953-961
    • Nunn, C.M.1    Jenkins, T.C.2    Neldle, S.3
  • 28
    • 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
  • 29
    • 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
  • 31
    • 0031576353 scopus 로고    scopus 로고
    • The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution
    • Phillips K., Dauter Z., Murchie A. I. H., Lilley D. M. J., Luisi B. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273:1997;171-182.
    • (1997) J. Mol. Biol. , vol.273 , pp. 171-182
    • Phillips, K.1    Dauter, Z.2    Murchie, A.I.H.3    Lilley, D.M.J.4    Luisi, B.5
  • 32
    • 0023626977 scopus 로고
    • Binding of Hoechst 33258 to the minor groove of B -DNA
    • Pjura P. E., Grzeskowiak K., Dickerson R. E. Binding of Hoechst 33258 to the minor groove of B -DNA. J. Mol. Biol. 197:1987;257-271.
    • (1987) J. Mol. Biol. , vol.197 , pp. 257-271
    • Pjura, P.E.1    Grzeskowiak, K.2    Dickerson, R.E.3
  • 33
    • 0025885778 scopus 로고
    • Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G
    • Quintana J. R., Lipanov A. A., Dickerson R. E. Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Biochemistry. 30:1991;10294-10306.
    • (1991) Biochemistry , vol.30 , pp. 10294-10306
    • Quintana, J.R.1    Lipanov, A.A.2    Dickerson, R.E.3
  • 34
    • 0029930932 scopus 로고    scopus 로고
    • The width of the minor-groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA
    • Rydzewski J. M., Leupin W., Chazin W. The width of the minor-groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA. Nucl. Acids Res. 24:1996;1287-1293.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 1287-1293
    • Rydzewski, J.M.1    Leupin, W.2    Chazin, W.3
  • 35
    • 0031195002 scopus 로고    scopus 로고
    • Conformations of the sugar-phosphate backbone in helical DNA crystal structures
    • Schneider B., Neidle S., Berman H. M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers. 42:1997;113-124.
    • (1997) Biopolymers , vol.42 , pp. 113-124
    • Schneider, B.1    Neidle, S.2    Berman, H.M.3
  • 36
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar R. S., Record M. T. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record, M.T.2
  • 37
    • 0023350241 scopus 로고
    • Nucleic acid model building: The multiple backbone solutions associated with a given base morphology
    • Srinivasan A. R., Olson W. K. Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. J. Biomol. Struct. Dynam. 4:1987;895-938.
    • (1987) J. Biomol. Struct. Dynam. , vol.4 , pp. 895-938
    • Srinivasan, A.R.1    Olson, W.K.2
  • 38
    • 0026569363 scopus 로고
    • Conformation of B -DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: Molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342
    • Sriram M., van der Marel G. A., Roelen H. L., van Boom J. H., Wang A. H. Conformation of B -DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. EMBO J. 11:1992a;225-232.
    • (1992) EMBO J. , vol.11 , pp. 225-232
    • Sriram, M.1    Van Der Marel, G.A.2    Roelen, H.L.3    Van Boom, J.H.4    Wang, A.H.5
  • 39
    • 0026475822 scopus 로고
    • Structural consequences of a carcinogenic alkylation lesion on DNA: Effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)-netropsin complex
    • Sriram M., van der Marel G. A., Roelen H. L., van Boom J. H., Wang A. H. Structural consequences of a carcinogenic alkylation lesion on DNA: effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)-netropsin complex. Biochemistry. 31:1992b;11823-11834.
    • (1992) Biochemistry , vol.31 , pp. 11823-11834
    • Sriram, M.1    Van Der Marel, G.A.2    Roelen, H.L.3    Van Boom, J.H.4    Wang, A.H.5
  • 40
    • 0030918413 scopus 로고    scopus 로고
    • Influence of sequence on the conformation of the B -DNA helix
    • Subirana J. A., Faria T. Influence of sequence on the conformation of the B -DNA helix. Biophys. J. 73:1997;333-338.
    • (1997) Biophys. J. , vol.73 , pp. 333-338
    • Subirana, J.A.1    Faria, T.2
  • 41
    • 0029866801 scopus 로고    scopus 로고
    • An in-the-groove view of DNA structures in complexes with proteins
    • Suzuki M., Yagi N. An in-the-groove view of DNA structures in complexes with proteins. J. Mol. Biol. 255:1996;677-687.
    • (1996) J. Mol. Biol. , vol.255 , pp. 677-687
    • Suzuki, M.1    Yagi, N.2
  • 42
    • 0024296533 scopus 로고
    • The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG)
    • Teng M. K., Usman N., Frederick C. A., Wang A. H. The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucl. Acids Res. 16:1988;2671-2690.
    • (1988) Nucl. Acids Res. , vol.16 , pp. 2671-2690
    • Teng, M.K.1    Usman, N.2    Frederick, C.A.3    Wang, A.H.4
  • 46
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek S. T., Clark T. W., Scott L. R., McCammon J. A. Molecular dynamics of acetylcholinesterase dimer complexed with tacrine. J. Am. Chem. Soc. 119:1997;9313-9322.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 9313-9322
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 48
    • 0025966606 scopus 로고
    • Analysis of local helix geometry in three B -DNA decamers and eight dodecamers
    • Yanagi K., Privé 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    Privé, G.G.2    Dickerson, R.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.