메뉴 건너뛰기




Volumn 40, Issue 8, 2012, Pages 3714-3722

B-DNA structure is intrinsically polymorphic: Even at the level of base pair positions

Author keywords

[No Author keywords available]

Indexed keywords

DNA B; MAGNESIUM ION;

EID: 84860376513     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1168     Document Type: Article
Times cited : (44)

References (47)
  • 1
    • 0034711942 scopus 로고    scopus 로고
    • Conformational flexibility of B-DNA at 0.74 angstrom resolution: D(CCAGTACTGG) 2
    • Kielkopf, C.L., Ding, S., Kuhn, P. and Reese, D.C. (2000) Conformational Flexibility of B-DNA at 0.74 Angstrom Resolution: d(CCAGTACTGG)2. J. Mol. Biol., 296, 787-801.
    • (2000) J. Mol. Biol. , vol.296 , pp. 787-801
    • Kielkopf, C.L.1    Ding, S.2    Kuhn, P.3    Reese, D.C.4
  • 2
    • 0034714010 scopus 로고    scopus 로고
    • 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium
    • Chiu, T.K. and Dickerson, R.E. (2000) 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J. Mol. Biol., 301, 915-945.
    • (2000) J. Mol. Biol. , vol.301 , pp. 915-945
    • Chiu, T.K.1    Dickerson, R.E.2
  • 4
    • 69449087887 scopus 로고    scopus 로고
    • Allosteric modulation of DNA by small molecules
    • Chenoweth, D.M. and Dervan, P.B. (2009) Allosteric modulation of DNA by small molecules. Proc. Natl Acad. Sci. USA, 106, 13175-13179.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 13175-13179
    • Chenoweth, D.M.1    Dervan, P.B.2
  • 5
    • 0024846232 scopus 로고
    • Crystallographic study of one turn of G/C-rich B-DNA
    • Heinemann, U. and Alings, C. (1989) Crystallographic study of one turn of G/C-rich B-DNA. J. Mol. Biol., 210, 369-381.
    • (1989) J. Mol. Biol. , vol.210 , pp. 369-381
    • Heinemann, U.1    Alings, C.2
  • 7
    • 0018077590 scopus 로고
    • Crystal structure of yeast phenylalanine tRNA. I. Crystallographic refinement
    • Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M. and Kim, S.-H. (1978) Crystal structure of yeast phenylalanine tRNA. I. Crystallographic refinement. J. Mol. Biol., 123, 607.
    • (1978) J. Mol. Biol. , vol.123 , pp. 607
    • Sussman, J.L.1    Holbrook, S.R.2    Warrant, R.W.3    Church, G.M.4    Kim, S.-H.5
  • 9
    • 0032387836 scopus 로고    scopus 로고
    • Structure of the potassium form of CGCGA ATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
    • Shui, X., Sines, C., McFail-Isom, L., VanDerveer, D. and Williams, L.D. (1998) Structure of the potassium form of CGCGA ATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry, 37, 16877-16887.
    • (1998) Biochemistry , vol.37 , pp. 16877-16887
    • Shui, X.1    Sines, C.2    McFail-Isom, L.3    Vanderveer, D.4    Williams, L.D.5
  • 10
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shui, X., McFail-Isom, L., Hu, G.G. and Williams, L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry, 37, 8341-8355.
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shui, X.1    McFail-Isom, L.2    Hu, G.G.3    Williams, L.D.4
  • 12
    • 0038713237 scopus 로고    scopus 로고
    • A unified model for the origin of DNA sequence-directed curvature
    • Hud, N.V. and Plavec, J. (2003) A unified model for the origin of DNA sequence-directed curvature. Biopolymers, 69, 144-158.
    • (2003) Biopolymers , vol.69 , pp. 144-158
    • Hud, N.V.1    Plavec, J.2
  • 13
    • 0031059866 scopus 로고    scopus 로고
    • Carter, J.C.W. and Sweet, R.M. (eds) Part A. Academic Press, New York
    • Otwinowski, Z. and Minor, W. (1997) In: Carter, J.C.W. and Sweet, R.M. (eds), Methods in Enzymol., Macromolecular Crystallography, Vol. 276. Part A. Academic Press, New York, pp. 307-326.
    • (1997) Methods in Enzymol., Macromolecular Crystallography , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 14
    • 0026597444 scopus 로고
    • Free R-value-a novel statistical quantity for assessing the accuracy of crystal-structures
    • Brunger, A.T. (1992) Free R-value-a novel statistical quantity for assessing the accuracy of crystal-structures. Nature, 355, 472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brunger, A.T.1
  • 18
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximumlikelihood method. Acta Crystallogr
    • Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximumlikelihood method. Acta Crystallogr., Sect D: Biol. Crystallogr., 53, 240-255.
    • (1997) Sect D: Biol. Crystallogr. , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 20
    • 33646767009 scopus 로고    scopus 로고
    • Ortep-3 for windows
    • Farrugia, L.J. (1997) Ortep-3 for Windows. J. Appl. Cryst., 30, 565.
    • (1997) J. Appl. Cryst. , vol.30 , pp. 565
    • Farrugia, L.J.1
  • 21
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX. Acta Crystallogr, Sect. A: Found
    • Sheldrick, G.M. (2008) A short history of SHELX. Acta Crystallogr., Sect. A: Found. Crystallogr., 64, 112-122.
    • (2008) Crystallogr. , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 22
    • 84944815329 scopus 로고
    • What factors determine cation coordination numbers
    • Brown, I.D. (1988) What factors determine cation coordination numbers. Acta Crystallogr. Sect. B., 44, 545-553.
    • (1988) Acta Crystallogr. Sect. B. , vol.44 , pp. 545-553
    • Brown, I.D.1
  • 23
    • 0015511563 scopus 로고
    • Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation
    • Altona, C. and Sundaralingam, M. (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc., 94, 8205-8212.
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 8205-8212
    • Altona, C.1    Sundaralingam, M.2
  • 24
    • 0035367927 scopus 로고    scopus 로고
    • DNA-cation interactions: The major and minor grooves are flexible ionophores
    • Hud, N.V. and Polak, M. (2001) DNA-cation interactions: the major and minor grooves are flexible ionophores. Curr. Opin. Struct. Biol., 11, 293-301.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 293-301
    • Hud, N.V.1    Polak, M.2
  • 25
    • 0027203986 scopus 로고
    • The crystal structure of the trigonal decamer C-G-A-T-C-G-6mea-T-C-G: A B-DNA helix with 10.6 base-pairs per turn
    • Baikalov, I., Grzeskowiak, K., Yanagi, K., Quintana, J. and Dickerson, R.E. (1993) The crystal structure of the trigonal decamer C-G-A-T-C-G-6mea-T-C- G: A B-DNA helix with 10.6 base-pairs per turn. J. Mol. Biol., 231, 768-784.
    • (1993) J. Mol. Biol. , vol.231 , pp. 768-784
    • Baikalov, I.1    Grzeskowiak, K.2    Yanagi, K.3    Quintana, J.4    Dickerson, R.E.5
  • 26
    • 0026738923 scopus 로고
    • CCAGGCm5CTGG. Helical fine structure, hydration, and comparison with CCAGGCCTGG
    • Heinemann, U. and Hahn, M. (1992) CCAGGCm5CTGG. Helical fine structure, hydration, and comparison with CCAGGCCTGG. J. Biol. Chem., 267, 7332-7341.
    • (1992) J. Biol. Chem. , vol.267 , pp. 7332-7341
    • Heinemann, U.1    Hahn, M.2
  • 27
    • 33845551411 scopus 로고
    • Geometry of the N-H O=C hydrogen bond. 1. Lone pair directionality
    • Taylor, R., Kennard, O. and Versichel, W. (1983) Geometry of the N-H O=C hydrogen bond. 1. Lone pair directionality. J. Am. Chem. Soc., 105, 5761-5766.
    • (1983) J. Am. Chem. Soc. , vol.105 , pp. 5761-5766
    • Taylor, R.1    Kennard, O.2    Versichel, W.3
  • 28
    • 0021494642 scopus 로고
    • 3-Center (Bifurcated) Hydrogen-bonding in the crystal-structures of amino-acids
    • Jeffrey, G.A. and Mitra, J. (1984) 3-Center (Bifurcated) Hydrogen-bonding in the crystal-structures of amino-acids. J. Am. Chem. Soc., 106, 5546-5553.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 5546-5553
    • Jeffrey, G.A.1    Mitra, J.2
  • 29
    • 0023494886 scopus 로고
    • A bifurcated hydrogen-bonded conformation in the d(A-T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin
    • Coll, M., Frederick, C.A., Wang, A.H.-J. and Rich, A. (1987) A bifurcated hydrogen-bonded conformation in the d(A-T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl Acad. Sci. USA, 84, 8385-8389.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 8385-8389
    • Coll, M.1    Frederick, C.A.2    Wang, A.H.-J.3    Rich, A.4
  • 30
    • 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. and Klug, A. (1987) The structure of an Oligo(dA) Oligo(dT) tract and its biological implications. Nature, 330, 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
  • 33
    • 0026601995 scopus 로고
    • Investigations on the dynamic structures of adenine-and thymine-containing DNA
    • Brahms, S., Fritsch, V., Brahms, J.G. and Westhof, E. (1992) Investigations on the dynamic structures of adenine-and thymine-containing DNA. J. Mol. Biol., 223, 455-476.
    • (1992) J. Mol. Biol. , vol.223 , pp. 455-476
    • Brahms, S.1    Fritsch, V.2    Brahms, J.G.3    Westhof, E.4
  • 36
    • 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. and Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 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
  • 37
    • 77649270492 scopus 로고    scopus 로고
    • Sequence recognition of DNA by protein-induced conformational transitions
    • Watkins, D., Mohan, S., Koudelka, G.B. and Williams, L.D. (2010) Sequence recognition of DNA by protein-induced conformational transitions. J. Mol. Biol., 396, 1145-1164.
    • (2010) J. Mol. Biol. , vol.396 , pp. 1145-1164
    • Watkins, D.1    Mohan, S.2    Koudelka, G.B.3    Williams, L.D.4
  • 38
    • 39749145842 scopus 로고    scopus 로고
    • P22 C2 repressor-operator complex: Mechanisms of direct and indirect readout
    • Watkins, D., Hsiao, C., Woods, K.K., Koudelka, G.B. and Williams, L.D. (2008) P22 C2 repressor-operator complex: mechanisms of direct and indirect readout. Biochemistry, 47, 2325-2338.
    • (2008) Biochemistry , vol.47 , pp. 2325-2338
    • Watkins, D.1    Hsiao, C.2    Woods, K.K.3    Koudelka, G.B.4    Williams, L.D.5
  • 40
    • 0031576353 scopus 로고    scopus 로고
    • The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution
    • Phillips, K., Dauter, Z., Murchie, A.I.H., Lilley, D.M.J. and Luisi, B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution. J. Mol. Biol., 273, 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
  • 42
    • 0020359857 scopus 로고
    • Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG
    • Fratini, A.V., Kopka, M.L., Drew, H.R. and Dickerson, R.E. (1982) Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J. Biol. Chem., 257, 14686-14707.
    • (1982) J. Biol. Chem. , vol.257 , pp. 14686-14707
    • Fratini, A.V.1    Kopka, M.L.2    Drew, H.R.3    Dickerson, R.E.4
  • 44
    • 0028184697 scopus 로고
    • Measuring the geometry of DNA grooves
    • Stofer, E. and Lavery, R. (1994) Measuring the geometry of DNA grooves. Biopolymers, 34, 337-346.
    • (1994) Biopolymers , vol.34 , pp. 337-346
    • Stofer, E.1    Lavery, R.2
  • 45
    • 0034725706 scopus 로고    scopus 로고
    • Solvent organization in an oligonucleotide crystal. The structure of d(GC GAATTCG)2 at atomic resolution
    • Soler-Lopez, M., Malinina, L. and Subirana, J.A. (2000) Solvent organization in an oligonucleotide crystal. The structure of d(GC GAATTCG)2 at atomic resolution. J. Biol. Chem., 275, 23034-23044.
    • (2000) J. Biol. Chem. , vol.275 , pp. 23034-23044
    • Soler-Lopez, M.1    Malinina, L.2    Subirana, J.A.3
  • 47
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.