-
1
-
-
0034711942
-
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
-
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
-
3
-
-
0038645688
-
Water and ions in a high resolution structure of B-DNA
-
Soler-Lopez, M., Malinina, L., Liu, J., Huynh-Dinh, T. and Subirana, J.A. (1999) Water and ions in a high resolution structure of B-DNA. J. Biol. Chem., 274, 23683-23686.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 23683-23686
-
-
Soler-Lopez, M.1
Malinina, L.2
Liu, J.3
Huynh-Dinh, T.4
Subirana, J.A.5
-
4
-
-
69449087887
-
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
-
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
-
6
-
-
0019558179
-
Structure of a B-DNA dodecamer. Conformation and dynamics
-
Drew, H.R., Wing, R.M., Takano, T., Broka, C., Itakura, K. and Dickerson, R.E. (1981) Structure of a B-DNA dodecamer. Conformation and dynamics. Proc. Natl Acad. Sci. USA, 78, 2179-2183.
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 2179-2183
-
-
Drew, H.R.1
Wing, R.M.2
Takano, T.3
Broka, C.4
Itakura, K.5
Dickerson, R.E.6
-
7
-
-
0018077590
-
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
-
8
-
-
0034669632
-
Cations mediate B-DNA conformational heterogeneity
-
Sines, C.C., McFail-Isom, L., Howerton, S.B., VanDerveer, D. and Williams, L.D. (2000) Cations mediate B-DNA conformational heterogeneity. J. Am. Chem. Soc., 122, 11048-11056.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 11048-11056
-
-
Sines, C.C.1
McFail-Isom, L.2
Howerton, S.B.3
Vanderveer, D.4
Williams, L.D.5
-
9
-
-
0032387836
-
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
-
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
-
11
-
-
0033150892
-
DNA structure: Cations in charge?
-
McFail-Isom, L., Sines, C.C. and Williams, L.D. (1999) DNA structure: cations in charge? Curr. Opin. Struct. Biol., 9, 298-304.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 298-304
-
-
McFail-Isom, L.1
Sines, C.C.2
Williams, L.D.3
-
12
-
-
0038713237
-
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
-
-
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
-
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
-
15
-
-
3543012707
-
Crystallography & Nmr system: A new software suite for macromolecular structure determination. Acta Crystallogr
-
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography & Nmr system: a new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D-Biol. Crystallogr., 54, 905-921.
-
(1998)
Sect. D-Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
-
16
-
-
0030071775
-
Geometric parameters in nucleic acids: Sugar and phosphate constitutents
-
Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K. and Berman, H.M. (1996) Geometric parameters in nucleic acids: sugar and phosphate constitutents. J. Am. Chem. Soc., 118, 519-529.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 519-529
-
-
Gelbin, A.1
Schneider, B.2
Clowney, L.3
Hsieh, S.-H.4
Olson, W.K.5
Berman, H.M.6
-
17
-
-
0030051966
-
Geometric parameters in nucleic acids: Nitrogenous bases
-
Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K. and Berman, H.M. (1996) Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc., 118, 509-518.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 509-518
-
-
Clowney, L.1
Jain, S.C.2
Srinivasan, A.R.3
Westbrook, J.4
Olson, W.K.5
Berman, H.M.6
-
18
-
-
0030924992
-
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
-
19
-
-
13244281317
-
Coot: Model-building tools for molecular graphics
-
Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect D: Biol. Crystallogr., 60, 2126-2132.
-
(2004)
Acta Crystallogr, Sect D: Biol. Crystallogr.
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
20
-
-
33646767009
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
31
-
-
9644302286
-
High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)] 2
-
Woods, K.K., Maehigashi, T., Howerton, S.B., Sines, C.C., Tannenbaum, S. and Williams, L.D. (2004) High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2. J. Am. Chem. Soc., 126, 15330-15331.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 15330-15331
-
-
Woods, K.K.1
Maehigashi, T.2
Howerton, S.B.3
Sines, C.C.4
Tannenbaum, S.5
Williams, L.D.6
-
33
-
-
0026601995
-
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
-
34
-
-
80051707464
-
High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A
-
Brzezinski, K., Brzuszkiewicz, A., Dauter, M., Kubicki, M., Jaskolski, M. and Dauter, Z. (2011) High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A. Nucleic Acids Res., 1, 1.
-
(2011)
Nucleic Acids Res.
, vol.1
, pp. 1
-
-
Brzezinski, K.1
Brzuszkiewicz, A.2
Dauter, M.3
Kubicki, M.4
Jaskolski, M.5
Dauter, Z.6
-
35
-
-
0018689799
-
Molecular structure of a left-handed double helical DNA fragment at atomic resolution
-
Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G. and Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature, 282, 680-686.
-
(1979)
Nature
, vol.282
, pp. 680-686
-
-
Wang, A.H.1
Quigley, G.J.2
Kolpak, F.J.3
Crawford, J.L.4
Van Boom, J.H.5
Van Der Marel, G.6
Rich, A.7
-
36
-
-
0032530555
-
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
-
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
-
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
-
39
-
-
0027948889
-
The tyranny of the Lattice
-
Dickerson, R.E., Goodsell, D.S. and Neidle, S. (1994) " . . . The Tyranny of the Lattice . . . ". Proc. Natl Acad. Sci. USA, 91, 3579-3583.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 3579-3583
-
-
Dickerson, R.E.1
Goodsell, D.S.2
Neidle, S.3
-
40
-
-
0031576353
-
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
-
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
-
43
-
-
0027335758
-
BI-BII transitions in B-DNA
-
Hartmann, B., Piazzola, D. and Lavery, R. (1993) BI-BII transitions in B-DNA. Nucleic Acids Res., 21, 561-568.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 561-568
-
-
Hartmann, B.1
Piazzola, D.2
Lavery, R.3
-
44
-
-
0028184697
-
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
-
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
-
46
-
-
0000742485
-
X-ray crystallographic analysis of the hydration of A-and B-form DNA at atomic resolution
-
Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H.Y. et al. (1998) X-ray crystallographic analysis of the hydration of A-and B-form DNA at atomic resolution. Biopolymers, 48, 234-252.
-
(1998)
Biopolymers
, vol.48
, pp. 234-252
-
-
Egli, M.1
Tereshko, V.2
Teplova, M.3
Minasov, G.4
Joachimiak, A.5
Sanishvili, R.6
Weeks, C.M.7
Miller, R.8
Maier, M.A.9
An, H.Y.10
-
47
-
-
0242396923
-
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
|