Crystal studies of B-DNA: the answers and the questions.

The history of DNA crystallography is reviewed and is followed by discussion of the methods used for structure determination. The features of B-DNA molecular and crystal structures are described.

[1]  M. Sundaralingam,et al.  Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition. , 1996, Biophysical journal.

[2]  Juan A. Subirana,et al.  Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met represser–operator complexes , 1996, Nature Structural Biology.

[3]  W. Olson,et al.  Simulating DNA at low resolution. , 1996, Current opinion in structural biology.

[4]  D. Goodsell,et al.  MPD and DNA bending in crystals and in solution. , 1996, Journal of molecular biology.

[5]  A. R. Srinivasan,et al.  Geometric parameters in nucleic acids: Nitrogenous bases , 1996 .

[6]  H. Berman,et al.  Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents , 1996 .

[7]  H. Berman,et al.  Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs. , 1995, Biochemistry.

[8]  H M Berman,et al.  Hydration of the DNA bases is local. , 1995, Biophysical journal.

[9]  H M Berman,et al.  Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  D. Moras,et al.  Self-fitting and self-modifying properties of the B-DNA molecule. , 1995, Journal of molecular biology.

[11]  A Klug,et al.  Rapid crystallization of chemically synthesized hammerhead RNAs using a double screening procedure. , 1995, Journal of molecular biology.

[12]  L. Tari,et al.  Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition. , 1995, Nucleic acids research.

[13]  H. Berman,et al.  Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. , 1995, Biophysical journal.

[14]  S. Harvey,et al.  Dehydrating agents sharply reduce curvature in DNAs containing A tracts. , 1995, Nucleic acids research.

[15]  M. Eisenstein,et al.  Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. , 1995, Journal of molecular biology.

[16]  B. Gallois,et al.  High-resolution structure of a DNA helix forming (C·G)*G base triplets , 1995, Nature.

[17]  V. Zhurkin,et al.  B-DNA twisting correlates with base-pair morphology. , 1995, Journal of molecular biology.

[18]  L. A. Lipscomb,et al.  X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[19]  D. Goodsell,et al.  Crystal structure of C-T-C-T-C-G-A-G-A-G. Implications for the structure of the Holliday junction. , 1995, Biochemistry.

[20]  D. Goodsell,et al.  The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps. , 1994, Journal of molecular biology.

[21]  U. Heinemann,et al.  Crystallographic studies of DNA helix structure. , 1994, Biophysical chemistry.

[22]  D. Goodsell,et al.  "...the tyranny of the lattice...". , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Joachimiak,et al.  Determinants of repressor/operator recognition from the structure of the trp operator binding site , 1994, Nature.

[24]  H M Berman,et al.  A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. , 1993, Biophysical journal.

[25]  W. Hunter,et al.  Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution. , 1993, Journal of molecular biology.

[26]  W. Denny,et al.  Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)-SN6999 complex. , 1993, Biochemistry.

[27]  D. Goodsell,et al.  Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA. , 1993, Biochemistry.

[28]  Eric Westhof,et al.  Water and Biological Macromolecules , 1993 .

[29]  Fritz Eckstein,et al.  Chiral phosphorothioate analogues of B-DNA: The crystal structure of Rp-d¦Gp(S)CpGp(S)CpGp(S)C¦☆ , 1993 .

[30]  T. Steitz,et al.  A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. , 1993, Journal of molecular biology.

[31]  R. Dickerson,et al.  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. , 1993, Journal of molecular biology.

[32]  D. Goodsell,et al.  Crystal structure of CATGGCCATG and its implications for A-tract bending models. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[33]  R. Dickerson,et al.  Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. , 1993, Biochemistry.

[34]  I. Weber,et al.  Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers. , 1992, Nucleic acids research.

[35]  R. Dickerson,et al.  Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G , 1992 .

[36]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[37]  S Neidle,et al.  Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution. , 1992, Journal of molecular biology.

[38]  H M Berman,et al.  Hydration of DNA bases: Analysis of crystallographic data , 1992, Biopolymers.

[39]  R. Dickerson,et al.  Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. , 1992, Journal of molecular biology.

[40]  J L Sussman,et al.  Three-dimensional structures of bulge-containing DNA fragments. , 1992, Journal of molecular biology.

[41]  M. Bansal,et al.  Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B‐DNA. , 1992, The EMBO journal.

[42]  D. Moras,et al.  Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures , 1991, Nature.

[43]  G. A. van der Marel,et al.  Molecular structure of a DNA decamber containing an anticancer nucleoside arabinosylcytosine: conformational perturbation by arabinosylcytosine in B-DNA. , 1991, Biochemistry.

[44]  R. Dickerson,et al.  The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. , 1991, The Journal of biological chemistry.

[45]  H. Berman,et al.  Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG). , 1991, Biochemistry.

[46]  R. Dickerson,et al.  Crystal structure analysis of the B-DNA dodecamer CGTGAATTCACG. , 1991, Biochemistry.

[47]  U Heinemann,et al.  C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G. , 1991, The Journal of biological chemistry.

[48]  R. Dickerson,et al.  Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. , 1991, Journal of molecular biology.

[49]  R. Dickerson,et al.  Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. , 1991, Journal of molecular biology.

[50]  A. Rich,et al.  Molecular structure of nicked DNA: a substrate for DNA repair enzymes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[51]  U. Heinemann,et al.  Crystallographic study of one turn of G/C-rich B-DNA. , 1989, Journal of molecular biology.

[52]  E. Westhof,et al.  Unusual helical packing in crystals of DNA bearing a mutation hot spot , 1989, Nature.

[53]  T. Steitz,et al.  Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[54]  A. Rich,et al.  Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution. , 1989, The Journal of biological chemistry.

[55]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[56]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[57]  D. Goodsell,et al.  Structure of an alternating-B DNA helix and its relationship to A-tract DNA. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[58]  R Lavery,et al.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. , 1988, Journal of biomolecular structure & dynamics.

[59]  P. Fitzgerald.  MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement , 1988 .

[60]  W. Olson,et al.  Base sequence effects in double‐helical DNA. III. Average properties of curved dna , 1988, Biopolymers.

[61]  A. Rich,et al.  A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[62]  E. Westhof.  Re-refinement of the B-dodecamer d(CGCGAATTCGCG) with a comparative analysis of the solvent in it and in the Z-hexamer d(5BrCG5BrCG5BrCG). , 1987, Journal of biomolecular structure & dynamics.

[63]  A. Klug,et al.  The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.

[64]  S. A. Salisbury,et al.  Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]. , 1986, Journal of molecular biology.

[65]  R. Dickerson,et al.  Anisotropic thermal‐parameter refinement of the DNA dodecamer CGCGAATTCGCG by the segmented rigid‐body method , 1985 .

[66]  E Westhof,et al.  Crystallographic refinement of yeast aspartic acid transfer RNA. , 1985, Journal of molecular biology.

[67]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[68]  H R Drew,et al.  Ordered water structure around a B-DNA dodecamer. A quantitative study. , 1983, Journal of molecular biology.

[69]  H R Drew,et al.  Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. , 1982, The Journal of biological chemistry.

[70]  Richard E. Dickerson,et al.  Structure of a B-DNA dodecamer at 16 K. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[71]  R. Dickerson,et al.  The molecular structure of d(ICpCpGpG), a fragment of right-handed double helical A-DNA , 1982, Nature.

[72]  R. Dickerson,et al.  Kinematic model for B-DNA. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[73]  R. Millane,et al.  Stereochemical details of the side-by-side model for DNA. , 1981, Nucleic acids research.

[74]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[75]  M. Bansal,et al.  Conformational flexibility of DNA: polymorphism and handedness. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[76]  Richard E. Dickerson,et al.  Crystal structure analysis of a complete turn of B-DNA , 1980, Nature.

[77]  A. R. Srinivasan,et al.  Yeast tRNAPhe conformation wheels: a novel probe of the monoclinic and orthorhombic models. , 1980, Nucleic acids research.

[78]  F. Crick,et al.  Is DNA really a double helix? , 1979, Journal of molecular biology.

[79]  R. K. Stodola,et al.  Drug-nucleic acid interactions: conformational flexibility at the intercalation site. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[80]  R. Lewitt,et al.  A possible conformation for double-stranded polynucleotides. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[81]  N C Seeman,et al.  RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate. , 1976, Journal of molecular biology.

[82]  N. Seeman,et al.  Double Helix at Atomic Resolution , 1973, Nature.

[83]  R. Franklin,et al.  Molecular Configuration in Sodium Thymonucleate , 1953, Nature.

[84]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[85]  R. T. Walker,et al.  The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides. , 1996, Nucleic acids research.

[86]  E. Pednault,et al.  Nucleic acid structure analysis: a users guide to a collection of new analysis programs. , 1993, Journal of biomolecular structure & dynamics.

[87]  D. Moras,et al.  Crystallization of DNA. , 1992, Methods in enzymology.

[88]  H. Berman,et al.  Crystal structures of fragments of DNA and RNA , 1981 .

[89]  S. Neidle.  Topics in Nucleic Acid Structure , 1981 .

[90]  R. Bechmann,et al.  Numerical data and functional relationships in science and technology , 1969 .