Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies | Quarterly Reviews of Biophysics | Cambridge Core (original) (raw)

References

Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the cro repressor of phage 434: a view at high resolution. Science 242, 899–907.Google Scholar

Anderson, J. E., Ptashne, M. & Harrison, S. C. (1985). A phage repressor-operator complex at 7 Å resolution. Nature 316, 596–601.Google Scholar

Arentzen, R., Van Boecke, C. A. A., Van Der Marel, G. & Van Boom, J. H. (1979). A convenient phosphorylating agent for the synthesis of DNA fragments by the phosphotriester approach. Synthesis 137–139.Google Scholar

Arndt, U. W. (1985). Television area detector diffractometers. In Methods in Enzymology, vol. 114 (ed. Wyckoff, H., Hirs, C. H. W. and Timasheff, S. N.), pp. 472–485. New York: Academic Press.Google Scholar

Arnott, S. & Hukins, D. W. J. (1972). Optimised parameters for A-DNA and B-DNA. Biochem. biophys. Res. Comm. 47, 1504–1509.Google Scholar

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: a computer based archival file for macromolecular structures. Eur. J. Biochem. 80, 319–324.Google Scholar

Blundell, T. & Johnson, L. N. (1976). Protein Crystallography. New York: Academic Press.Google Scholar

Brennan, R. G., Westhof, E. & Sundaralingam, M. (1986). The structure of a ZDNA with 2 different backbone conformations. Stabilisation of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine. J. Biomolec. Struct. Dynam. 3, 649–665.CrossRefGoogle Scholar

Brown, T., Kennard, O., Kneale, G. & Rabinovich, D. (1985). High resolution structure of a DNA helix containing mismatched base pairs. Nature 315, 604–606.CrossRefGoogle ScholarPubMed

Brown, T., Hunter, W. N., Kneale, G. & Kennard, O. (1986 a). Molecular structure of the G. A base pair and it's implications for the mechanism of tranversion mutations. Proc. natn. Acad. Sci. U.S.A. 83, 2402–2406.Google Scholar

Brown, T., Kneale, G., Hunter, W. N. & Kennard, O. (1986 b). Structural characterisation of the bromouracil.guanine base pair mismatch in a Z-DNA fragment. Nucl. Acids Res. 14, 1801–1809.CrossRefGoogle Scholar

Brown, T., Leonard, G. A., Booth, E. D. & Chambers, J. (1989). Crystal structure and stability of a DNA duplex containing A(anti). G(syn) base pairs. J. molec. Biol. 207, 445–457.Google Scholar

Calladine, C. R. (1982). Mechanics of sequence-dependent stacking of bases in BDNA. J. molec. Biol. 161, 343–352.CrossRefGoogle ScholarPubMed

Calladine, C. R. & Drew, H. R. (1984). A base centred explanation of the B-to-A transition in DNA. J. molec. Biol. 178, 773–782.Google Scholar

Calladine, C. R. & Drew, H. R. (1986). Principles of sequence-dependent flexure of DNA. J. molec. Biol. 192, 907–918.CrossRefGoogle ScholarPubMed

Calladine, C. R., Drew, H. R. & McCall, M. J. (1988). The intrinsic curvature of DNA in solution. J. molec. Biol. 201, 127–137.CrossRefGoogle ScholarPubMed

Chattopadhaya, R. & Chakrabarti, P. (1988). Solving structures by MERLOT. Acta crystallogr. B 44, 651–657.Google Scholar

Chattopadhyaya, R., Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1988). X-ray structure of a DNA hairpin molecule. Nature 334, 175–179.Google Scholar

Chevrier, B., Dock, A. C., Hartmann, B., Leng, M., Moras, D., Thoung, M. T. & Westhof, E. (1986). Solvation of the left-handed hexamer d(5BrCG5BrCG5BrCG) in crystals grown at two temperatures. J. molec. Biol. 188, 707–719.CrossRefGoogle Scholar

Coll, M., Wang, A. H.-J., Van Der Marel, G. A., Van Boom, J. H. & Rich, A. (1986). Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs. J. Biomolec. Struct. Dynam. 4, 157–172.CrossRefGoogle ScholarPubMed

Coll, M., Frederick, C. A., Wang, A. H.-J. & Rich, A. (1987). A bifurcated hydrogen bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG). Proc. natn. Acad. Sci. U.S.A. 84, 8385–8389.Google Scholar

Coll, M., Pita, I., Lloveras, J., Subirana, J. A., Bardella, P., Huynh-Dinh, T. & Igolen, J. (1988). Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs. Nucl. Acids Res. 16, 8695–8705.Google Scholar

Coll, M., Saal, D., Frederick, C. A., Aymami, J., Rich, A. & Wang, A. H.-J. (1989 a). Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA. Molecular and crystal structure of d(CGCGFG). Nucl. Acids Res. 17, 911–923.Google Scholar

Coll, M., Aymami, J., Van Der Marel, G. A., Van Boom, J. H., Rich, A. & Wang, A. H.-J. (1989 b). Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Biochemistry 28, 310–320.Google Scholar

Conner, B. N., Takano, T., Tanaka, S., Itakura, K. & Dickerson, R. E. (1982). The molecular structure of d(IoCCGG) a fragment of right-handed double helical ADNA. Nature 295, 294–299.CrossRefGoogle Scholar

Conner, B. N., Yoon, C., Dickerson, J. L. & Dickerson, R. E. (1984). Helix geometry and hydration in an A-DNA tetramer: IoCCGG. J. molec. Biol. 174, 663–695.CrossRefGoogle Scholar

Corfield, P. W. R., Hunter, W. N., Brown, T., Robinson, P. & Kennard, O. (1987). Inosine. adenine base-pairs in a B-DNA duplex. Nucl. Acids Res. 15, 7935–7949.Google Scholar

Crawford, J. L., Kolpak, E. J., Wang, A. H.-J., Quigley, G. J., Van Boom, J. H., Van Der Marel, G. & Rich, A. (1980). The tetramer d(CGCG) crystallises as a lefthanded double helix. Proc. natn. Acad. Set. U.S.A. 77, 4016–4020.Google Scholar

Cruse, W. B. T., Salisbury, S. A., Brown, T., Eckstein, F., Cosstick, R. & Kennard, O. (1986). Chiral phosphorothioate analogues of B-DNA: The crystal structure of Rp-d(GpSCGpSCGpSC). J. molec. Biol. 192, 891–905.Google Scholar

Cruse, W. B. T., Aymami, J., Kennard, O., Brown, T., Jack, A. G. C. & Leonard, G. A. (1989). Refined crystal structure of an octanucleotide duplex with I.T mismatched base pairs. Nucl. Acids Res. 17, 55–72.Google Scholar

Dickerson, R. E. (1983). Base sequence and helix structure variations in B and A-DNA. J. molec. Biol. 166, 419–441.CrossRefGoogle Scholar

Dickerson, R. E. & Drew, H. R. (1981). Structure of a B-DNA dodecamer: influence of base sequence on helix structure. J. molec. Biol. 149, 761–786.Google Scholar

Dickerson, R. E. et al. (1989). Definitions and nomenclature of nucleic acid structure parameters. EMBO. J. 8, 1–4.Google Scholar

Di Gabriele, A. D., Sanderson, M. R. & Steitz, T. A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natn. Acad. Sci. U.S.A. 86, 1816–1820.CrossRefGoogle ScholarPubMed

Dock-Bregeon, A. C., Chevrier, B., Podjarny, A., Moras, D., Debear, J. S., Gough, G. R., Gilham, P. T. & Johnson, J. E. (1988). High resolution structure of the RNA duplex [U(U-A)6A]2. Nature 335, 375–378.CrossRefGoogle Scholar

Doucet, J., Benoit, J.-P., Cruse, W. B. T., Prange, T. & Kennard, O. (1989). Coexistence of A- and B-form DNA in a single crystal lattice. Nature 337, 190–192.Google Scholar

Drew, H. R. & Dickerson, R. E. (1981 a). Structure of a B-DNA dodecamer: geometry of hydration. J. molec. Biol. 151, 535–556.Google Scholar

Drew, H. R. & Dickerson, R. E. (1981 b). Conformation and dynamics in a Z-DNA tetramer. J. molec. Biol. 152, 723–736.Google Scholar

Drew, H. R. & Travers, A. A. (1984). DNA structural variations in the tyrT promoter. Cell 37, 491–502.Google Scholar

Drew, H. R., Dickerson, R. E. & Itakura, K. (1978). A salt-induced conformational change in crystals of the synthetic DNA tetramer d(CGCG). J. molec. Biol. 125,535–543.Google Scholar

Drew, H. R., Takano, T., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). High salt d(CGCG): A left-handed Z-DNA double helix. Nature 286, 567–573.CrossRefGoogle Scholar

Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer; conformation and dynamics. Proc. natn. Acad. Sci. U.S.A. 78, 2179–2183.Google Scholar

Drew, H. R., Samson, S. & Dickerson, R. E. (1982). Structure of a B-DNA dodecamer at 16 K. Proc. natn. Acad. Set. U.S.A. 79, 4040–4044.Google Scholar

Drew, H. R., McCall, M. J. & Calladine, C. R. (1988). Recent studies of DNA in the crystal. A. Rev. Cell. Biol. 4, 1–20.Google Scholar

Eisenstein, M., Hope, H., Haran, T. E., Frolow, P., Sharked, Z. & Rabinovich, D. (1988). Low-temperature study of the A-DNA fragment d(GGGCGCCC). Acta crystallogr. B 44, 625–628.Google Scholar

Fairall, L., Martin, S. & Rhodes, D. (1989). The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure. EMBO. J. 8, 1809–1817.Google Scholar

Fazakerley, G. V., Quignard, E., Woisard, A., Guschlbauer, W., Van Der Marel, G. A., Van Boom, J. H., Jones, M. & Radman, M. (1986). Structures of mismatched base pairs in DNA and their recognition by the E. coli mismatch repair system. EMBO.J. 5, 3697–3703.Google Scholar

Fersht, A. R., Knill-Jones, J. W. & Tsui, W. C. (1982). Kinetic basis of spontaneous frequencies, proofreading specificities and cost of proofreading by DNA polymerases of E. coli. J. molec. Biol. 156, 37–51.Google Scholar

Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. (1982). Reversible bending in a B-DNA dodecamer: CGCGAATTBrCGCG. J. biol. Chem. 257, 14686–14707.Google Scholar

Frederick, C. A., Saal, D., Van Der Marel, G. A., Van Boom, J. H., Wang, A. H.-J. & Rich, A. (1987). The crystal structure of d(GGmCCGGCC): the effect of methylation on A-DNA structure and stability. Biopolymers 26, 145–160.Google Scholar

Frederick, C. A., Quigley, G. J., Van Der Marel, G. A., Van Boom, J. H., Wang, A. H.-J. & Rich, A. (1988). Methylation of the Ecorl recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 20 Å resolution. J. biol. Chem. 263, 17872–17879.Google Scholar

Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., Van Der Marel, G. A., Van Boom, J. H., Rich, A. & Wang, A. H.-J. (1989). Molecular structure of an A-DNA decamer d(ACCGGCCGGT). Eur. J. Biochem. 181, 295–307.CrossRefGoogle ScholarPubMed

Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R. & Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. natn. Acad. Sci. U.S.A. 85, 8924–8928.CrossRefGoogle ScholarPubMed

Fujii, S., Wang, A. H.-J., Van Der Marel, G., Van Boom, J. H. & Rich, A. (1982). Molecular structure of (msdC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilising Z-DNA. Nucl. Acids Res. 10, 7879–7892.CrossRefGoogle Scholar

Fujii, S., Wang, A. H.-J., Van Der Marel, G., Van Boom, J. H. & Rich, A. (1985). The octamers d(CGCGCGCG) and d(CGCATGCG) both crystallise as Z-DNA in the same hexagonal lattice. Biopolymers 24, 243–250.CrossRefGoogle Scholar

Gait, M. J., Matthes, H. W. D., Singh, M., Sproat, B. S. & Titmus, R. C. (1982). Rapid synthesis of oligodeoxyribonucleotides VII. Solid phase synthesis by a continuous flow phosphotriester method on a kieselguhr-polyamide support. Nucl. Acids Res. 10, 6243–6248.Google Scholar

Gao, X. & Patel, D. (1988). G(syn).A(anti) mismatch formation in DNA dodecamers at acidic pH:pH dependent conformational transition of G.A mispairs detected by proton NMR. J. Am. chem. Soc. 110, 5178–5182.CrossRefGoogle Scholar

Gottesfeld, J. M., Blanco, J. & Tennant, L. L. (1987). The 5S internal control region is B-form both free in solution and in a complex with TFIIIA. Nature 329, 460–462.Google Scholar

Hamlin, R. (1985). Multiwire area X-ray diffractometers. In Methods in Enzymology, vol. 114 (ed. Wyckoff, H., Hirs, C. H. W. and Timasheff, S. N.), pp. 416–452. New York: Academic Press.Google Scholar

Haran, T. E., Shakked, Z., Wang, A. H.-J. & Rich, A. (1987). The crystal structure of d(CCCCGGGG): a new A-form variant with an extended backbone conformation. J. Biomolec. Struct. Dynam. 5, 199–217.Google Scholar

Heinemann, U., Lauble, H., Frank, R. & Blocker, H. (1987). Crystal structure analysis of an A-DNA fragment at 18 Å resolution: d(GCCCGGGC). Nucl. Acids Res. 15, 9531–9550.Google Scholar

Hendrickson, W., Smith, J. L. & Sheriff, S. (1985). Direct phase determination based on anomalous scattering. In Methods in Enzymology, vol. 115 (ed. Wyckoff, H., Hirs, C. H. W. and Timasheff, S. N.), pp. 41–55. New York: Academic Press.Google Scholar

Ho, P. S., Frederick, C. A., Quigley, G., Van Der Marel, G. A., Van Boom, J. H., Wang, A. H.-J. & Rich, A. (1985). G.T wobble pairing in Z-DNA at 10 Å atomic resolution; the crystal structure of d(CGCGTG). EMBO. J. 4, 3617–3623.Google Scholar

Holbrook, S. R. & Kim, S.-H. (1985). Crystallisation and heavy atom derivatives of polynucleotides. In Methods in Enzymology, vol. 114 (ed. Wyckoff, H., Hirs, C. H. W. and Timasheff, S. N.), pp. 167–175. New York: Academic Press.Google Scholar

Hoogsteen, K. (1963). The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr. 16,907–916.Google Scholar

Hoppe, H. (1988). Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr. B 44, 22–26.Google Scholar

Hunter, W. N., Brown, T., Anand, N. N. & Kennard, O. (1986 a). Structure of an adenine-cytosine base pair in DNA and it's implications for mismatch repair. Nature 320, 552–555.CrossRefGoogle Scholar

Hunter, W. N., Brown, T. & Kennard, O. (1986 b). Structural features and hydration of d(CGCGAATTAGCG): a double helix containing two G. A mispairs. J. Biomol. Struct. Dynam. 4, 173–191.Google Scholar

Hunter, W. N., Kneale, G., Brown, T., Rabinovich, D. & Kennard, O. (1986 b). Refined crystal structure of an octanucleotide duplex with G.T mismatched base pairs. J. molec. Biol. 190, 605–618.Google Scholar

Hunter, W. N., Brown, T. & Kennard, O. (1987 a). Structural features and hydration of d(CGCAAATTCGCG): a double helix containing two C. A mispairs. Nucl. Acids Res. 15, 6589–6606.Google Scholar

Hunter, W. N., Brown, T., Kneale, G., Anand, N. N., Rabinovich, D. & Kennard, O. (1987 b). The structure of guanine.thymine mismatches in B-DNA at 2·5 Å revolution. J. biol. Chem. 262, 9962–9970.Google Scholar

Hunter, W. N., Langlois D'Estaintot, B. & Kennard, O. (1989). Structural variation in d(CTCTAGAG): implications for protein-nucleic acid interactions. Biochemistry 28, 2444–2451.CrossRefGoogle Scholar

Iupac-Iub Joint Commission on Biochemical Nomenclature (1983). Abbreviations and symbols for the description of conformations of polynucleotide chains. Eur. J. Biochem. 131, 9–15.Google Scholar

Jain, S., Zon, G. & Sundaralingam, M. (1987). The potentially Z-DNA forming sequence d(GTGTACAC) crystallises as A-DNA. J. molec. Biol. 197, 141–145.Google Scholar

Jain, S., Zon, G. & Sundaralingam, M. (1989). Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC). Biochemistry 28, 2360–2364.CrossRefGoogle ScholarPubMed

Jordan, S. R. & Pabo, C. O. (1988). Structure of the lambda complex at 2·5 Å resolution: details of the repressor-operator interactions. Science 242, 4917–4921.Google Scholar

Joshua-Tor, L., Rabinovich, D., Hoppe, H.Frolow, F.Appella, E. & Sussman, J. L. (1988). The three-dimensional structure of a DNA duplex containing loopedout bases. Nature 334, 82–84.Google Scholar

Jovin, T. M., Soumpasis, D. M. & McIntosh, L. P. (1987). The transition between BDNA and Z-DNA. A. Rev. phys. Chem. 38, 521–560.CrossRefGoogle Scholar

Kan, L.-S., Chandrasegaran, S., Pulford, S. M. & Miller, P. S. (1983). Detection of a guanine adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc. natn. Acad. Set. U.S.A. 80, 4263–4265.Google Scholar

Kennard, O. (1985). Structural studies of DNA fragments: The G.T wobble base pair in A, B and Z-DNA. The G.A base pair in B-DNA. J. Biomol. Struct. Dynam. 3, 205–226.Google Scholar

Kennard, O. (1987). The molecular structure of base-pair mismatches. In Nucleic acidsand Molecular Biology, vol. 1 (ed. Lilley, D., and Eckstein, E.), pp. 25–52. Berlin: Springer-Verlag.Google Scholar

Kennard, O. & Hunter, W. N. (1989). Crystal structures of oligonucleotides. In Landolt-Bornstein Tables, Group VII, vol. 1, pp. 255–360. Berlin: Springer-Verlag.Google Scholar

Kennard, O., Cruse, W. B. T., Nachman, J., Prange, T., Shakked, Z. & Rabinovich, D. (1986). Ordered water structure in an A-DNA octamer at 1·7 Å resolution. J. Biomol. Struct. Dynam. 3, 623–647.CrossRefGoogle Scholar

Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z. & Steitz, T. A. (1979). A hypothesis on a specific sequence dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. molec. Biol. 131, 669–680.CrossRefGoogle Scholar

Kneale, G., Brown, T., Kennard, O. & Rabinovich, D. (1985). G.T. base pairs in a DNA helix: The crystal structure of d(GGGGTCCC). J. molec. Biol. 186, 805–814.Google Scholar

Kopka, M. L., Fratini, A. V., Drew, H. R. & Dickerson, R. E. (1983). Ordered water structure around a B-DNA dodecamer. J. molec. Biol. 163, 129–146.Google Scholar

Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. (1985 a). The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. natn. Acad. Sci. U.S.A. 82, 1376–1380.Google Scholar

Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. (1985 b). Binding of an anti-tumor drug to DNA: Netropsin and CGCGAATTBrCGCG. J. molec. Biol. 183, 553–563.Google Scholar

Lauble, H., Frank, R., Blocker, H. & Heinemann, U. (1988). Three-dimensional structure of d(GGGATCCC) in the crystalline state. Nucl. Acids Res. 16, 7799–7816.Google Scholar

Lerman, L. S. (1961). Structural considerations in the interaction of DNA and acridines. J. molec. Biol. 3, 18–30.CrossRefGoogle ScholarPubMed

McBride, L. J. & Caruthers, M. H. (1983). An investigation of several deoxynucleoside phosphoramidites useful for synthesising deoxyoligonucleotides. Tetrahedron Letts. 24, 245–248.Google Scholar

McCall, M., Brown, T. & Kennard, O. (1985). The crystal structure of d(GGGGCCC) – A model for poly(dG).poly(dC). J. molec. Biol. 183, 385–396.CrossRefGoogle Scholar

McCall, M., Brown, T., Hunter, W. N. & Kennard, O. (1986). The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA. Nature 322, 661–664.Google Scholar

McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grable, J. & Rosenberg, J. M. (1986). Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution. Science 234, 1526–1541.Google Scholar

McPherson, A. (1982). Preparation and Analysis of Protein Crystals. San Francisco: John Wiley and Sons.Google Scholar

McPherson, A., Brayer, G. D. & Morrison, R. D. (1986). Crystal structure of Rnase A complexed with d(pA)4. J. molec. Biol. 189, 305–327.CrossRefGoogle ScholarPubMed

Miller, M., Harrison, R. W., Wlodawer, A., Appella, E. & Sussman, J. L. (1988). Crystal structure of 15-mer DNA duplex containing unpaired bases. Nature 334, 85–86.Google Scholar

Moore, M. H., Hunter, W. N., Langlois D'Estaintot, B. & Kennard, O. (1989). Drug-DNA interactions in the crystal structure of d(CGATCG) complexed with daunomycin. J. molec. Biol. 206, 693–705.Google Scholar

Neidle, S., Pearl, L. & Skelly, J. V. (1987). DNA structure and perturbation by drug binding. Biochem. J. 243, 1–13.Google Scholar

Nelson, H. C. M., Finch, J. T., Luisi, B. E. & Klug, A. (1987). The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature 330, 221–226.Google Scholar

Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. O., Luisi, B. F. & Sigler, P. B. (1988). Crystal structure of trp repressor/operator complex at atomic resolution. Nature 355, 321–329.Google Scholar

Patel, D. J., Shapiro, L. & Hare, D. (1987). Conformation of DNA base pair mismatches in solution. In Nucleic Acids and Molecular Biology (ed. Eckstein, F. and Lilley, D. M. J.), pp. 70–84. Berlin: Springer-Verlag.Google Scholar

Pjura, P. E., Grzeskowiak, K. & Dickerson, R. E. (1987). Binding of Hoechst 33258 to the minor groove of B-DNA. J. molec. Biol. 197, 257–271.Google Scholar

Prive, G. G., Heinemann, U., Chandrasegaran, S., Kan, L. S.Kopka, M. L. & Dickerson, R. E. (1987). Helix geometry, hydration and G. A mismatch in a B-DNA decamer. Science 238, 498–504.Google Scholar

Prive, G. G., Heinemann, U., Chandrasegaran, S., Kan, L. S., Kopka, M. L. & Dickerson, R. E. (1988). A mismatch decamer as a model for general-sequence BDNA. In Structure and Expression, vol. 2 (ed. Sarma, R. H. and Sarma, M. H.), pp. 27–47. Schenectady: Adenine Press.Google Scholar

Quigley, G. J., Wang, A. H.-J., Ughetto, G., Van Der Marel, G., Van Boom, J. H. & Rich, A. (1980). Molecular structure of an anticancer drug-DNA complex: Daunomycin plus d(CGTACG). Proc. natn. Acad. Sci. U.S.A. 77, 7204–7208.Google Scholar

Quigley, G. J., Ughetto, G., Van Der Marel, G., Van Boom, J. H., Wang, A. H.-J. & Rich, A. (1986). Non-Watson-Crick G.C and A.T base pairs in a DNA-antibiotic complex. Science 232, 1255–1258.Google Scholar

Rabinovich, D., Haran, T. E., Eisenstein, M. & Shakked, Z. (1988). Structures of the mismatched duplex d(GGGTGCCC) and one of its Watson-Crick analogues d(GGGCGCCC) J. molec. Biol. 200, 151–161.Google Scholar

Rabinovich, D. & Shakked, Z. (1984). A new approach to structure determination of large molecules by multi-dimensional search methods. Ada Crystallogr A 40, 195–200.Google Scholar

Rosenberg, B., Van Camp, J., Trosko, J. E. & Mansour, V. H. (1969). Platinum compounds: a new class of potent antitumour agents. Nature 222, 385–386.CrossRefGoogle ScholarPubMed

Rich, A., Nordheim, A. & Wang, A. H.-J. (1984). The chemistry and biology of lefthanded Z-DNA. A. Rev. Biochem. 53, 791–846.Google Scholar

Richmond, T. J., Finch, J. T., Rushton, B., Rhodes, D. & Klug, A. (1984). Structure of the nucleosome core particle at 7 Å resolution. Nature 311, 532–537.Google Scholar

Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag.Google Scholar

Saenger, W. (1987). Structure and dynamics of water surrounding biomolecules. A. Rev. Biophys. biophys. Chem. 16, 93–114.Google Scholar

Saenger, W., Hunter, W. N. & Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385–388.Google Scholar

Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. molec. Biol. 191, 659–675.Google Scholar

Seeman, N. C., Rosenberg, J. M. & Rich, A. (1976). Sequence-specific recognition of double helical nucleic acids by proteins. Proc. natn. Acad. Sci. U.S.A. 73, 804–808.Google Scholar

Shakked, Z. & Kennard, O. (1984). The A form of DNA. In Biological Macromolecules and Assemblies, vol. 2. Nucleic Acids and Interactive Proteins (ed. McPherson, A. and Jurnak, F.), pp. 2–36. New York: Wiley and Sons.Google Scholar

Shakked, Z. & Rabinovich, D. (1986). The effect of the base sequence on the fine structure of the DNA double helix. Prog. Biophys. molec. Biol. 47, 159–195.Google Scholar

Shakked, Z., Rabinovich, D., Cruse, W. B. T., Egert, E., Kennard, O., Sala, G., Salisbury, S. A. & Viswamitra, M. A. (1981). Crystalline A-DNA: the X-ray analysis of the fragment d(GGTATACC). Proc. R. Soc. Land. B. 213, 479–487.Google Scholar

Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W. B. T., Salisbury, S. A. & Viswamitra, M. A. (1983). Sequence dependent conformation of an A-DNA double helix: the crystal structure of the octamer d(GGTATACC). J. molec. Biol. 166, 183–201.Google Scholar

Sherman, S. E., Gibson, D., Wang, A. H.-J. & Lippard, S. J. (1985). X-ray structure of the major adduct of the anticancer drug cisplatin with DNA: cis-[Pt(NH3)2-(pGpG)]. Science 230, 412–417.Google Scholar

Sherman, S. E., Gibson, D., Wang, A. H.-J. & Lippard, S. J. (1988). Crystal and molecular structure of cis-[Pt(NH3)2(pGpG)], the principal adduct formed by cisdiamminedichloroplatinum(II) with DNA. J. Am. Chem. Soc. 110, 7368–7381.Google Scholar

Suck, D., Lahm, A. & Oefner, C. (1988). Structure refined to 20 Å of a nicked DNA octanucleotide complex with DNAse I. Nature 332, 464–468.Google Scholar

Teng, M.-K., Usman, N., Frederick, C.A. & Wang, A. H.-J. (1988). The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucl. Acids Res. 16, 2671–2690.Google Scholar

Ughetto, G., Wang, A. H.-J., Quigley, G. J., Van Der Marel, G. A., Van Boom, J. H. & Rich, A. (1985). A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. Nucl. Acids Res. 13, 2305–2323.Google Scholar

Viswamitra, M. A., Kennard, O., Jones, P. G., Sheldrick, G. M., Salisbury, S. A., Favello, L. & Shakked, Z. (1978). Structure of the deoxytetranucleotide d(pATAT) and a sequence dependant model for poly(dA-dT). Nature 273, 687–688.CrossRefGoogle Scholar

Viswamitra, M. A., Shakked, Z., Jones, P. G., Sheldrick, G. M., Salisbury, S. A. & Kennard, O. (1982). Structure of the deoxytetranucleotide d-pATAT and a sequence-dependant model for poly(dA-dT). Biopolymers 21, 513–533.Google Scholar

Wang, A. H.-J., Quigley, G. J., Kolpak, R. J., Crawford, J. L., Van Boom, J. H., Van Der Marel, G. A. & Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680–686.Google Scholar

Wang, A. H.-J., Quigley, G. J., Kolpak, R. J., Van Der Marel, G. A., Boom, J. H. & Rich, A. (1981). Left handed double helical DNA: variations in the backbone conformation. Science 211, 171–176.Google Scholar

Wang, A. H.-J., Fujii, S., Van Boom, J. H. & Rich, A. (1982 a). Molecular structure of the octamer d(GGCCGGCC): Modified A-DNA. Proc. natn. Acad. Sci. U.S.A. 79,3968–3972.Google Scholar

Wang, A. H.-J., Fujii, S., Van Boom, J. H., Van Der Marel, G. A., Van Boeckel, S. A. A. & Rich, A. (1982 b). Molecular structure of r(GCG)d(TATACGC): A DNARNA hybrid helix joined to double helical DNA. Nature 299, 601–604.Google Scholar

Wang, A. H.-J., Hakoshima, T., Van Der Marel, G. A., Van Boom, J. H. & Rich, A. (1984 a). A.T base pairs are less stable than G.C base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell 37, 321–331.Google Scholar

Wang, A. H.-J., Ughetto, G., Quigley, G. J., Hakoshima, T., Van Der Marel, G. A., Van Boom, J. H. & Rich, A. (1984 b). The molecular structure of a DNA-triostin A complex. Science 225, 1115–1121.Google Scholar

Wang, A. H.-J., Gessner, R. V., Van Der Marel, G. A., Van Boom, J. H. & Rich, A. (1985). Crystal structure of a Z-DNA without an alternating purine-pyrimidine sequence. Proc. natn. Acad. Sci. U.S.A. 82, 3611–3615.Google Scholar

Wang, A. H.-J., Ughetto, G., Quigley, G. J. & Rich, A. (1986). Interactions of a quinoxaline antibiotic and DNA: The molecular structure of a triostin Ad(GCGTACGC) complex. J. Biomol. Struct. Dynam. 4, 319–342.Google Scholar

Wang, A. H.-J., Ughetto, G., Quigley, G. J. & Rich, A. (1987). The interaction between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CGTACG) at 1·2Å resolution. Biochemistry 26, 1152–1163.Google Scholar

Watson, J. D. & Crick, F. H. C. (1953). A structure for deoxyribose nucleic acid. Nature 171, 737–738.Google Scholar

Westhof, E. (1987). Water: an integral part of nucleic acid structure. A. Rev. Biophys. biophys. Chem. 17, 125–144.Google Scholar

Westhof, E. (1988). Hydration of oligonucleotides in crystals. Int. J. Biol. Macromol. 9, 185–192.Google Scholar

Westhof, E., Dumas, P. & Moras, D. (1985). Crystallographic refinement of yeast aspartic transfer RNA. J. molec. Biol. 184, 119–145.Google Scholar

Westhof, E., Hosur, M. V. & Sundaralingam, M. (1988). Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrCG5BrCG) and proflavin. Biochemistry 27, 5742–5747.Google Scholar

Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature 287 755–758.CrossRefGoogle ScholarPubMed

Wing, R. M., Pjura, P., Drew, H. R. & Dickerson, R. E. (1984). The primary mode of binding of cisplatin to a B-DNA dodecamer: CGCGAATTCGCG. EMBO J. 3, 1201–1206.Google Scholar

Wolberger, C., Dong, Y., Ptashne, M. & Harrison, S. C. (1988). Structure of a phage 434 cro/DNA complex. Nature 335, 789–795.Google Scholar

Woodbury, C. P. & Von Hippel, P. H. (1981). Relaxed sequence specificities of EcoRI endonuclease and methylase: mechanisms, possible practical applications and uses in defining protein-nucleic acid recognition mechanisms. Gene Amplification and Analysis 1, 181–207.Google Scholar

Yoon, C., Prive, G. G., Goodsell, D. S. & Dickerson, R. E. (1988). Structure of an alternating B-DNA helix and its relationship to A-tract DNA. Proc. natn. Acad. Sci. U.S.A. 85, 6332–6336.Google Scholar