Abstract
STUDIES of the crystal structures of more than 30 synthetic DNA fragments have provided structural information about three basic forms of the double helix: A-, B- and Z-form DNA1–5. These studies have demonstrated that the DNA double helix adopts a highly variable structure which is related to its base sequence. The extent to which such observed structures are influenced by the crystalline environment can be found by studying the same molecule in different crystalline forms. We have recently crystallized one particular oligomer in various crystal forms. Here we report the results of structural analyses of the different crystal structures and demonstrate that the DNA double helix can adopt a range of conformations in the crystalline state depending on hydration, molecular packing and temperature. These results have implications on our understanding of the influence of the environment on DNA structure, and on the modes of DNA recognition by proteins.
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Shakked, Z. & Kennard, O. in Biological Macromolecules and Assemblies: Nucleic Acids and Interactive Proteins Vol. 2 (eds Jurnak, F. A. & McPherson, A.) 1–36. (Wiley, New York, 1985).
Dickerson, R. E., Kopka, K. L. & Pjura, P. in Biological Macromolecules and Assemblies: Nucleic Acids and Interactive Proteins Vol. 2 (eds Jurnak, F. A. & McPherson, A.) 38–126 (Wiley, New York, 1985).
Wang, A. H.J-. & Rich, A. in Biological Macromolecules and Assemblies: Nucleic Acids and Interactive Proteins Vol. 2 (eds Jurnak, F. A. & McPherson, A.) 128–170 (Wiley, New York, 1985).
Shakked, Z. & Rabinovich, D. Progr. Biophys. molec. Biol. 47, 159–195 (1986).
Haran, T. E. & Shakked, Z. J. molec. Struct. 179, 367–391 (1988).
Rabinovich, D., Haran, T. E., Eisenstein, M. & Shakked, Z. J. molec. Biol. 200, 151–161 (1988).
Eisenstein, M. et al. Acta crystallogr. B44, 625–628 (1988).
Shakked, Z. et al. Proc. R. Soc. B213, 479–487 (1981).
Haran, T. E., Shakked, Z., Wang, A., & Rich, A. J. biomolec. Struct. Dynam. 5, 199–217 (1987).
Wang, A. H.-J., Fujii, S., van Boom, J. H. & Rich, A. Proc. natn. Acad. Sci. U.S.A. 79, 3968–3972 (1982).
Haran, T. E. thesis, Feinberg Grad. Sch. Weizmann Inst. Sci. (1986).
Heinemann, U., Lauble, H., Frank, R. & Blocker, H. Nucleic Acids Res.
von Hippel, P. H. & Berg, O. G. Proc. natn. Acad. Sci. U.S.A. 83, 1608–1612 (1986).
Otwinowski, Z. et al. Nature 335, 321–329 (1988).
Beaucage, S. L. & Caruthers, M. H. Tetrahedron Lett. 2, 1859–1862 (1981).
Hope, H. Acta Crystallogr. B44, 22–26 (1988).
Rabinovich, D. & Shakked, Z. Acta crystallogr. A40, 195–200 (1984).
Hendrickson, W. A. & Konnert, J. H. in Biomolecular Structure, Conformation, Function and Evolution Vol. 1 (eds Srinivasan, R. Subramanian, E. & Yatindra, N.) 43–57 (Pergamon, Oxford, 1981).
Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. J. biol. Chem. 257, 14686–14707 (1982).
Dickerson, R. E. et al. EMBO J. 8, 1–4 (1989).
Jain, S. & Sundaralingam, M. J. J. biol. Chem. 264, 12780–12784 (1989).
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Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M. et al. The conformation of the DNA double helix in the crystal is dependent on its environment. Nature 342, 456–460 (1989). https://doi.org/10.1038/342456a0
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DOI: https://doi.org/10.1038/342456a0
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