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DNA—Ligand Interactions pp 63–83Cite as

Unusual DNA Structures and Gene Regulation

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Part of the book series: NATO ASI Series ((volume 137))

Abstract

Left-handed Z-DNA, cruciforms, purine·pyrimidine (pur·pyr) sequences, and bent DNA have been studied with supercoiled recombinant plasmids, restriction fragments, and DNA polymers. Different types of sequences of cellular and viral origin as well as synthetic polymers and plasmid inserts have been investigated.

Left-handed Z-DNA is stabilized by negative supercoiling for a variety of suitable sequences. Strictly alternating purine-pyrimidine sequences are neither necessary nor sufficient for Z-DNA formation. The junctions between right-handed B and left-handed Z helices contain few, if any, nonpaired bases. Consecutive AT pairs can adopt left-handed Z conformations.

DNA cruciforms are stabilized by negative supercoiling at inverted repeat sequences. The influence of salts, temperature, and stem length indicates a sensitive interrelationship between these factors for cruciform stability.

Segments of recombinant plasmids containing pur·pyr sequences adopt unusual helical conformations under the influence of negative supercoiling. This feature is recognized and specifically cleaved by Sl nuclease. The major late promoter of adenovirus exhibits this property at the TATA box. A variety of other studies led to the conclusion that the B-helix deformation was not due to a previously recognized DNA conformation. Furthermore, the direct repeat sequences at the cleavage-packaging signal of herpes simplex virus type 1 adopts a novel DNA structure under the influence of negative supercoiling. The properties of this direct repeat have been previously unrecognized with any other system. This DNA (anisomorphic DNA) has different conformations in the complementary strands, which give rise to an aberrant DNA structure in the center of the direct repeat sequences.

Bent DNA occurs in fragments of kinetoplast DNA from Crithidia as well as other trypanosomes. Most fragments contain numerous runs of 4 to 6 A’s which are spaced with a periodicity of 1 per helical repeat.

The chemical and biological properties of these unusual DNA conformations are described.

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References

  1. R.D. Wells, T.C. Goodman, W. Hillen, G.T. Horn, R.D. Klein, J.E. Larson, U.R. Muller, S.K. Neuendorf, N. Panayotatos, and S.M. Stirdivant, Prog. Nucleic Acids Res. Mol. Biol. 24, 167–267 (1980).

    Article  CAS  Google Scholar 

  2. S.B. Zimmerman, Ann. Rev. Biochem. 51, 395–427 (1982).

    Article  PubMed  CAS  Google Scholar 

  3. R.E. Dickerson, H.R. Drew, B.N. Connor, R.M. Wing, A.V. Fratini, and M.L. Kopka, Science 216, 475–478 (1982).

    Article  PubMed  CAS  Google Scholar 

  4. C.K. Singleton in: Cell Proliferation: Recent Advances (Leffert, H.L. and Boynton, A.L., eds., 1984), Academic Press, New York.

    Google Scholar 

  5. A.H.-J. Wang, G.J. Quigley, F.J. Kolpak, J.L. Crawford, J.H. van Boom, G. van der Marel, and A. Rich, Nature 282, 680–686 (1979).

    Article  PubMed  CAS  Google Scholar 

  6. H.R. Drew, T. Takano, K. Itakura, and R.E. Dickerson, Nature 286, 567–573 (1980).

    Article  PubMed  CAS  Google Scholar 

  7. A. Rich, A. Nordheim, and A.H.-J. Wang, Ann. Rev. Biochem. 53, 791–846 (1984).

    Article  PubMed  CAS  Google Scholar 

  8. R.D. Wells, B.F. Erlanger, H.B. Gray, L.H. Hanau, T.M. Jovin, M.W. Kilpatrick, J. Klysik, J.E. Larson, J.C. Martin, J.J. Miglietta, C.K. Singleton, S.M. Stirdivant, C.M. Veneziale, R.M. Wartell, C.F. Wei, W. Zacharias, and D. Zarling, Gene Expression, UCLA Symp. Mol. Cell. Biol. 8, 3–18 (1983).

    CAS  Google Scholar 

  9. C.K. Singleton, J. Klysik, S.M. Stirdivant, and R.D. Wells’, Nature 299, 312–316 (1982).

    Article  PubMed  CAS  Google Scholar 

  10. L.J. Peck, A. Nordheim. A. Rich, and J.C Wang, Proc. Natl. Acad. Sci. USA 79, 4560–4564 (1982).

    Article  PubMed  CAS  Google Scholar 

  11. M.J. Ellison, R.J. Kelleher, III, A.H.-J. Wang, J.F. Habener, and A. Rich, Proc. Natl. Acad. Sci. USA 82, 8320–8324 (1985).

    Article  PubMed  CAS  Google Scholar 

  12. M. McLean, J.A. Blaho, M.W. Kilpatrick, and R.D. Wells, Proc. Natl. A Acad. Sci. USA 83, 5884–5888 (1986).

    Article  CAS  Google Scholar 

  13. C.K. Singleton, J. Klysik, and R.D. Wells, Proc. Natl. Acad. Sci. USA 80, 2447–2451 (1983).

    Article  PubMed  CAS  Google Scholar 

  14. C.K. Singleton, M.W. Kilpatrick, and R.D. Wells, J. Biol. Chem. 259, 1963–1967 (1984).

    PubMed  CAS  Google Scholar 

  15. M.W. Kilpatrick, J. Klysik, C.K. Singleton, D. Zarling, T.M. Jovin, L.H. Hanau, B.F. Erlanger, and R.D. Wells, J. Biol. Chem. 259, 7268–7274 (1984).

    PubMed  CAS  Google Scholar 

  16. H. Haraada, M.G. Petrino, T. Kakunaga, and A. Novel, Proc. Natl. Acad. Sci. USA 79, 6465 (1982).

    Article  Google Scholar 

  17. R. Thomas, S. Beck, and F.M. Pohl, Proc. Natl. Acad. Sci. USA 80, 5550–5553 (1983).

    Article  Google Scholar 

  18. E.M. Lafer, R.P.C. Valle, A. Moller, A. Nordheim, P.H. Schur, A. Rich, and B.D. Stollar, J. Clin. Invest. 71, 314–321 (1983).

    Article  PubMed  CAS  Google Scholar 

  19. H.R. Bergen, III, M.J. Losman, T.R. O’Connor, W. Zacharias, J.E. Larson, R.D. Wells, and W.J. Koopman, J. Immun., submitted 1986.

    Google Scholar 

  20. B.H. Johnston and A. Rich, Cell 42, 713–724 (1986).

    Article  Google Scholar 

  21. G. Galazka, E. Palacek, R.D. Wells, and J. Klysik, J. Biol. Chem. in press, 1986.

    Google Scholar 

  22. T.E. Hayes and J.E. Dixon, J. Biol. Chem. 260, 8145–8156 (1985).

    PubMed  CAS  Google Scholar 

  23. T.R. O’Connor, D.S. Kang, and R.D. Wells, J. Biol. Chem., in the press 1986.

    Google Scholar 

  24. D.S. Kang and R.D. Wells, J. Biol. Chem. 260, 7783–7790 (1985).

    PubMed  CAS  Google Scholar 

  25. F. Azorin, A. Nordheim, and A. Rich, EMBO J. 2, 649–655 (1983).

    PubMed  CAS  Google Scholar 

  26. L.J. Peck and J.C. Wang, Proc. Natl. Acad. Sci. USA 80, 6206–6210 (1983).

    Article  PubMed  CAS  Google Scholar 

  27. E. Schon, T. Evans, J. Welsh, and A. Efstratiadis, A, Cell 35, 837–848 (1983).

    Article  CAS  Google Scholar 

  28. D.E. Pulleyblank, D.B. Haniford, and A.R. Morgan, Cell 42, 271–280 (1985).

    Article  PubMed  CAS  Google Scholar 

  29. C.R. Cantor and A. Efstratiadis, Nucleic Acids Res. 21, 8059–8072 (1984).

    Article  Google Scholar 

  30. M.W. Kilpatrick, C.-F. Wei, H.B. Gray, and R.D. Wells, Nucleic Acids Res. 11, 3811–3818 (1983).

    Article  PubMed  CAS  Google Scholar 

  31. D.B. Haniford and D.E. Pulleyblank, Nucleic Acids Res. 13, 4343–4363 (1985).

    Article  PubMed  CAS  Google Scholar 

  32. M. Behe and G. Felsenfeld, Proc. Natl. Acad. Sci. USA 78, 1619–1623 (1981).

    Article  PubMed  CAS  Google Scholar 

  33. J. Feigon, A.H.-J. Wang, G.A. van der Marel, J.H. van Boom, and A. Rich, Nucleic Acids Res. 12, 1243–1263 (1984).

    Article  PubMed  CAS  Google Scholar 

  34. J. Klysik, S.M. Stirdivant, C.K. Singleton, W. Zacharias, and R.D. Wells, J. Mol. Biol. 168, 51–71 (1983).

    Article  PubMed  CAS  Google Scholar 

  35. L. Vardimon and A. Rich, Proc. Natl. Acad. Sci. USA 81, 3268–3272 (1984).

    Article  PubMed  CAS  Google Scholar 

  36. W. Zacharias, J.E. Larson, M.W. Kilpatrick and R.D. Wells, Nucleic Acids Res. 12, 7677–7692 (1984).

    Article  PubMed  CAS  Google Scholar 

  37. F. Azorin, R. Hahn, and A. Rich, Proc. Natl. Acad. Sci. USA 81, 3268–3272 (1984).

    Article  Google Scholar 

  38. R.M. Wartell, J. Klysik, W. Hillen, and R.D. Wells, Proc. Natl. Acad. Sci. USA 79, 2549–2553 (1982).

    Article  PubMed  CAS  Google Scholar 

  39. J. Feigon, A.H.-J. Wang, G.A. van der Marel, J.H. van Boom, and A. Rich, Science 230, 82–84 (1985).

    Article  PubMed  CAS  Google Scholar 

  40. M.J. Ellison, J. Feigon, R.J. Kelleher III, A. H.-J. Wang, J.F. Habener, and A. Rich, Biochem 25, 3648–3655 (1986).

    Article  CAS  Google Scholar 

  41. T.R. O’Connor, D.S. Kang, and R.D. Wells, J. Biol. Chem., in the press (1986).

    Google Scholar 

  42. R.D. Wells, T.C. Goodman, W. Hillen, G.T. Horn, R. D. Klein, J. E. Larson, U.R. Muller, S.K. Neuendorf, N. Panayotatos, and S.M. Stirdivant, Prog. Nucleic Acids Res. Mol. Biol. 24, 167–267 (1980).

    Article  CAS  Google Scholar 

  43. R.D. Wells, R.W. Blakesley, J.F. Burd, H.W. Chan, J.B. Dodgson, S.C. Hardies, G.T. Horn, K.F. Jensen, J. Larson, I.F. Nés, E. Seising, and R.M. Wartell. Critical Reviews in Biochemistry 4, 305–340 (1977).

    Article  PubMed  CAS  Google Scholar 

  44. R.D. Wells, J.E. Larson, R.C. Grant, B.E. Shortle, and Cantor, C.R., J. Mol. Biol. 54, 465-497.

    Google Scholar 

  45. H.A.F. Mace, H.R.B. Pelham, and A.A. Travers, Nature 304, 555–557 (1983).

    Article  PubMed  CAS  Google Scholar 

  46. C. McKeon, A. Schmidt, and B. de Crombrugghe, J. Biol. Chem. 259, 6636–6640 (1984).

    PubMed  CAS  Google Scholar 

  47. C-K.J. Shen, Nuc. Acids Res. 11, 7899–7911 (1983).

    Article  CAS  Google Scholar 

  48. G.C. Glikin, G. Garguils, L. Rena-Descalzi, and A. Worcel, Nature 303, 770–774 (1983).

    Article  PubMed  CAS  Google Scholar 

  49. D. Dybvig, D.D. Clark, G. Aliperti, and M.J. Schlesinger, Nucl. Acids Res. 11, 8495-8505.

    Google Scholar 

  50. S.B. Selleck, S.C.R. Elgin, and I.L. Cartwright, J. Mol. Biol. 178, 17–33 (1984).

    Article  PubMed  CAS  Google Scholar 

  51. J.M. Nickol and G. Felsenfeld, Cell 35, 467–477 (1983).

    Article  PubMed  CAS  Google Scholar 

  52. E. Schon, T. Evans, J. Welsh, and A. Efstratiadis, Cell 35, 838–848 (1983).

    Article  Google Scholar 

  53. H. Htun, E. Lund, and J.E. Dahlberg, Proc. Natl. Acad. Sci, USA 81, 7288–7292 (1984).

    Article  PubMed  CAS  Google Scholar 

  54. A. J. Nahmias. in: Viruses, Evolution and Cancer (E. Kurstak and K. Maramorosch, eds.) 605–634, Academic Press, New York (1980).

    Google Scholar 

  55. P.G. Spear and B. Roizman in: DNA Tumor Viruses (J. Tooze, ed.) 615-746, Cold Spring Harbor (1980).

    Google Scholar 

  56. S. Wadsworth, R.J. Jacob, and B. Roizman, J. Virol. 15, 1487–1497 (1975).

    PubMed  CAS  Google Scholar 

  57. P. Sheldrick and N. Berthelot, Cold Spring Harbor Symp. Quant. Biol. 39, 667–678 (1975).

    Article  PubMed  Google Scholar 

  58. M.J. Wagner and W.C. Summers, J. Virol. 27, 374–387 (1978).

    PubMed  CAS  Google Scholar 

  59. B.J. Graham, H. Ludwig, D.L. Bronson, M. Benyesh-Melnick, and N. Biswal, Biochim, Biophys. Acta 259 13–23 (1972).

    Article  CAS  Google Scholar 

  60. A.J. Davison and N.M. Wilkie, J. Gen. Virol 55, 315–331 (1981).

    Article  PubMed  CAS  Google Scholar 

  61. E.S. Mocarski and B. Roizman, Proc. Natl. Acad. Sci. USA 78, 7047–7051 (1981).

    Article  PubMed  CAS  Google Scholar 

  62. R.W. Honess, J. Gen. Virol. 65, 2077–2107 (1984).

    Article  PubMed  CAS  Google Scholar 

  63. E.S. Mocarski and B. Roizman, Cell 31, 89–97 (1982).

    Article  PubMed  CAS  Google Scholar 

  64. F. Wohlrab, M.J. McLean, and R.D. Wells, submitted (1986).

    Google Scholar 

  65. M.W. Kilpatrick, A. Torri, D.S. Kang, J.A. Engler, and R.D. Wells, J. Biol. Chem. 261, 11350–11354 (1986).

    PubMed  CAS  Google Scholar 

  66. Y.-T. Yu and J.L. Manley, Cell 45, 743–751 (1986).

    Article  PubMed  CAS  Google Scholar 

  67. E. Seising, R.D. Wells, C.J. Alden, and S. Arnott, J. Biol. Chem., 254, 5555–5561 (1979).

    Google Scholar 

  68. J.C. Marini, S.D. Levene, D.M. Crothers, and P.T. Englund, Proc. Natl. Acad. Sci. USA 79, 7664–7668 (1982).

    Article  PubMed  CAS  Google Scholar 

  69. P.A. Kitchin, V.A. Klein, K.A. Ryan, K.L. Gann, C.A. Raush, D.S. Kang, R.D. Wells, and P.T. Englund, J. Biol. Chem. 261, 11302–11309 (1986).

    PubMed  CAS  Google Scholar 

  70. F. Wohlrab and R.D. Wells, Gene Amplification and Analysis, Vol. 5, in the press (1986).

    Google Scholar 

  71. T.R. O’Connor, M.W. Kilpatrick, J. Klysik, J.E. Larson, J.C. Martin, C.K. Singleton, S.M. Stirdivant, W. Zacharias, and R.D. Wells, J. of Biomole. Str. and Dyn., 1, 999–1009 (1983).

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA

    Robert D. Wells

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  1. Robert D. Wells
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Editors and Affiliations

  1. Service de Biochimie, Bat. 142, Département de Biologie, Centre d’Etudes Nucléaires de Saclay, F-91191, Gif-sur-Yvette Cedex, France

    Wilhelm Guschlbauer (Director) (Director)

  2. Institut für Kristallographie, Freie Universität, Takustrasse 6, D-1000, Berlin 33, German Federal Republic

    Wolfram Saenger (Codirector) (Codirector)

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© 1987 Plenum Press, New York

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Wells, R.D. (1987). Unusual DNA Structures and Gene Regulation. In: Guschlbauer, W., Saenger, W. (eds) DNA—Ligand Interactions. NATO ASI Series, vol 137. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-5383-6_4

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  • DOI: https://doi.org/10.1007/978-1-4684-5383-6_4

  • Publisher Name: Springer, Boston, MA

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