Advertisement

Metal-Mediated Base Pairs in Nucleic Acids with Purine- and Pyrimidine-Derived Nucleosides

  • Dominik A. Megger
  • Nicole Megger
  • Jens MüllerEmail author
Chapter
Part of the Metal Ions in Life Sciences book series (MILS, volume 10)

Abstract

Metal-mediated base pairs are transition metal complexes formed from complementary nucleosides within nucleic acid double helices. Instead of relying on hydrogen bonds, they are stabilized by coordinative bonds. The nucleosides acting as ligands do not necessarily have to be artificial. In fact, several examples are known of naturally occurring nucleobases (e.g., thymine, cytosine) capable of forming stable metal-mediated base pairs that are highly selective towards certain metal ions. This chapter provides a comprehensive overview of metal-mediated base pairs formed from natural nucleosides or from closely related artificial nucleosides that are pyrimidine or purine derivatives. It addresses the different strategies that lead to the development of these base pairs. The article focuses on structural models for metal-mediated base pairs, their experimental characterization within a nucleic acid, and on their possible applications.

Keywords

cytosine deazaadenine M-DNA metal-mediated base pairs polymerase sensor thymine 

Notes

Acknowledgment

Financial support of our research by the Deutsche Forschungsgemeinschaft is gratefully acknowledged.

References

  1. 1.
    J. Müller, Metallomics 2010, 2, 318–327.CrossRefPubMedGoogle Scholar
  2. 2.
    G. L. Eichhorn, Y. A. Shin, J. Am. Chem. Soc. 1968, 90, 7323–7328.CrossRefPubMedGoogle Scholar
  3. 3.
    G. L. Eichhorn, J. J. Butzow, P. Clark, E. Tarien, Biopolymers 1967, 5, 283–296.CrossRefPubMedGoogle Scholar
  4. 4.
    R. M. Izatt, J. J. Christensen, J. H. Rytting, Chem. Rev. 1971, 71, 439–481.CrossRefPubMedGoogle Scholar
  5. 5.
    R. H. Jensen, N. Davidson, Biopolymers 1966, 4, 17–32.CrossRefGoogle Scholar
  6. 6.
    S. Katz, Nature 1962, 194, 569.CrossRefGoogle Scholar
  7. 7.
    J. Müller, Eur. J. Inorg. Chem. 2008, 3749–3763.Google Scholar
  8. 8.
    G. H. Clever, C. Kaul, T. Carell, Angew. Chem. Int. Ed. 2007, 46, 6226–6236.CrossRefGoogle Scholar
  9. 9.
    K. Tanaka, M. Shionoya, Coord. Chem. Rev. 2007, 251, 2732–2742.CrossRefGoogle Scholar
  10. 10.
    S. Atwell, E. Meggers, G. Spraggon, P. G. Schultz, J. Am. Chem. Soc. 2001, 123, 12364–12367.CrossRefPubMedGoogle Scholar
  11. 11.
    S. Johannsen, N. Megger, D. Böhme, R. K. O. Sigel, J. Müller, Nat. Chem. 2010, 2, 229–234.CrossRefPubMedGoogle Scholar
  12. 12.
    G. H. Clever, M. Shionoya, Chapter 10 of this book.Google Scholar
  13. 13.
    J. S. Lee, L. J. P. Latimer, R. S. Reid, Biochem. Cell Biol. 1993, 71, 162–168.CrossRefPubMedGoogle Scholar
  14. 14.
    P. Aich, S. L. Labiuk, L. W. Tari, L. J. T. Delbaere, W. J. Roesler, K. J. Falk, R. P. Steer, J. S. Lee, J. Mol. Biol. 1999, 294, 477–485.CrossRefPubMedGoogle Scholar
  15. 15.
    B. Lippert, Prog. Inorg. Chem. 2005, 54, 385–447.CrossRefGoogle Scholar
  16. 16.
    M. Fuentes-Cabrera, B. G. Sumpter, J. E. Šponer, J. Šponer, L. Petit, J. C. Wells, J. Phys. Chem. B 2007, 111, 870–879.CrossRefPubMedGoogle Scholar
  17. 17.
    S. S. Alexandre, J. M. Soler, L. Seijo, F. Zamora, Phys. Rev. B 2006, 73, 205112.CrossRefGoogle Scholar
  18. 18.
    E. C. Fusch, B. Lippert, J. Am. Chem. Soc. 1994, 116, 7204–7209.CrossRefGoogle Scholar
  19. 19.
    S. L. Labiuk, L. T. J. Delbaere, J. S. Lee, J. Biol. Inorg. Chem. 2003, 8, 715–720.CrossRefPubMedGoogle Scholar
  20. 20.
    A. Rakitin, P. Aich, C. Papadopoulos, Y. Kobzar, A. S. Vedeneev, J. S. Lee, J. M. Xu, Phys. Rev. Lett. 2001, 86, 3670–3673.CrossRefPubMedGoogle Scholar
  21. 21.
    C.-Z. Li, Y.-T. Long, H.-B. Kraatz, J. S. Lee, J. Phys. Chem. B 2003, 107, 2291–2296.CrossRefGoogle Scholar
  22. 22.
    M. J. Dinsmore, J. S. Lee, J. Electroanal. Chem. 2008, 617, 71–77.CrossRefGoogle Scholar
  23. 23.
    X. Li, Y. Zhou, T. C. Sutherland, B. Baker, J. S. Lee, H.-B. Kraatz, Anal. Chem. 2005, 77, 5766–5769.CrossRefPubMedGoogle Scholar
  24. 24.
    S. D. Wettig, D. O. Wood, P. Aich, J. S. Lee, J. Inorg. Biochem. 2005, 99, 2093–2101.CrossRefPubMedGoogle Scholar
  25. 25.
    K. Mizoguchi, S. Tanaka, T. Ogawa, N. Shiobara, H. Sakamoto, Phys. Rev. B 2005, 72, 0033106.CrossRefGoogle Scholar
  26. 26.
    F. Moreno-Herrero, P. Herrero, F. Moreno, J. Colchero, C. Gómez-Navarro, J. Gómez-Herrero, A. M. Baró, Nanotechnology 2003, 14, 128–133.CrossRefGoogle Scholar
  27. 27.
    B. Liu, A. J. Bard, C.-Z. Li, H.-B. Kraatz, J. Phys. Chem. B 2005, 109, 5193–5198.CrossRefPubMedGoogle Scholar
  28. 28.
    B. Q. Spring, R. M. Clegg, J. Phys. Chem. B 2007, 111, 10040–10052.CrossRefPubMedGoogle Scholar
  29. 29.
    G. H. Clever, M. Shionoya, Coord. Chem. Rev. 2010, 254, 2391–2402.CrossRefGoogle Scholar
  30. 30.
    S. Katz, J. Am. Chem. Soc. 1952, 74, 2238–2245.CrossRefGoogle Scholar
  31. 31.
    C. A. Thomas, J. Am. Chem. Soc. 1954, 76, 6032–6034.CrossRefGoogle Scholar
  32. 32.
    S. Katz, Biochim. Biophys. Acta 1963, 68, 240–253.CrossRefPubMedGoogle Scholar
  33. 33.
    L. D. Kosturko, C. Folzer, R. F. Stewart, Biochemistry 1974, 13, 3949–3952.CrossRefPubMedGoogle Scholar
  34. 34.
    Z. Kuklenyik, L. G. Marzilli, Inorg. Chem. 1996, 35, 5654–5662.CrossRefPubMedGoogle Scholar
  35. 35.
    Y. Miyake, H. Togashi, M. Tashiro, H. Yamaguchi, S. Oda, M. Kudo, Y. Tanaka, Y. Kondo, R. Sawa, T. Fujimoto, T. Machinami, A. Ono, J. Am. Chem. Soc. 2006, 128, 2172–2173.CrossRefPubMedGoogle Scholar
  36. 36.
    H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010, 16, 13218–13225.CrossRefPubMedGoogle Scholar
  37. 37.
    Y. Tanaka, S. Oda, H. Yamaguchi, Y. Kondo, C. Kojima, A. Ono, J. Am. Chem. Soc. 2007, 129, 244–245.CrossRefPubMedGoogle Scholar
  38. 38.
    A. Ono, H. Togashi, Angew. Chem. Int. Ed. 2004, 43, 4300–4302.CrossRefGoogle Scholar
  39. 39.
    R.-M. Kong, X.-B. Zhang, L.-L. Zhang, X.-Y. Jin, S.-Y. Huan, G.-L. Shen, R.-Q. Yu, Chem. Commun. 2009, 5633–5635.Google Scholar
  40. 40.
    C.-X. Tang, Y. Zhao, X.-W. He, X.-B. Yin, Chem. Commun. 2010, 46, 9022–9024.CrossRefGoogle Scholar
  41. 41.
    Y. Miyake, A. Ono, Tetrahedron Lett. 2005, 46, 2441–2443.CrossRefGoogle Scholar
  42. 42.
    E. Ennifar, P. Walter, P. Dumas, Nucleic Acids Res. 2003, 31, 2671–2682.CrossRefPubMedGoogle Scholar
  43. 43.
    S. Johannsen, S. Paulus, N. Düpre, J. Müller, R. K. O. Sigel, J. Inorg. Biochem. 2008, 102, 1141–1151.CrossRefPubMedGoogle Scholar
  44. 44.
    T. Yamane, N. Davidson, Biochim. Biophys. Acta 1962, 55, 609–621.CrossRefPubMedGoogle Scholar
  45. 45.
    L. G. Marzilli, T. J. Kistenmacher, M. Rossi, J. Am. Chem. Soc. 1977, 99, 2797–2798.CrossRefPubMedGoogle Scholar
  46. 46.
    T. J. Kistenmacher, M. Rossi, L. G. Marzilli, Inorg. Chem. 1979, 18, 240–244.CrossRefGoogle Scholar
  47. 47.
    A. Ono, S. Cao, H. Togashi, M. Tashiro, T. Fujimoto, T. Machinami, S. Oda, Y. Miyake, I. Okamoto, Y. Tanaka, Chem. Commun. 2008, 4825–4827.Google Scholar
  48. 48.
    H. Torigoe, Y. Miyakawa, A. Ono, T. Kozasa, Nucleosides Nucleotides Nucleic Acids 2011, 30, 149–167.CrossRefPubMedGoogle Scholar
  49. 49.
    D. A. Megger, J. Müller, Nucleosides Nucleotides Nucleic Acids 2010, 29, 27–38.CrossRefPubMedGoogle Scholar
  50. 50.
    H. Urata, E. Yamaguchi, Y. Nakamura, S.-i. Wada, Chem. Commun. 2011, 47, 941–943.CrossRefGoogle Scholar
  51. 51.
    T. Ono, K. Yoshida, Y. Saotome, R. Sakabe, I. Okamoto, A. Ono, Chem. Commun. 2011, 47, 1542–1544.CrossRefGoogle Scholar
  52. 52.
    D. A. Megger, C. Fonseca Guerra, F. M. Bickelhaupt, J. Müller, J. Inorg. Biochem. 2011, 105, 1398–1404.Google Scholar
  53. 53.
    Y. Wen, F. Xing, S. He, S. Song, L. Wang, Y. Long, D. Li, C. Fan, Chem. Commun. 2010, 46, 2596–2598.CrossRefGoogle Scholar
  54. 54.
    I. Okamoto, K. Iwamoto, Y. Watanabe, Y. Miyake, A. Ono, Angew. Chem. Int. Ed. 2009, 48, 1648–1651.CrossRefGoogle Scholar
  55. 55.
    K. Aoki, W. Saenger, Acta Cryst. 1984, C40, 775–778.Google Scholar
  56. 56.
    B. Lippert, Coord. Chem. Rev. 2000, 200–202, 487–516.CrossRefGoogle Scholar
  57. 57.
    J. Ruiz, M. D. Villa, V. Rodríguez, N. Cutillas, C. Vicente, G. López, D. Bautista, Inorg. Chem. 2007, 46, 5448–5449.CrossRefPubMedGoogle Scholar
  58. 58.
    C. Switzer, D. Shin, Chem. Commun. 2005, 1342–1344.Google Scholar
  59. 59.
    D. Shin, C. Switzer, Chem. Commun. 2007, 4401–4403.Google Scholar
  60. 60.
    F.-A. Polonius, J. Müller, Angew. Chem. Int. Ed. 2007, 46, 5602–5604.CrossRefGoogle Scholar
  61. 61.
    T. Ihara, T. Ishii, N. Araki, A. W. Wilson, A. Jyo, J. Am. Chem. Soc. 2009, 131, 3826–3827.CrossRefPubMedGoogle Scholar
  62. 62.
    M. G. Santangelo, P. M. Antoni, B. Spingler, G. Jeschke, ChemPhysChem 2010, 11, 599–606.CrossRefPubMedGoogle Scholar
  63. 63.
    F. Seela, T. Wenzel, Helv. Chim. Acta 1994, 77, 1485–1499.CrossRefGoogle Scholar
  64. 64.
    D. A. Megger, C. Fonseca Guerra, J. Hoffmann, B. Brutschy, F. M. Bickelhaupt, J. Müller, Chem. Eur. J. 2011, 17, 6533–6544.Google Scholar
  65. 65.
    F. Seela, T. Wenzel, Helv. Chim. Acta 1995, 78, 833–846.CrossRefGoogle Scholar
  66. 66.
    L. E. Kapinos, A. Holý, J. Günter, H. Sigel, Inorg. Chem. 2001, 40, 2500–2508.CrossRefPubMedGoogle Scholar
  67. 67.
    C. Switzer, S. Sinha, P. H. Kim, B. D. Heuberger, Angew. Chem. Int. Ed. 2005, 44, 1529–1532.CrossRefGoogle Scholar
  68. 68.
    B. D. Heuberger, D. Shin, C. Switzer, Org. Lett. 2008, 10, 1091–1094.CrossRefPubMedGoogle Scholar
  69. 69.
    H. Urata, E. Yamaguchi, T. Funai, Y. Matsumura, S.-i. Wada, Angew. Chem. Int. Ed. 2010, 49, 6516–6519.CrossRefGoogle Scholar
  70. 70.
    K. S. Park, C. Jung, H. G. Park, Angew. Chem. Int. Ed. 2010, 49, 9757–9760.CrossRefGoogle Scholar
  71. 71.
    R. Freeman, T. Finder, I. Willner, Angew. Chem. Int. Ed. 2009, 48, 7818–7821.CrossRefGoogle Scholar
  72. 72.
    N. Kanayama, T. Takarada, M. Maeda, Chem. Commun. 2011, 47, 2077–2079.CrossRefGoogle Scholar
  73. 73.
    H. Torigoe, T. Kozasa, A. Ono, Nucleic Acids Symp. Ser. 2006, 50, 89–90.CrossRefGoogle Scholar
  74. 74.
    J. Joseph, G. B. Schuster, Org. Lett. 2007, 9, 1843–1846.CrossRefPubMedGoogle Scholar
  75. 75.
    Z.-G. Wang, J. Elbaz, I. Willner, Nano Lett. 2011, 11, 304–309.CrossRefPubMedGoogle Scholar
  76. 76.
    J. Müller, D. Böhme, P. Lax, M. Morell Cerdà, M. Roitzsch, Chem. Eur. J. 2005, 11, 6246–6253.CrossRefPubMedGoogle Scholar
  77. 77.
    L. Benda, M. Straka, Y. Tanaka, V. Sychrovský, Phys. Chem. Chem. Phys. 2011, 13, 100–103.CrossRefPubMedGoogle Scholar
  78. 78.
    M. K. Schlegel, L. Zhang, N. Pagano, E. Meggers, Org. Biomol. Chem. 2009, 7, 476–482.CrossRefPubMedGoogle Scholar
  79. 79.
    R. M. Franzini, R. M. Watson, G. K. Patra, R. M. Breece, D. L. Tierney, M. P. Hendrich, C. Achim, Inorg. Chem. 2006, 45, 9798–9811.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Dominik A. Megger
    • 1
  • Nicole Megger
    • 1
  • Jens Müller
    • 1
    Email author
  1. 1.Institute for Inorganic and Analytical ChemistryUniversity of MünsterMünsterGermany

Personalised recommendations