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G-Quadruplex Structures and G-Quadruplex-Interactive Compounds

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Telomeres and Telomerase

Part of the book series: Methods in Molecular Biology ((MIMB,volume 735))

Abstract

G-quadruplexes are noncanonical secondary structures formed in DNA sequences containing consecutive runs of guanines. DNA G-quadruplexes have recently emerged as attractive cancer therapeutic targets. It has been shown that the 3′ G-rich single-stranded overhangs of human telomeres can form G-quadruplex structures. G-quadruplex-interactive compounds have been shown to inhibit telomerase access as well as telomere capping. Nuclear magnetic resonance (NMR) spectroscopy has been shown to be a powerful method in determining the G-quadruplex structures under physiologically relevant conditions. We present the NMR methodology used in our research group for structure determination of G-quadruplexes in solution and their interactions with small molecule compounds. An example of a G-quadruplex structure formed in the human telomere sequence recently solved in our laboratory is used as an example.

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References

  1. Yang, D., and Okamoto, K. (2010) Structural Insights into G-quadruplexes: Towards New Anti-Cancer Drugs., Fut. Med. Chem. In press.

    Google Scholar 

  2. Sen, D., and Gilbert, W. (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA, Nature 344, 410–414.

    Article  PubMed  CAS  Google Scholar 

  3. Hud, N. V., and Plavec, J. (2006) The role of cations in determining quadruplex structure and stability, in Quadruplex Nucleic Acids (Neidle, S., Ed.), pp 100–130, Royal Society of Chemistry, RSC Publishing, Cambridge.

    Google Scholar 

  4. Neidle, S., and Parkinson, G. (2002) Telomere maintenance as a target for anticancer drug discovery, Nature Reviews Drug Discovery 1, 383–393.

    Article  PubMed  CAS  Google Scholar 

  5. Qin, Y., and Hurley, L. H. (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions, Biochimie 90, 1149–1171.

    Article  PubMed  CAS  Google Scholar 

  6. Punchihewa, C., and Yang, D. Z. (2009) Therapeutic Targets and Drugs-G-quadruplex inhibitors., in Telomeres and Telomerase in Cancer (Hiyama, K., Ed.), pp 251–280, Springer, NJ, USA.

    Chapter  Google Scholar 

  7. Henderson, E., Hardin, C. C., Walk, S. K., Tinoco, I., Jr., and Blackburn, E. H. (1987) Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs, Cell 51, 899–908.

    Article  PubMed  CAS  Google Scholar 

  8. Moyazis, R. K., Buckingham, J. M., Cram, L. S., Dani, M., Deaven, L. L., Jones, M. D., Meyne, J., Ratliff, R. L., and Wu, J. R. (1988) A highly conserved repetitive DNA sequence (TTAGGG)n, present at the telomere of human chromosomes., Proc. Natl. Acad. Sci. USA 85, 6622–6626.

    Article  Google Scholar 

  9. Wright, W. E., Tesmer, V. M., Huffman, K. E., Levene, S. D., and Shay, J. W. (1997) Normal human chromosomes have long G-rich telomeric overhangs at one end, Genes Dev. 11, 2801–2809.

    Article  PubMed  CAS  Google Scholar 

  10. Bodnar, A. G., Ouellette, M., Frolkis, M., Holt, S. E., Chiu, C. P., Morin, G. B., Harley, C. B., Shay, J. W., Lichtsteiner, S., and Wright, W. E. (1998) Extension of life-span by introduction of telomerase into normal human cells, Science 279, 349–352.

    Article  PubMed  CAS  Google Scholar 

  11. Sun, D., Lopez, C., Von Hoff, D. D., and Hurley, L. H. (1998) Modulation of the catalytic activity and processivity of human telomerase from HeLa cell, Proc. Am. Assoc. Cancer Res. 39, 569.

    Google Scholar 

  12. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J., and Pluckthun, A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei, Proc. Natl. Acad. Sci. USA 98, 8572–8577.

    Article  PubMed  CAS  Google Scholar 

  13. Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D., and Lipps, H. J. (2005) Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo, Nat. Struct. Mol. Biol. 12, 847–854.

    Article  PubMed  CAS  Google Scholar 

  14. Oganesian, L., and Bryan, T. M. (2007) Physiological relevance of telomeric G-quadruplex formation: a potential drug target, Bioessays 29, 155–165.

    Article  PubMed  CAS  Google Scholar 

  15. Granotier, C., Pennarun, G., Riou, L., Hoffschir, F., Gauthier, L. R., De Cian, A., Gomez, D., Mandine, E., Riou, J. F., Mergny, J. L., Mailliet, P., Dutrillaux, B., and Boussin, F. D. (2005) Preferential binding of a G-quadruplex ligand to human chromosome ends, Nucleic Acids Res. 33, 4182–4190.

    Article  PubMed  CAS  Google Scholar 

  16. Chang, C. C., Kuo, I. C., Lin, J. J., Lu, Y. C., Chen, C. T., Back, H. T., Lou, P. J., and Chang, T. C. (2004) A novel carbazole derivative, BMVC: A potential antitumor agent and fluorescence marker of cancer cells, Chemistry & Biodiversity 1, 1377–1384.

    Article  CAS  Google Scholar 

  17. Harley, C. B., Futcher, A. B., and Greider, C. W. (1990) Telomeres shorten during ageing of human fibroblasts, Nature 345, 458–460.

    Article  PubMed  CAS  Google Scholar 

  18. Greider, C. W., and Blackburn, E. H. (1985) Identification of a specific telomere terminal transferase activity in Tetrahymena extracts, Cell 43, 405–413.

    Article  PubMed  CAS  Google Scholar 

  19. Kim, N. W., Piatyszek, M. A., Prowse, K. R., Harley, C. B., West, M. D., Ho, P. L. C., Coviello, G. M., Wright, W. E., Weinrich, S. L., and Shay, J. W. (1994) Specific Association of Human Telomerase Activity with Immortal Cells and Cancer, Science 266, 2011–2015.

    Article  PubMed  CAS  Google Scholar 

  20. Hanahan, D., and Weinberg, R. A. (2000) The hallmarks of cancer, Cell. 100, 57–70.

    Article  PubMed  CAS  Google Scholar 

  21. Zahler, A. M., Williamson, J. R., Cech, T. R., and Prescott, D. M. (1991) Inhibition of Telomerase by G-Quartet DNA Structures, Nature 350, 718–720.

    Article  PubMed  CAS  Google Scholar 

  22. Wang, Y., and Patel, D. J. (1993) Solution Structure of the Human Telomeric Repeat D[Ag(3)(T(2)Ag(3))3] G-Tetraplex, Structure 1, 263–282.

    Article  PubMed  CAS  Google Scholar 

  23. Parkinson, G. N., Lee, M. P. H., and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA, Nature 417, 876–880.

    Article  PubMed  CAS  Google Scholar 

  24. Ambrus, A., Chen, D., Dai, J. X., Bialis, T., Jones, R. A., and Yang, D. Z. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution, Nucleic Acids Res. 34, 2723–2735.

    Article  PubMed  CAS  Google Scholar 

  25. Dai, J. X., Carver, M., Punchihewa, C., Jones, R. A., and Yang, D. Z. (2007) Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence, Nucleic Acids Res. 35, 4927–4940.

    Article  PubMed  CAS  Google Scholar 

  26. Dai, J. X., Punchihewa, C., Ambrus, A., Chen, D., Jones, R. A., and Yang, D. Z. (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation, Nucleic Acids Res. 35, 2440–2450.

    Article  PubMed  CAS  Google Scholar 

  27. Xu, Y., Noguchi, Y., and Sugiyama, H. (2006) The new models of the human telomere d[AGGG(TTAGGG)(3)] in K+ solution, Bioorg. Med. Chem. 14, 5584–5591.

    Article  PubMed  CAS  Google Scholar 

  28. Luu, K. N., Phan, A. T., Kuryavyi, V., Lacroix, L., and Patel, D. J. (2006) Structure of the human telomere in K+ solution: An intramolecular (3+1) G-quadruplex scaffold, J. Am. Chem. Soc. 128, 9963–9970.

    Article  PubMed  CAS  Google Scholar 

  29. Phan, A. T., Kuryavyi, V., Luu, K. N., and Patel, D. J. (2007) Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution, Nucleic Acids Res. 35, 6517–6525.

    Article  PubMed  CAS  Google Scholar 

  30. Phan, A. T., Luu, K. N., and Patel, D. J. (2006) Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution, Nucleic Acids Res. 34, 5715–5719.

    Article  PubMed  CAS  Google Scholar 

  31. Dai, J. X., Carver, M., and Yang, D. Z. (2008) Polymorphism of human telomeric quadruplex structures, Biochimie. 90, 1172–1183.

    Article  PubMed  CAS  Google Scholar 

  32. Ambrus, A., Chen, D., Dai, J. X., Jones, R. A., and Yang, D. Z. (2005) Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization, Biochemistry 44, 2048–2058.

    Google Scholar 

  33. Dai, J. X., Chen, D., Jones, R. A., Hurley, L. H., and Yang, D. Z. (2006) NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region, Nucleic Acids Res. 34, 5133–5144.

    Article  PubMed  CAS  Google Scholar 

  34. Sun, D. Y., Thompson, B., Cathers, B. E., Salazar, M., Kerwin, S. M., Trent, J. O., Jenkins, T. C., Neidle, S., and Hurley, L. H. (1997) Inhibition of human telomerase by a G-quadruplex-interactive compound, J. Med. Chem. 40, 2113–2116.

    Article  PubMed  CAS  Google Scholar 

  35. White, E. W., Tanious, F., Ismail, M. A., Reszka, A. P., Neidle, S., Boykin, D. W., and Wilson, W. D. (2007) Structure-specific recognition of quadruplex DNA by organic cations: Influence of shape, substituents and charge, Biophys. Chem. 126, 140–153.

    Article  PubMed  CAS  Google Scholar 

  36. Muller, S., Pantos, G. D., Rodriguez, R., and Balasubramanian, S. (2009) Controlled-folding of a small molecule modulates DNA G-quadruplex recognition, Chem. Commun. 80–82.

    Google Scholar 

  37. Read, M., Cuesta, J., Basra, I., Harrison, J., Reszka, A., Gowan, S., Kelland, L. R., and Neidle, S. (2001) Rational design approaches to increase the potency of G-quadruplex-mediated telomerase inhibitors, Clin. Cancer Res. 7, 713.

    Google Scholar 

  38. Shin-ya, K., Wierzba, K., Matsuo, K., Ohtani, T., Yamada, Y., Furihata, K., Hayakawa, Y., and Seto, H. (2001) Telomestatin, a novel telomerase inhibitor from Streptomyces anulatus, J. Am. Chem. Soc. 123, 1262–1263.

    Article  PubMed  CAS  Google Scholar 

  39. Wheelhouse, R. T., Han, F. X., Sun, D., and Hurley, L. H. (1998) The interaction of telomerase inhibitory porphyrines with G-quadruplex DNA., Proc. Am. Assoc. Cancer Res. 39, 430.

    Google Scholar 

  40. Dai, J. X., Punchihewa, C., Mistry, P., Ooi, A. T., and Yang, D. Z. (2004) Novel DNA Bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug, J. Biol. Chem. 279, 46096–46103.

    Google Scholar 

  41. Goddard, T. D., and Kneller, D. G. (2004) University of California, San Francisco.

    Google Scholar 

  42. Brünger, A. T. (1993) Version 3.1: A system for X-ray crystallography and NMR. Yale University press, Neww Haven, CT, USA., Version 3.1: A system for X-ray crystallography and NMR. Yale University press, New Haven, CT, USA.

    Google Scholar 

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Acknowledgments

This research was supported by the National Institutes of Health funding (1S10RR16659 and CA122952). We thank Dr. Megan Carver for proofreading the manuscript.

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Authors and Affiliations

  1. Department of Chemistry, BIO5 Institute, College of Pharmacy, The University of Arizona, Tucson, AZ, USA

    Danzhou Yang

  2. Arizona Cancer Center, Tucson, AZ, USA

    Danzhou Yang

Authors
  1. Raveendra I. Mathad
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  2. Danzhou Yang
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Corresponding author

Correspondence to Danzhou Yang .

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Editors and Affiliations

  1. , Dept. Biochemistry & Molecular Biology, Baylor College of Medicine, Baylor Plaza One, Houston, 77030, Texas, USA

    Zhou Songyang

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Mathad, R.I., Yang, D. (2011). G-Quadruplex Structures and G-Quadruplex-Interactive Compounds. In: Songyang, Z. (eds) Telomeres and Telomerase. Methods in Molecular Biology, vol 735. Humana Press. https://doi.org/10.1007/978-1-61779-092-8_8

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  • DOI: https://doi.org/10.1007/978-1-61779-092-8_8

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-091-1

  • Online ISBN: 978-1-61779-092-8

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