G-Quartet, G-Quadruplex, and G-Wire Regulated by Chemical Stimuli

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 749)

Abstract

Guanine-rich DNA, which is widely distributed in the human genome, can fold into a supramolecular structure called the G-wire. The G-wire possesses promising characteristics as a functional element for various applications in vitro and in vivo. Here, we describe the preparative procedures for the G-wire and signatures of G-wire formation. Procedures for the regulation of G-wire formation by chemical stimuli will be useful for in vivo and in vitro applications.

Key words

G-wire G-quadruplex G-quartet Guanine Molecular crowding Metal ion Polymorphism 

Notes

Acknowledgments

This work was supported in part by Grants-in-Aid for Scientific Research, the Academic Frontier Project (2004–2009), and the Core Research project (2009–2014) of the Ministry of Education, Culture, Sport, Science and Technology (MEXT) of Japan; by the Long-range Research Initiative; and by the Hirao Taro Foundation of the Konan University Association for Academic Research.

References

  1. 1.
    International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931–945.Google Scholar
  2. 2.
    Seeman, N. C. (2003) DNA in a material world. Nature 421, 427–431.Google Scholar
  3. 3.
    Jaeger, L. and Chworos, A. (2006) The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16, 531–543.CrossRefGoogle Scholar
  4. 4.
    Sharma, J., Chhabra, R., Cheng, A., Brownell, J., Liu, Y., and Yan, H. (2009) Control of self-assembly of DNA tubules through ­integration of gold nanoparticles. Science 323, 112–116.Google Scholar
  5. 5.
    Liu, Y., Kuzuya, A., Sha, R., Guillaume, J., Wang, R., Canary, J. W., and Seeman, N. C. (2008) Coupling across a DNA helical turn yields a hybrid DNA/organic catenane doubly tailed with functional termini. J. Am. Chem. Soc. 130, 10882–10883.CrossRefGoogle Scholar
  6. 6.
    He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A. E., Jiang, W., Mao, C. (2008) Nature 452, 198–201.Google Scholar
  7. 7.
    Rothemund, P. W. (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302.Google Scholar
  8. 8.
    Goodman, R. P., Schaap, I. A. T., Tardin, C. F., Erben, C. M., Berry, R. M., Schmidt, C. F., and Turberfield, A. J. (2005) Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661–1665.Google Scholar
  9. 9.
    Kumari, S., Bugaut, A., Huppert, J., and Balasubramanian, S. (2007) An RNA G-quadruplex in the 5’ UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 3, 218–221.CrossRefGoogle Scholar
  10. 10.
    Rankin, S., Reszka, A. P., Huppert, J., Zloh, M., Parkinson, G. N., Todd, A. K., Ladame, S., Balasubramanian, S., and Neidle, S. (2005) Putative DNA quadruplex formation within the human c-kit oncogene. J. Am. Chem. Soc. 127, 10584–10589.CrossRefGoogle Scholar
  11. 11.
    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.CrossRefGoogle Scholar
  12. 12.
    Scaria, V., Hariharan, M., Arora, A., and Maiti, S. (2006) Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. Nucleic Acids Res. 34 (Web Server issue), W683–685.Google Scholar
  13. 13.
    Du, Z., Zhao, Y., and Li, N. (2008) Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription Genome Res. 18, 233–241.Google Scholar
  14. 14.
    Gellert, M., Lipsett, M. N., and Davies, D. R. (1962) Helix formation by guanylic acid. Proc. Natl. Acad. Sci. USA, 48, 2013–2018.CrossRefGoogle Scholar
  15. 15.
    Miyoshi, D., Nakao, A., Toda, T., and Sugimoto, N. (2001) Effect of divalent cations on antiparallel G-quartet structure of d(G4T4G4). FEBS Lett. 496, 128–133.CrossRefGoogle Scholar
  16. 16.
    Miyoshi, D., Nakao, A., and Sugimoto, N. (2002) Molecular crowding regulates the structural switch of the DNA G-quadruplex. Biochemistry 41, 15017–15024.Google Scholar
  17. 17.
    Miyoshi D, Matsumura S, Nakano S, Sugimoto N. (2004) Duplex dissociation of telomere DNAs induced by molecular crowding. J. Am. Chem. Soc. 126, 165–169.CrossRefGoogle Scholar
  18. 18.
    Davis, J. T. (2004) G-quartets 40 years later: from 5’-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed. 43, 668–698.CrossRefGoogle Scholar
  19. 19.
    Chen, F. M. (1992) Sr2+ facilitates intermolecular G-quadruplex formation of telomeric sequences. Biochemistry, 21, 3769–3776.CrossRefGoogle Scholar
  20. 20.
    Marsh, T. C. and Henderson, E. (1994) G-wires: self-assembly of a telomeric ­oligonucleotide, d(GGGGTTGGGG), into large superstructures. Biochemistry 33, 10718–10724.Google Scholar
  21. 21.
    Marsh, T. C., Vesenka, J., and Henderson, E. (1995) new DNA nanostructure, the G-wire, imaged by scanning probe microscopy. Nucleic Acids Res. 23, 696–700.CrossRefGoogle Scholar
  22. 22.
    Kotlyar, A., Borovok, N., Molotsky, T., Cohen, H., Shapir E., and Porath, D. (2005) Long Monomolecular G4-DNA Nanowires”. Adv. Mat. 17, 1901–1905.CrossRefGoogle Scholar
  23. 23.
    Borovok, N., Molotsky, T., Ghabboun, J., Porath, D., and Kotlyar, A. (2008) Efficient procedure of preparation and properties of long uniform G4-DNA nanowires. Anal. Biochem. 374, 71–78.CrossRefGoogle Scholar
  24. 24.
    Protozanova, E. and Macgregor, R. B. Jr. (1996) Frayed wires: a thermally stable form of DNA with two distinct structural domains. Biochemistry 35, 16638–16645.Google Scholar
  25. 25.
    Yanze, M. F., Lee, W. S., Poon, K., Piquette-Miller, M., and Macgregor, R. B. Jr. (2003) Cellular uptake and metabolism of DNA frayed wires. Biochemistry 42, 11427–11433.Google Scholar
  26. 26.
    Miyoshi, D., Nakao, A., and Sugimoto, N. (2003) Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+. Nucleic Acids Res. 31, 1156–1163.CrossRefGoogle Scholar
  27. 27.
    Miyoshi, D., Karimata, H., and Sugimoto, N. (2005) Drastic effect of a single base ­difference between human and tetrahymena telomere sequences on their structures under molecular crowding conditions. Angew. Chem. Int. Ed. 44, 3740–3744.CrossRefGoogle Scholar
  28. 28.
    Porath, D., Bezryadin, A., de Vries, S., and Dekker, C. (2000) Direct measurement of electrical transport through DNA molecules. Nature 403, 635–638.Google Scholar
  29. 29.
    Calzolari, A., Felice, R. D., Molinari, E. (2002) G-quartet biomolecular nanowires. Appl. Phys. Lett. 80, 3331–3333.CrossRefGoogle Scholar
  30. 30.
    Vesenka, J., Bagg, D., Wolff, A., Reichert, A., Moeller, R., and Fritzsche, W. (2007) Auto-orientation of G-wire DNA on mica. Colloids Surf B Biointerfaces 58, 256–263.Google Scholar
  31. 31.
    Davis, J. T. and Spada, G. P. (2007) Supramolecular architectures generated by self-assembly of guanosine derivatives. Chem. Soc. Rev. 36, 296–313.CrossRefGoogle Scholar
  32. 32.
    Spada, G. P. and Gottarelli, G. (2004) Synlett 596–602.Google Scholar
  33. 33.
    Lorieau. J., Yao, L., and Bax, A. (2008) Liquid crystalline phase of G-tetrad DNA for NMR study of detergent-solubilized proteins. J. Am. Chem. Soc. 130, 7536–7537.CrossRefGoogle Scholar
  34. 34.
    Sanger. W. (1984) Principle of Nucleic Acids and Structure, Springer-Verlag, New York.Google Scholar
  35. 35.
    Richards, E. G. (1975) Use of tables in calculation of absorption, optical rotatory dispersion and circular dichroism of polyribonucleotides. In Fasman,G.D. (ed.), Handbook of Biochemistry and Molecular Biology, 3rd edn. CRC Press, Cleveland, OH, USA, Vol. 1, pp. 596–603.Google Scholar
  36. 36.
    Mergny, J. L., Phan, A. T., and Lacroix L. (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett. 435, 74–78.CrossRefGoogle Scholar
  37. 37.
    Miyoshi, D., Nakamura, K. Karimata, H., Ohmichi, T., and Sugimoto, N. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J. Am. Chem. Soc., 130, in press (2009).Google Scholar
  38. 38.
    Mergny, J. L., Li, J., Lacroix, L., Amrane, S., and Chaires, J. B. (2005) Thermal difference spectra: a specific signature for nucleic acid structures. Nucleic Acids Res. 33, e138.CrossRefGoogle Scholar
  39. 39.
    Kunstelj, K., Federiconi, F., Spindler, L., and Drevensek-Olenik, I. (2007) Self-organization of guanosine 5’-monophosphate on mica. Colloids Surf B Biointerfaces 59, 120–127.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), and Frontier Institute for Biomolecular Engineering Research (FIBER)Konan UniversityKobeJapan

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