Table of Contents Author Guidelines Submit a Manuscript
Journal of Nucleic Acids
Volume 2010 (2010), Article ID 468017, 6 pages
http://dx.doi.org/10.4061/2010/468017
Research Article

Structure and Stability of a Dimeric G-Quadruplex Formed by Cyclic Oligonucleotides

1Departament de Química Orgànica, Universitat de Barcelona, C/. Martí i Franquès 1, 08028 Barcelona, Spain
2The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
3Instituto de Química Física “Rocasolano”, CSIC, C/. Serrano 119, 28006 Madrid, Spain

Received 15 January 2010; Accepted 12 March 2010

Academic Editor: Daniela Montesarchio

Copyright © 2010 Joan Casals et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Burge, G. N. Parkinson, P. Hazel, A. K. Todd, and S. Neidle, “Quadruplex DNA: sequence, topology and structure,” Nucleic Acids Research, vol. 34, no. 19, pp. 5402–5415, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. P. Bates, J.-L. Mergny, and D. Yang, “Quartets in G-major. The first international meeting on quadruplex DNA,” EMBO Journal, vol. 8, no. 11, pp. 1003–1010, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. J. L. Huppert, “Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes,” Chemical Society Reviews, vol. 37, no. 7, pp. 1375–1384, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. J. T. Davis, “G-quartets 40 years later: from 5-GMP to molecular biology and supramolecular chemistry,” Angewandte Chemie International Edition, vol. 43, no. 6, pp. 668–698, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. D. Margulies and A. D. Hamilton, “Protein recognition by an ensemble of fluorescent DNA G-quadruplexes,” Angewandte Chemie International Edition, vol. 48, no. 10, pp. 1771–1774, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. P. Alberti, A. Bourdoncle, B. Saccà, L. Lacroix, and J.-L. Mergny, “DNA nanomachines and nanostructures involving quadruplexes,” Organic and Biomolecular Chemistry, vol. 4, no. 18, pp. 3383–3391, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. S. Balasubramanian and S. Neidle, “G-quadruplex nucleic acids as therapeutic targets,” Current Opinion in Chemical Biology, vol. 13, no. 3, pp. 345–353, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. M. A. Blasco, “Telomeres and human disease: ageing, cancer and beyond,” Nature Reviews Genetics, vol. 6, no. 8, pp. 611–622, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. D. J. Patel, A. T. Phan, and V. Kuryavyi, “Human telomere, oncogenic promoter and 5-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics,” Nucleic Acids Research, vol. 35, no. 22, pp. 7429–7455, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. D. Monchaud and M.-P. Teulade-Fichou, “A hitchhiker's guide to G-quadruplex ligands,” Organic and Biomolecular Chemistry, vol. 6, no. 4, pp. 627–636, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. B. Gatto, M. Palumbo, and C. Sissi, “Nucleic acid aptamers based on the G-quadruplex structure: therapeutic and diagnostic potential,” Current Medicinal Chemistry, vol. 16, no. 10, pp. 1248–1265, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. K. Paeschke, T. Simonsson, J. Postberg, D. Rhodes, and H. J. Lipps, “Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo,” Nature Structural and Molecular Biology, vol. 12, no. 10, pp. 847–854, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. M. L. Duquette, P. Handa, J. A. Vincent, A. F. Taylor, and N. Maizels, “Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA,” Genes and Development, vol. 18, no. 13, pp. 1618–1629, 2004. View at Publisher · View at Google Scholar · View at Scopus
  14. N. Maizels, “Dynamic roles for G4 DNA in the biology of eukaryotic cells,” Nature Structural and Molecular Biology, vol. 13, no. 12, pp. 1055–1059, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. E. T. Kool, “Circular oligonucleotides: new concepts in oligonucleotide design,” Annual Review of Biophysics and Biomolecular Structure, vol. 25, pp. 1–28, 1996. View at Google Scholar · View at Scopus
  16. E. T. Kool, “Recognition of DNA, RNA, and proteins by circular oligonucleotides,” Accounts of Chemical Research, vol. 31, no. 8, pp. 502–510, 1998. View at Google Scholar · View at Scopus
  17. G. W. Ashley and D. M. Kushlan, “Chemical synthesis of oligonucleotide dumbbells,” Biochemistry, vol. 30, pp. 2927–2933, 1991. View at Google Scholar
  18. J. H. Ippel, V. Lanzotti, A. Galeone et al., “Conformation of the circular dumbbell d<pCGC-TT-GCG-TT>: structure determination and molecular dynamics,” Journal of Biomolecular NMR, vol. 6, no. 4, pp. 403–422, 1995. View at Publisher · View at Google Scholar · View at Scopus
  19. C.-T. Lin, Y. L. Lyu, and L. F. Liu, “A cruciform-dumbbell model for inverted dimer formation mediated by inverted repeats,” Nucleic Acids Research, vol. 25, no. 15, pp. 3009–3016, 1997. View at Publisher · View at Google Scholar · View at Scopus
  20. N. Escaja, E. Pedroso, M. Rico, and C. González, “Dimeric solution structure of two cyclic octamers: four-stranded DNA structures stabilized by A:T:A:T and G:C:G:C tetrads,” Journal of the American Chemical Society, vol. 122, no. 51, pp. 12732–12742, 2000. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Viladoms, N. Escaja, M. Frieden, I. Gomez-Pinto, E. Pedroso, and C. González, “Self-association of short DNA loops through minor groove C:G:G:C tetrads,” Nucleic Acids Research, vol. 37, no. 10, pp. 3264–3275, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. J. Qi and R. H. Shafer, “Covalent ligation studies on the human telomere quadruplex,” Nucleic Acids Research, vol. 33, no. 10, pp. 3185–3192, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. T. Zhou, G. Chen, Y. Wang, Q. Zhang, M. Yang, and T. Li, “Synthesis of unimolecularly circular G-quadruplexes as prospective molecular probes,” Nucleic Acids Research, vol. 32, no. 21, article e173, 2004. View at Google Scholar
  24. J. Chen, D. Liu, A. H. F. Lee, J. Qi, A. S. C. Chan, and T. Li, “Formation of circular oligodeoxyribonucleotides on the structural basis of G-quadruplex and product analysis,” Chemical Communications, pp. 2686–2687, 2002. View at Google Scholar
  25. A. T. Phan and D. J. Patel, “Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics,” Journal of the American Chemical Society, vol. 125, no. 49, pp. 15021–15027, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. G. N. Parkinson, M. P. H. Lee, and S. Neidle, “Crystal structure of parallel quadruplexes from human telomeric DNA,” Nature, vol. 417, no. 6891, pp. 876–880, 2002. View at Publisher · View at Google Scholar · View at Scopus
  27. Y. Wang and D. J. Patel, “Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex,” Structure, vol. 1, no. 4, pp. 263–282, 1993. View at Google Scholar · View at Scopus
  28. N. Zhang, A. T. Phan, and D. J. Patel, “(3 + 1) assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex,” Journal of the American Chemical Society, vol. 127, no. 49, pp. 17277–17285, 2005. View at Publisher · View at Google Scholar · View at Scopus
  29. A. T. Phan, V. Kuryavyi, K. N. Luu, and D. J. Patel, “Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution,” Nucleic Acids Research, vol. 35, no. 19, pp. 6517–6525, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. A. T. Phan, K. N. Luu, and D. J. Patel, “Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution,” Nucleic Acids Research, vol. 34, no. 19, pp. 5715–5719, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. J. Dai, M. Carver, C. Punchihewa, R. A. Jones, and D. Yang, “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 Research, vol. 35, no. 15, pp. 4927–4940, 2007. View at Publisher · View at Google Scholar · View at Scopus
  32. A. T. Phan, “Human telomeric G-quadruplex: structures of DNA and RNA sequences,” FEBS Journal, vol. 277, no. 5, pp. 1107–1117, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. E. Alazzouzi, N. Escaja, A. Grandas, and E. Pedroso, “A straightforward solid-phase synthesis of cyclic oligodeoxyribonucleotides,” Angewandte Chemie International Edition, vol. 36, no. 13-14, pp. 1506–1508, 1997. View at Google Scholar · View at Scopus
  34. M. Piotto, V. Saudek, and V. Sklenář, “Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions,” Journal of Biomolecular NMR, vol. 2, no. 6, pp. 661–665, 1992. View at Publisher · View at Google Scholar · View at Scopus
  35. D. T. Goddard and G. Kneller, SPARKY 3, University of California, San Francisco, Calif, USA, 2003.
  36. I. N. Rujan, J. C. Meleney, and P. H. Bolton, “Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium,” Nucleic Acids Research, vol. 33, no. 6, pp. 2022–2031, 2005. View at Publisher · View at Google Scholar · View at Scopus
  37. M. Webba da Silva, M. Trajkovski, Y. Sannohe, N. Ma'ani Hessari, H. Sugiyama, and J. Plavec, “Design of a G-quadruplex topology through glycosidic bond angles,” Angewandte Chemie International Edition, vol. 48, no. 48, pp. 9167–9170, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. P. Hazel, G. N. Parkinson, and S. Neidle, “Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures,” Nucleic Acids Research, vol. 34, no. 7, pp. 2117–2127, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. N. Smargiasso, F. Rosu, W. Hsia et al., “G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation,” Journal of the American Chemical Society, vol. 130, no. 31, pp. 10208–10216, 2008. View at Publisher · View at Google Scholar · View at Scopus
  40. K. J. Breslauer, “Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions,” Methods in Enzymology, vol. 259, pp. 221–242, 1995. View at Publisher · View at Google Scholar · View at Scopus
  41. J.-L. Mergny, A.-T. Phan, and L. Lacroix, “Following G-quartet formation by UV-spectroscopy,” FEBS Letters, vol. 435, no. 1, pp. 74–78, 1998. View at Publisher · View at Google Scholar · View at Scopus