Table of Contents Author Guidelines Submit a Manuscript
Journal of Nucleic Acids
Volume 2011, Article ID 316079, 5 pages
http://dx.doi.org/10.4061/2011/316079
Research Article

Direct Detection of Thrombin Binding to 8-Bromodeoxyguanosine-Modified Aptamer: Effects of Modification on Affinity and Kinetics

Department of Nanobiochemistry, FIRST, Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan

Received 14 May 2011; Revised 15 July 2011; Accepted 21 July 2011

Academic Editor: Daisuke Miyoshi

Copyright © 2011 Shou Goji and Jun Matsui. 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. E. Osborne, R. J. Cain, and G. D. Glick, “Structure and dynamics of disulfide cross-linked DNA triple helices,” Journal of the American Chemical Society, vol. 119, no. 6, pp. 1171–1182, 1997. View at Publisher · View at Google Scholar · View at Scopus
  2. K. S. Schmidt, S. Borkowski, J. Kurreck et al., “Application of locked nucleic acids to improve aptamer in vivo stability and targeting function,” Nucleic Acids Research, vol. 32, no. 19, pp. 5757–5765, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. B. Saccà, L. Lacroix, and J. L. Mergny, “The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides,” Nucleic Acids Research, vol. 33, no. 4, pp. 1182–1192, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Shangguan, Z. Tang, P. Mallikaratchy, Z. Xiao, and W. Tan, “Optimization and modifications of aptamers selected from live cancer cell lines,” A European Journal of Chemical Biology, vol. 8, no. 6, pp. 603–606, 2007. View at Google Scholar
  5. E. B. Pedersen, J. T. Nielsen, C. Nielsen, and V. V. Filichev, “Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids,” Nucleic Acids Research, vol. 39, no. 6, pp. 2470–2481, 2011. View at Google Scholar
  6. L. C. Bock, L. C. Griffin, J. A. Latham, E. H. Vermaas, and J. J. Toole, “Selection of single-stranded DNA molecules that bind and inhibit human thrombin,” Nature, vol. 355, no. 6360, pp. 564–566, 1992. View at Publisher · View at Google Scholar · View at Scopus
  7. R. F. Macaya, P. Schultze, F. W. Smith, J. A. Roe, and J. Feigon, “Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 8, pp. 3745–3749, 1993. View at Google Scholar · View at Scopus
  8. P. Schultze, R. F. Macaya, and J. Feigon, “Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG),” Journal of Molecular Biology, vol. 235, no. 5, pp. 1532–1547, 1994. View at Publisher · View at Google Scholar · View at Scopus
  9. K. Y. Wang, S. McCurdy, R. G. Shea, S. Swaminathan, and P. H. Bolton, “A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA,” Biochemistry, vol. 32, no. 8, pp. 1899–1904, 1993. View at Google Scholar · View at Scopus
  10. K. Padmanabhan, K. P. Padmanabhan, J. D. Ferrara, J. E. Sadler, and A. Tulinsky, “The structure of α-thrombin inhibited by a 15-mer single-stranded DNA aptamer,” Journal of Biological Chemistry, vol. 268, no. 24, pp. 17651–17654, 1993. View at Google Scholar · View at Scopus
  11. K. Padmanabhan and A. Tulinsky, “An ambiguous structure of a DNA 15-mer thrombin complex,” Acta Crystallographica Section D, vol. 52, no. 2, pp. 272–282, 1996. View at Google Scholar · View at Scopus
  12. A. Virno, A. Randazzo, C. Giancola, M. Bucci, G. Cirino, and L. Mayol, “A novel thrombin binding aptamer containing a G-LNA residue,” Bioorganic and Medicinal Chemistry, vol. 15, no. 17, pp. 5710–5718, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. L. Bonifacio, F. C. Church, and M. B. Jarstfer, “Effect of locked-nucleic acid on a biologically active G-quadruplex. A structure-activity relationship of the thrombin aptamer,” International Journal of Molecular Sciences, vol. 9, no. 3, pp. 422–433, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. C. G. Peng and M. J. Damha, “G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA),” Nucleic Acids Research, vol. 35, no. 15, pp. 4977–4988, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. G. X. He, S. H. Krawczyk, S. Swaminathan et al., “N2- and C8-substituted oligodeoxynucleotides with enhanced thrombin inhibitory activity in vitro and in vivo,” Journal of Medicinal Chemistry, vol. 41, no. 13, pp. 2234–2242, 1998. View at Publisher · View at Google Scholar · View at Scopus
  16. V. Esposito, A. Randazzo, G. Piccialli, L. Petraccone, C. Giancola, and L. Mayol, “Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)]4,” Organic and Biomolecular Chemistry, vol. 2, no. 3, pp. 313–318, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. L. Petraccone, I. Duro, A. Randazzo, A. Virno, L. Mayol, and C. Giancola, “Biophysical properties of quadruplexes containing two or three 8-bromodeoxyguanosine residues,” Nucleosides, Nucleotides and Nucleic Acids, vol. 26, no. 6-7, pp. 669–674, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. E. Dias, J. L. Battiste, and J. R. Williamson, “Chemical probe for glycosidic conformation in telomeric DNAs,” Journal of the American Chemical Society, vol. 116, no. 10, pp. 4479–4480, 1997. View at Google Scholar · View at Scopus
  19. J. Matsui and S. Goji, to be submitted.
  20. F. Pröll, B. Möhrle, M. Kumpf, and G. Gauglitz, “Label-free characterisation of oligonucleotide hybridisation using reflectometric interference spectroscopy,” Analytical and Bioanalytical Chemistry, vol. 382, no. 8, pp. 1889–1894, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. B. P. Möhrle, M. Kumpf, and G. Gauglitz, “Determination of affinity constants of locked nucleic acid (LNA) and DNA duplex formation using label free sensor technology,” Analyst, vol. 130, no. 12, pp. 1634–1638, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. J. Piehler, A. Brecht, G. Gauglitz, and M. Zerin, “Label-free monitoring of DNA-ligand interactions,” Analytical Biochemistry, vol. 249, no. 1, pp. 94–102, 1997. View at Publisher · View at Google Scholar · View at Scopus
  23. T. Hattori, M. Umetsu, T. Nakanishi et al., “High affinity anti-inorganic material antibody generation by integrating graft and evolution technologies: potential of antibodies as biointerface molecules,” Journal of Biological Chemistry, vol. 285, no. 10, pp. 7784–7793, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. H. Hasegawa, K. I. Taira, K. Sode, and K. Ikebukuro, “Improvement of aptamer affinity by dimerization,” Sensors, vol. 8, no. 2, pp. 1090–1098, 2008. View at Google Scholar · View at Scopus
  25. A. Pastemak, F. J. Hernandez, L. M. Rasmussen, B. Vester, and J. Wengel, “Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer,” Nucleic Acids Research, vol. 39, pp. 1155–1164, 2011. View at Google Scholar
  26. T. Hianik, V. Ostatná, M. Sonlajtnerova, and I. Grman, “Influence of ionic strength, pH and aptamer configuration for binding affinity to thrombin,” Bioelectrochemistry, vol. 70, no. 1, pp. 127–133, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. S. R. Nallagatla, B. Heuberger, A. Haque, and C. Switzer, “Combinatorial synthesis of thrombin-binding aptamers containing iso-guanine,” Journal of Combinatorial Chemistry, vol. 11, no. 3, pp. 364–369, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. X. Li, L. Shen, D. Zhang et al., “Electrochemical impedance spectroscopy for study of aptamer-thrombin interfacial interactions,” Biosensors and Bioelectronics, vol. 23, no. 11, pp. 1624–1630, 2008. View at Publisher · View at Google Scholar · View at Scopus