Table of Contents Author Guidelines Submit a Manuscript
Journal of Sensors
Volume 2016, Article ID 3561863, 8 pages
http://dx.doi.org/10.1155/2016/3561863
Research Article

Nanogravimetric and Optical Characterizations of Thrombin Interaction with a Self-Assembled Thiolated Aptamer

1Institute for Microelectronics and Microsystems, National Research Council, Unit of Naples, Via P. Castellino 111, 80131 Naples, Italy
2Department of Chemistry, University of Naples “Federico II”, Via Cynthia, 80126 Naples, Italy
3Department of Pharmacy, University of Naples Federico II, 80138 Naples, Italy

Received 12 February 2016; Accepted 3 April 2016

Academic Editor: Maria Luz Rodríguez-Méndez

Copyright © 2016 Jane Politi 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. H. Jerius, A. Beal, D. Woodrum, A. Epstein, and C. Brophy, “Thrombin-induced vasospasm: cellular signaling mechanisms,” Surgery, vol. 123, no. 1, pp. 46–50, 1998. View at Publisher · View at Google Scholar · View at Scopus
  2. N. Vergnolle, M. D. Hollenberg, and J. L. Wallace, “Pro- and anti-inflammatory actions of thrombin: a distinct role for proteinase-activated receptor-1 (PAR1),” British Journal of Pharmacology, vol. 126, no. 5, pp. 1262–1268, 1999. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Zain, Y.-Q. Huang, X. Feng, M. L. Nierodzik, J.-J. Li, and S. Karpatkin, “Concentration-dependent dual effect of thrombin on impaired growth/apoptosis or mitogenesis in tumor cells,” Blood, vol. 95, no. 10, pp. 3133–3138, 2000. View at Google Scholar · View at Scopus
  4. D. M. Tasset, M. F. Kubik, and W. Steiner, “Oligonucleotide inhibitors of human thrombin that bind distinct epitopes,” Journal of Molecular Biology, vol. 272, no. 5, pp. 688–698, 1997. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Tsiang, A. K. Jain, K. E. Dunn, M. E. Rojas, L. L. K. Leung, and C. S. Gibbs, “Functional mapping of the surface residues of human thrombin,” The Journal of Biological Chemistry, vol. 270, no. 28, pp. 16854–16863, 1995. View at Publisher · View at Google Scholar · View at Scopus
  6. U. Abildgaard, “Inhibition of the thrombin-fibrinogen reaction by heparin in the absence of cofactor,” Scandinavian Journal of Haematology, vol. 5, no. 6, pp. 432–439, 1968. View at Google Scholar · View at Scopus
  7. H. Yang, J. Ji, Y. Liu, J. Kong, and B. Liu, “An aptamer-based biosensor for sensitive thrombin detection,” Electrochemistry Communications, vol. 11, no. 1, pp. 38–40, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. A. D. Ellington and J. W. Szostak, “In vitro selection of RNA molecules that bind specific ligands,” Nature, vol. 346, no. 6287, pp. 818–822, 1990. View at Publisher · View at Google Scholar · View at Scopus
  9. T.-C. Chiu and C.-C. Huang, “Aptamer-functionalized nano-biosensors,” Sensors, vol. 9, no. 12, pp. 10356–10388, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. R. D. Jenison, S. C. Gill, A. Pardi, and B. Polisky, “High-resolution molecular discrimination by RNA,” Science, vol. 263, no. 5152, pp. 1425–1429, 1994. View at Publisher · View at Google Scholar · View at Scopus
  11. A. A. Haller and P. Sarnow, “In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 16, pp. 8521–8526, 1997. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Sassanfar and J. W. Szostak, “An RNA motif that binds ATP,” Nature, vol. 364, no. 6437, pp. 550–553, 1993. View at Publisher · View at Google Scholar · View at Scopus
  13. C. Mannironi, A. Di Nardo, P. Fruscoloni, and G. P. Tocchini-Valentini, “In vitro selection of dopamine RNA ligands,” Biochemistry, vol. 36, no. 32, pp. 9726–9734, 1997. View at Publisher · View at Google Scholar · View at Scopus
  14. A. Geiger, P. Burgstaller, H. Von der Eltz, A. Roeder, and M. Famulok, “RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity,” Nucleic Acids Research, vol. 24, no. 6, pp. 1029–1036, 1996. View at Publisher · View at Google Scholar · View at Scopus
  15. T. Mairal, V. C. Özalp, P. Lozano Sánchez, M. Mir, I. Katakis, and C. K. O'Sullivan, “Aptamers: molecular tools for analytical applications,” Analytical and Bioanalytical Chemistry, vol. 390, no. 4, pp. 989–1007, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Song, L. Wang, J. Li, C. Fan, and J. Zhao, “Aptamer-based biosensors,” TrAC—Trends in Analytical Chemistry, vol. 27, no. 2, pp. 108–117, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. C. Sun, Q. Han, D. Wang et al., “A label-free and high sensitive aptamer biosensor based on hyperbranched polyester microspheres for thrombin detection,” Analytica Chimica Acta, vol. 850, pp. 33–40, 2014. View at Publisher · View at Google Scholar · View at Scopus
  18. T. Coppola, M. Varra, G. Oliviero et al., “Synthesis, structural studies and biological properties of new TBA analogues containing an acyclic nucleotide,” Bioorganic and Medicinal Chemistry, vol. 16, no. 17, pp. 8244–8253, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. N. Borbone, M. Bucci, G. Oliviero et al., “Investigating the role of T7 and T12 residues on the biological properties of thrombin-binding aptamer: Enhancement of anticoagulant activity by a single nucleobase modification,” Journal of Medicinal Chemistry, vol. 55, no. 23, pp. 10716–10728, 2012. View at Publisher · View at Google Scholar · View at Scopus
  20. 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
  21. S. Balamurugan, A. Obubuafo, S. A. Soper, R. L. McCarley, and D. A. Spivak, “Designing highly specific biosensing surfaces using aptamer monolayers on gold,” Langmuir, vol. 22, no. 14, pp. 6446–6453, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. M. C. Dixon, “Quartz crystal microbalance with dissipation monitoring: enabling real-time characterization of biological materials and their interactions,” Journal of Biomolecular Techniques, vol. 19, no. 3, pp. 151–158, 2008. View at Google Scholar · View at Scopus
  23. D. R. P. Morris, J. Fatisson, A. L. J. Olsson, N. Tufenkji, and A. R. Ferro, “Real-time monitoring of airborne cat allergen using a QCM-based immunosensor,” Sensors and Actuators B: Chemical, vol. 190, pp. 851–857, 2014. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Politi, A. Caliò, P. Dardano, M. Iodice, I. Rea, and L. De Stefano, “Bioconjugation of heavy metal-binding proteins on surface: an optical and gravimetric characterization,” Procedia Engineering, vol. 87, pp. 292–295, 2014. View at Publisher · View at Google Scholar
  25. R. Spera, T. T. B. Correia, and C. Nicolini, “NAPPA based nanogravimetric biosensor: preliminary characterization,” Sensors and Actuators B: Chemical, vol. 182, pp. 682–688, 2013. View at Publisher · View at Google Scholar · View at Scopus
  26. D. Musumeci, G. Oliviero, G. N. Roviello, E. M. Bucci, and G. Piccialli, “G-quadruplex-forming oligonucleotide conjugated to magnetic nanoparticles: synthesis, characterization, and enzymatic stability assays,” Bioconjugate Chemistry, vol. 23, no. 3, pp. 382–391, 2012. View at Publisher · View at Google Scholar · View at Scopus
  27. HoribaJobinYvon DELTA PSI Software manual, ver. 2.4.3 158. (Horiba Scientific, 2011).
  28. S. Nagatoishi, Y. Tanaka, and K. Tsumoto, “Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions,” Biochemical and Biophysical Research Communications, vol. 352, no. 3, pp. 812–817, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Scuotto, E. Rivieccio, A. Varone et al., “Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative,” Nucleic Acids Research, vol. 43, no. 16, pp. 7702–7716, 2015. View at Publisher · View at Google Scholar · View at Scopus
  30. P. He, L. Liu, W. Qiao, and S. Zhang, “Ultrasensitive detection of thrombin using surface plasmon resonance and quartz crystal microbalance sensors by aptamer-based rolling circle amplification and nanoparticle signal enhancement,” Chemical Communications, vol. 50, no. 12, pp. 1481–1484, 2014. View at Publisher · View at Google Scholar · View at Scopus
  31. W. Tang, D. Wang, Y. Xu, N. Li, and F. Liu, “A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids,” Chemical Communications, vol. 48, no. 53, pp. 6678–6680, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. B. Pagano, L. Martino, A. Randazzo, and C. Giancola, “Stability and binding properties of a modified thrombin binding aptamer,” Biophysical Journal, vol. 94, no. 2, pp. 562–569, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. G. W. Lehman and J. P. McTague, “Melting of DNA,” The Journal of Chemical Physics, vol. 49, pp. 3170–3179, 1968. View at Publisher · View at Google Scholar
  34. A. V. Hill, “The possible effects of the aggregation of the molecules of hµmoglobin on its dissociation curves,” Journal of Physiology, vol. 40, pp. 40–46, 1910. View at Google Scholar
  35. J. Politi, J. Spadavecchia, M. Iodice, and L. De Stefano, “Oligopeptide-heavy metal interaction monitoring by hybrid gold nanoparticle based assay,” Analyst, vol. 140, no. 1, pp. 149–155, 2015. View at Publisher · View at Google Scholar · View at Scopus
  36. J. Politi, J. Spadavecchia, G. Fiorentino, I. Antonucci, S. Casale, and L. De Stefano, “Interaction of Thermus thermophilus ArsC enzyme and gold nanoparticles naked-eye assays speciation between As(III) and As(V),” Nanotechnology, vol. 26, no. 43, Article ID 435703, 2015. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Goutelle, M. Maurin, F. Rougier et al., “The Hill equation: a review of its capabilities in pharmacological modelling,” Fundamental & Clinical Pharmacology, vol. 22, no. 6, pp. 633–648, 2008. View at Publisher · View at Google Scholar · View at Scopus
  38. J. E. L. E. A. Sánchez, E. Baldrich, A. E. E. G. Radi et al., “Electronic ‘off-on’ molecular switch for rapid detection of thrombin,” Electroanalysis, vol. 18, no. 19-20, pp. 1957–1962, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. A. Poturnayová, M. Šnejdárková, and T. Hianik, “DNA aptamer configuration affects the sensitivity and binding kinetics of thrombin,” Acta Chimica Slovenica, vol. 5, no. 1, pp. 53–58, 2012. View at Google Scholar
  40. T. Hianik, “Detection of protein-aptamer interactions by means of electrochemical indicators and transverse shear mode method,” in Aptamers in Bioanalysis, M. Mascini, Ed., chapter 5, pp. 101–128, John Wiley & Sons Inc, Hoboken, NJ, USA, 2009. View at Publisher · View at Google Scholar
  41. Y. Xiao, A. A. Lubin, A. J. Heeger, and K. W. Plaxco, “Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor,” Angewandte Chemie International Edition, vol. 44, no. 34, pp. 5456–5459, 2005. View at Google Scholar
  42. L. De Stefano, I. Rea, P. Giardina, A. Armenante, and I. Rendina, “Protein-modified porous silicon nanostructures,” Advanced Materials, vol. 20, no. 8, pp. 1529–1533, 2008. View at Publisher · View at Google Scholar · View at Scopus
  43. Y. Xiao, B. D. Piorek, K. W. Plaxco, and A. J. Heegert, “A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement,” Journal of the American Chemical Society, vol. 127, no. 51, pp. 17990–17991, 2005. View at Publisher · View at Google Scholar · View at Scopus
  44. F. Le Floch, H. A. Ho, and M. Leclerc, “Label-free electrochemical detection of protein based on a ferrocene-bearing cationic polythiophene and aptamer,” Analytical Chemistry, vol. 78, no. 13, pp. 4727–4731, 2006. View at Publisher · View at Google Scholar · View at Scopus
  45. H. Wei, B. Li, J. Li, E. Wang, and S. Dong, “Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes,” Chemical Communications, vol. 36, pp. 3735–3737, 2007. View at Publisher · View at Google Scholar · View at Scopus
  46. T. Hianik, V. Ostatná, Z. Zajacová, E. Stoikova, and G. Evtugyn, “Detection of aptamer-protein interactions using QCM and electrochemical indicator methods,” Bioorganic & Medicinal Chemistry Letters, vol. 15, no. 2, pp. 291–295, 2005. View at Publisher · View at Google Scholar · View at Scopus
  47. I. Rea, P. Giardina, S. Longobardi et al., “Hydrophobin Vmh2-glucose complexes self-assemble in nanometric biofilms,” Journal of the Royal Society Interface, vol. 9, no. 75, pp. 2450–2456, 2012. View at Publisher · View at Google Scholar · View at Scopus
  48. M. Terracciano, I. Rea, J. Politi, and L. De Stefano, “Optical characterization of aminosilane-modified silicon dioxide surface for biosensing,” Journal of the European Optical Society, vol. 8, Article ID 13075, 2013. View at Publisher · View at Google Scholar · View at Scopus
  49. P. Brocos, Á. Piñeiro, R. Bravo, and A. Amigo, “Refractive indices, molar volumes and molar refractions of binary liquid mixtures: concepts and correlations,” Physical Chemistry Chemical Physics, vol. 5, no. 3, pp. 550–557, 2003. View at Publisher · View at Google Scholar · View at Scopus
  50. P. A. Cuypers, J. W. Corsel, M. P. Janssen, J. M. Kop, W. T. Hermens, and H. C. Hemker, “The adsorption of prothrombin to phosphatidylserine multilayers quantitated by ellipsometry,” The Journal of Biological Chemistry, vol. 258, no. 4, pp. 2426–2431, 1983. View at Google Scholar · View at Scopus
  51. C. Polonschii, S. David, S. Tombelli, M. Mascini, and M. Gheorghiu, “A novel low-cost and easy to develop functionalization platform. Case study: aptamer-based detection of thrombin by surface plasmon resonance,” Talanta, vol. 80, no. 5, pp. 2157–2164, 2010. View at Publisher · View at Google Scholar · View at Scopus