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Comparative thermodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct

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Abstract

Aptamers interacting selectively with the anion-binding exosites 1 and 2 of thrombin were merged into dimeric oligonucleotide constructs by means of a poly-(dT)-linker of 35 nucleotides (nt) in length. Complexes of thrombin with the aptamers and their hetero- and homodimeric constructs were measured using an optical biosensor Biacore-3000. The K D values obtained for the hetero- and homodimeric constructs were correspondingly 25–30- and 2–3-fold lower than those for the primary aptamers. Analysis of temperature dependencies of the K D values within the temperature interval of 10–40°C has shown that affinity increases with the temperature decrease. The values of the enthalpy change ΔH upon formation of complexes of thrombin with the aptamers and the heterodimeric construct were basically the same. The value of the entropy change ΔS upon complex formation of thrombin with the aptamer heterodimeric construct was 1.5–2-fold higher than the ΔS values for the complexes with the aptamers. The complex formation and dissociation rates increased with the elevation of temperature from 10 to 37°C. However, at both temperatures the dissociation rate for the complex of thrombin with the heterodimeric construct was evidently lower that for the complexes with the aptamers.

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References

  1. Jayasena, S.D., Clin. Chem., 1999, vol. 45, pp. 1628–1650.

    CAS  Google Scholar 

  2. Radko, S.P., Rakhmetova, S.Yu., Bodoev, N.V., and Archakov, A.I., Biomed. Khim., 2007, vol. 53, pp. 5–24.

    CAS  Google Scholar 

  3. Mairal, T., Ozalp, V.C., Lozano Sánchez, P., Mir, M., Katakis, I., and O’sullivan, C.K., Anal. Bioanal. Chem., 2008, vol. 390, pp. 989–1007.

    Article  CAS  Google Scholar 

  4. Davis, K.A., Abrams, B., Lin, Y., and Jayasena, S.D., Nucleic Acids Res., 1996, vol. 24, pp. 702–706.

    Article  CAS  Google Scholar 

  5. Lin, Y. and Jayasena, S.D., J. Mol. Biol., 1997, vol. 271, pp. 100–111.

    Article  CAS  Google Scholar 

  6. Ringquist, S. and Parma, D., Cytometry, 1998, vol. 33, pp. 394–405.

    Article  CAS  Google Scholar 

  7. Santulli-Marotto, S., Nair, S.K., Rusconi, C., Sullenger, B., and Gilboa, E., Cancer Res., 2003, vol. 63, pp. 7483–7489.

    CAS  Google Scholar 

  8. Di Giusto, D.A. and King, G.C., J. Biol. Chem., 2004, vol. 279, pp. 46483–46489.

    Article  Google Scholar 

  9. Umehara, T., Fukuda, K., Nishikawa, F., Kohara, M., Hasegawa, T., and Nishikawa, S., J. Biochem. (Tokyo), 2005, vol. 137, pp. 339–347.

    CAS  Google Scholar 

  10. Müller, J., Wulffen, B., Pötzsch, B., and Mayer, G., Chembiochem., 2007, vol. 8, pp. 2223–2226.

    Article  Google Scholar 

  11. Hasegawa, H., Taira, K., Sode, K., and Ikebukuro, K., Sensors, 2008, vol. 8, pp. 1090–1098.

    Article  CAS  Google Scholar 

  12. Kim, Y., Cao, Z., and Tan, W., Pros. Natl. Acad. Sci. USA, 2008, vol. 105, pp. 5664–5669.

    Article  CAS  Google Scholar 

  13. Tian, L. and Heyduk, T., Biochemistry, 2009, vol. 48, pp. 264–275.

    Article  CAS  Google Scholar 

  14. Rakhmetova, S.Yu., Radko, S.P., Gnedenko, O.V., Bodoev, N.V., Ivanov, A.S., and Archakov, A.I., Biomed. Khim., 2010, vol. 56, pp. 72–80.

    CAS  Google Scholar 

  15. Nimjee, S.M., Rusconi, C.P., Harrington, R.A., and Sullenger, B.A., Trends. Cardiovasc. Med., 2005, vol. 15, pp. 41–45.

    Article  CAS  Google Scholar 

  16. Andre, C., Xicluna, A., and Guillaume, Y.-C., Electrophoresis, 2005, vol. 26, pp. 3247–3255.

    Article  CAS  Google Scholar 

  17. Gilbert, S.D., Stoddard, S.D., Wise, S.J., and Batey, R.T., J. Mol. Biol., 2006, vol. 359, pp. 754–768.

    Article  CAS  Google Scholar 

  18. Bishop, G.R., Ren, J., Polander, B.C., Jeanfreaua, B.D., Trent, J.O., and Chaires, J.B., Biophys. Chem., 2007, vol. 126, pp. 165–175.

    Article  CAS  Google Scholar 

  19. Michaud, M., Jourdan, E., Ravelet, C., Villet, A., Ravel, A., Grosset, C., and Peyrin, E., Anal. Chem., 2004, vol. 76, pp. 1015–1020.

    Article  CAS  Google Scholar 

  20. Muller, M., Weigand, J. E., Weichenrieder, O., and Suess, B., Nucl. Acids Res., 2006, vol. 34, pp. 2607–2617.

    Article  Google Scholar 

  21. Berezovski, M., and Krylov, S.N., Anal. Chem., 2005, vol. 77, pp. 1526–1529.

    Article  CAS  Google Scholar 

  22. Pagano, B., Martino, L., Randazzo, A., and Giancola, C., Biophys. J., 2008, vol. 94, pp. 562–569.

    Article  CAS  Google Scholar 

  23. Tasset, D.M., Kubik, M.F., and Steiner, W.J., Mol. Biol., 1997, vol. 272, pp. 688–698.

    Article  CAS  Google Scholar 

  24. Bock, L.C., Griffin, L.C., Latham, J.A., Vermass, E.H., and Toole, J.J., Nature, 1992, vol. 355, pp. 564–566.

    Article  CAS  Google Scholar 

  25. Macaya, R.F., Waldron, J.A., Beutel, B.A., Gao, H., Joeston, M.E., Yang, M., Patel, R., Bertelsen, A.H., and Cook, A.G., Biochemistry, 1995, vol. 34, pp. 4478–4492.

    Article  CAS  Google Scholar 

  26. Majka, J. and Speck, C., Adv. Biochem. Eng. Biotechnol., 2007, vol. 104, pp. 13–36.

    CAS  Google Scholar 

  27. Baerga-Ortiz, A., Bergqvist, S., Mandell, J.G., and Komives, E.A., Protein Sci., 2004, vol. 13, pp. 166–176.

    Article  CAS  Google Scholar 

  28. Crothers, D.M. and Metzger, H., Immunochemistry, 1972, vol. 9, pp. 341–357.

    Article  CAS  Google Scholar 

  29. Zhou, X.H., Biochemistry, 2001, vol. 40, pp. 15069–15073.

    Article  CAS  Google Scholar 

  30. Fredenburgh, J.C., Stafford, A.R.., and Weitz, J.I., J. Biol. Chem., 1997, vol. 272, pp. 25493–25499.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, Moscow, 119121, Russia

    S. Yu. Rakhmetova, S. P. Radko, O. V. Gnedenko, N. V. Bodoev, A. S. Ivanov & A. I. Archakov

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  1. S. Yu. Rakhmetova
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  2. S. P. Radko
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  3. O. V. Gnedenko
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  4. N. V. Bodoev
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  5. A. S. Ivanov
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  6. A. I. Archakov
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Correspondence to S. P. Radko.

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Original Russian Text © S.Yu. Rakhmetova, S.P. Radko, O.V. Gnedenko, N.V. Bodoev, A.S. Ivanov, A.I. Archakov, 2011, published in Biomeditsinskaya Khimiya.

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Rakhmetova, S.Y., Radko, S.P., Gnedenko, O.V. et al. Comparative thermodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct. Biochem. Moscow Suppl. Ser. B 5, 139–143 (2011). https://doi.org/10.1134/S1990750811020144

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  • DOI: https://doi.org/10.1134/S1990750811020144

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