A Network of Networks to Reproduce the Electrical Features of an Aptamer-ligand Complex - What an Electrical Network Tells about Affinity

Eleonora Alfinito, Rosella Cataldo, Lino Reggiani

2017

Abstract

The increasing interest in the production and selection of aptamers for therapeutic and diagnostic applications yields many studies in recent years. Most of them investigated the production techniques, usually performed in vitro, but also the possibility of an in silico selection. Due to their specific ability of target-inhibition, some aptamers are under clinical trials, and some other were just patented by several pharmaceutical companies. However, the mechanism of aptamer-ligand formation is not completely understood. In this paper we explore the possibility to describe some topological and electrical features of the aptamer TBA alone and complexed with thrombin, its specific ligand, by using a network consisting of two different networks. The results are quite intriguing, confirming some conjectures about the different role of two cations, i.e. Na+ and K+, in stabilizing the compound. Furthermore, this study suggests the use of resistance measurements to discriminate among different affinities.

References

  1. Akimov, V., Alfinito, E., Bausells, J., Benilova, I., Paramo, I.C., Errachid, A., Ferrari, G., Fumagalli, L., Gomila, G., Grosclaude, J. and Hou, Y., 2008. Nanobiosensors based on individual olfactory receptors. Analog Integrated Circuits and Signal Processing, 57(3), pp.197-203.
  2. Alfinito, E., Pennetta, C. and Reggiani, L., 2009. Topological change and impedance spectrum of rat olfactory receptor I7: A comparative analysis with bovine rhodopsin and bacteriorhodopsin. Journal of Applied Physics, 105(8), p.084703.
  3. Alfinito, E., Pennetta, C. and Reggiani, L., 2010. Olfactory receptor-based smell nanobiosensors: an overview of theoretical and experimental results. Sensors and Actuators B: Chemical, 146(2), pp.554-558.
  4. Alfinito E., Pousset J., and Reggiani L.,2015 Proteotronics: Development of Protein-Based Electronics. CRC Press.
  5. Alfinito, E. and Reggiani, L., 2016. Current-voltage characteristics of seven-helix proteins from a cubic array of amino acids. Physical Review E, 93(6), p.062401.
  6. Alfinito, E., Reggiani, L., Cataldo, R., De Nunzio, G., Giotta, L. and Guascito, M.R., 2017. Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors. Nanotechnology, 28(6), p.065502.
  7. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E., 2000. The protein data bank. Nucleic acids research, 28(1), pp.235-242.
  8. De Arcangelis, L., Redner, S. and Coniglio, A., 1985. Anomalous voltage distribution of random resistor networks and a new model for the backbone at the percolation threshold. Physical Review B, 31(7), p.4725.
  9. Du, X., Li, Y., Xia, Y. L., Ai, S. M., Liang, J., Sang, P., Ji, X.-L. and Liu, S. Q., 2016. Insights into Protein-Ligand interactions: mechanisms, models, and methods. International journal of molecular sciences, 17(2), pp.144-177.
  10. Iliuk, A.B., Hu, L. and Tao, W.A., 2011. Aptamer in bioanalytical applications. Analytical chemistry. 83(12), pp. 4440-52.
  11. Ellington, A.D. and Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature, 346, pp.818-822.
  12. Jo, H. and Ban, C., 2016. Aptamer-nanoparticle complexes as powerful diagnostic and therapeutic tools. Experimental & Molecular Medicine. 48(5). e230.
  13. Kobilka, B.K. and Deupi, X., 2007. Conformational complexity of G-protein-coupled receptors. Trends in pharmacological sciences, 28(8), pp.397-406.
  14. Ni, X., Castanares, M., Mukherjee, A., Lupold, SE., 2011. Nucleic acid aptamers: clinical applications and promising new horizons. Current medicinal chemistry. 18(27), p.4206.
  15. Ohshiro, T., Matsubara, K., Tsutsui, M., Furuhashi, M., Taniguchi, M. and Kawai, T., 2012. Single-molecule electrical random resequencing of DNA and RNA. Scientific reports, 2, p.501.
  16. Oliphant, AR, Brandl, C.J. and Struhl, K., 1989. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 proteins. Mol. Cell. Biol. 9, pp. 2944-2949.
  17. Onuchic, J.N., Luthey-Schulten, Z. and Wolynes, P.G., 1997. Theory of protein folding: the energy landscape perspective. Annual review of physical chemistry, 48(1), pp.545-600.
  18. Pennetta, C., Alfinito, E., Reggiani, L., Fantini, F., DeMunari, I. and Scorzoni, A., 2004. Biased resistor network model for electromigration failure and related phenomena in metallic lines. Physical Review B, 70(17), p.174305.
  19. Russo-Krauss, I., Merlino, A., Randazzo, A., Novellino, E., Mazzarella, L. and Sica, F.,2012. High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Nucleic Acids Research. 40, gks 512.
  20. Schultze, P., Macaya, R.F. and Feigon, J., 1994. Threedimension al solution structure of the thrombin-binding DNA aptamer d (GGTTGGTGTGGTTGG). Journal of molecular biology. 235, pp. 1532-1547.
  21. Šponer, J., Leszczynski, J. and Hobza, P ., 2001. Electronic Properties, Hydrogen Bonding, Stacking,and Cation Binding of DNA and RNA Bases. Nucleic Acid Sci., (61), pp.3-31.
  22. Sun, H., Zhu, X., Lu, P. Y., Rosato, R.R., Tan, W. and Zu, Y., 2014. Oligonucleotide aptamers: new tools for targeted cancer therapy, Molecular Therapy-Nucleic Acids 3, e182.
  23. Tuerk, C. and Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249, pp.505-510.
  24. Yüce M., Ullah N. and Budak H., 2015. Trends in aptamer selection methods and applications. Analyst., 140(16) , pp.5379-99
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Paper Citation


in Harvard Style

Alfinito E., Cataldo R. and Reggiani L. (2017). A Network of Networks to Reproduce the Electrical Features of an Aptamer-ligand Complex - What an Electrical Network Tells about Affinity . In Proceedings of the 2nd International Conference on Complexity, Future Information Systems and Risk - Volume 1: COMPLEXIS, ISBN 978-989-758-244-8, pages 62-69. DOI: 10.5220/0006361000620069


in Bibtex Style

@conference{complexis17,
author={Eleonora Alfinito and Rosella Cataldo and Lino Reggiani},
title={A Network of Networks to Reproduce the Electrical Features of an Aptamer-ligand Complex - What an Electrical Network Tells about Affinity},
booktitle={Proceedings of the 2nd International Conference on Complexity, Future Information Systems and Risk - Volume 1: COMPLEXIS,},
year={2017},
pages={62-69},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006361000620069},
isbn={978-989-758-244-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 2nd International Conference on Complexity, Future Information Systems and Risk - Volume 1: COMPLEXIS,
TI - A Network of Networks to Reproduce the Electrical Features of an Aptamer-ligand Complex - What an Electrical Network Tells about Affinity
SN - 978-989-758-244-8
AU - Alfinito E.
AU - Cataldo R.
AU - Reggiani L.
PY - 2017
SP - 62
EP - 69
DO - 10.5220/0006361000620069