Effect of ligand binding on functionality of DNA field-effect transistor

E. Sh. Mamasakhlisov ; A. P. Antonyan ; A. A. Akopyan

Proceedings of the Yerevan State University. Physical and mathematical sciences, Tome 51 (2017) no. 1, pp. 66-70.

Résumé

Motivated by the prospects of developing DNA field-effect transistors, as tools for a variety of application fields such as medical diagnostics, environmental pollutants monitoring, biological weapons defense, and taking into account that the efficiency of DNA-sensors depends on the precise prediction of experimental parameters responsible for thermostability of nucleic acids duplexes and specific times of formation of DNA duplexes, we analyze the factors influencing both the thermodynamics of hybridization and the stability of DNA–DNA and DNA–RNA duplexes. In this work the case of competition-free DNA hybridization is analyzed. It is shown how the intercalating ligands effectively increase the binding constant for the target sequences and thus affects the sensitivity of the DNA-chip.

Détail

Keywords: ligand binding, thermostability, hybridization, DNA-chip.

Bibliographie

[1] D. Ivnitski, I. Abdel-Hamid, P. Atanesov, E. Wilkins, “Biosensors for Detection of Pathogenic Bacteria”, Biosensors and Bioelectronics, 14 (1999), 599–624 | DOI

[2] J. Labuda, A.M.O. Brett, G. Evtugyn, M. Fojta, M. Mascini, M. Ozsoz, I. Palchetti, E. Palecek, J. Wang, “Electrochemical Nucleic Acid-Based Biosensors: Concepts, Terms and Methodology (IUPAC Technical Report)”, Pure Appl. Chem., 82 (2010), 1161–1187 | DOI

[3] J.H. Watterson, P.A.E. Piunno, U.J. Krull, “Towards the Optimization of an Optical DNA Sensor: Control of Selectivity Coefficients and Relative Surface Affinities”, Anal. Chem. Acta, 457 (2002), 29–38 | DOI

[4] A. Halperin, A. Buhot, E.B. Zhulina, “On the Hybridization Isotherms of DNA Microarrays: The Langmuir Model and Its Extensions”, J. Phys.: Condens. Matter., 18 (2006), S463–S490 | DOI

[5] G. Ananyan, A. Avetisyan, L. Aloyan, Ye. Dalyan, “The Stability of DNA–Porphyrin Complexes in the Presence of Mn(II) Ions”, Biophys. Chem., 156 (2011), 96–101 | DOI

[6] A.A. Ghazaryan Ye.B. Dalyan, S.G. Haroutiunian, A. Tikhomirova, T.V. Chalikian, “Thermodynamics of Interactions of Water-Soluble Porphyrins with RNA Duplexes”, J. Am. Chem. Soc., 128 (2006), 1914–1921 | DOI

[7] R.F. Pasternack, J.I. Goldsmith, S. Szep, E.J. Gibbs, “A Spectroscopic and Thermodynamic Study of Porphyrin/DNA Supramolecular Assemblies”, Biophys. J., 75 (1998), 1024–1031 | DOI

[8] P.O. Vardevanyan, A.P. Antonyan, L.A. Hambardzumyan, M.A. Shahinyan, A.T. Karapetian, “Thermodynamic Analysis of DNA Complexes with Methylene Blue, Ethidium Bromide and Hoechst 33258”, Biopolymers and Cell, 29:6 (2013), 515–520 | DOI

[9] D.M. Hinckley, G.S. Freeman, J.K. Whitmer, J.J. de Pablo, “An Experimentally-Informed Coarse-Grained 3-Site-Per-Nucleotide Model of DNA: Structure, Thermodynamics and Dynamics of Hybridization”, J. Chem. Phys., 139 (2013), 144903 | DOI

[10] D.M. Hinckley, J.P. Lequieu, J.J. de Pablo, “Coarse-Grained Modeling of DNA Oligomer Hybridization: Length, Sequence and Salt Effects”, J. Chem. Phys., 141 (2014), 35102 | DOI

[11] A.W. Peterson, R.J. Heaton, R.M. Georgiadis, “The Effect of Surface Probe Density on DNA Hybridization”, Nucl. Acids Res., 29 (2001), 5163–5168 | DOI

[12] A. Halperin, A. Buhot, E.B. Zhulina, “Sensitivity, Specificity and the Hybridization Isotherms of DNA Chips”, Biophys. J., 86 (2004), 718–730 | DOI

[13] M.F. Hagan, A.K. Chakraborty, “Hybridization Dynamics of Surface Immobilized DNA”, J. Chem. Phys., 120 (2004), 4958–4968 | DOI

[14] M.M.A. Seckar, W. Bloch, P.M.S. John, “Comparative Study of Sequence-Dependent Hybridization Kinetics in Solution and on Microspheres”, Nucleic Acids Res., 33 (2005), 366–375 | DOI

[15] N.V. Sorokin, D.Y. Yurasov, A.I. Cherepanov, J.M. Kozhekbaeva, V.R. Chechetkin, O.A. Gra, M.A. Livshits, T.V. Nasedkina, A.S. Zasedatelev, “Effects of External Transport on Discrimination between Perfect and Mismatch Duplexes on Gel-Based Oligonucleotide Microchips”, J. Biomol. Struct. Dyn., 24 (2007), 571–578 | DOI

[16] D. Irving, P. Gong, R. Levicky, “DNA Surface Hybridization: Comparison of Theory and Experiment”, J. Phys. Chem. B, 114 (2010), 7631–7640 | DOI

[17] T.J. Schmitt, T.A. Knotts, “IV. Thermodynamics of DNA Hybridization on Surfaces”, J. Chem. Phys., 134 (2011), 205105 | DOI

[18] S.M. Nelson, L.R. Ferguson, W.A. Denny, “Non-Covalent Ligand/DNA Interactions: Minor Groove Binding Agents”, Mutat. Res., 623 (2007), 24–40 | DOI

[19] V.V. Kostjukov, A.A.H. Santiago, F.R. Rodriquez, S.R. Castilla, J.A. Parkinson, M.P. Evsigneev, “Energetics of Ligand Binding to the DNA Minor Groove”, Phys. Chem. Chem. Phys., 14 (2012), 5588–5600 | DOI

[20] C.G. Ricci, P.A. Netz, “Docking Studies on DNA-Ligand Interactions: Building and Application of a Protocol to Identify the Binding Mode”, J. Chem. Inf. Model., 49 (2009), 1925–2935 | DOI

[21] C. Tanford, “Chemical Potential of Bound Ligand, an Important Parameter for Free Energy Transduction”, Proceed. Nat. Acad. USA, 78 (1981), 270–273 | DOI

[22] P. Pincus, “Colloid Stabilization with Grafted Polyelectrolytes”, Macromolecules, 24 (1991), 2912–2919 | DOI

[23] J. Wittmer, J.F. Joanny, “Charged Diblock Copolymers at Interfaces”, Macromolecules, 26 (1993), 2691–2697 | DOI

[24] O.V. Borisov, E.B. Zhulina, T.M. Birshtein, “Diagram of the States of a Grafted Polyelectrolyte Layer”, Macromolecules, 27 (1994), 4795–4803 | DOI

[25] I.Y. Wong, N.A. Melosh, “An Electrostatic Model for DNA Surface Hybridization”, Biophys. J., 98 (2010), 2954–2963 | DOI