Influence of adsorption of ligands on output signal of DNA-biosensor
Abstract
Background: The important advantage of the application of DNA-biosensors as compared to traditional molecular-biological methods is connected to the miniaturization of the studied samples and analyzers, which significantly decreases the analysis value as well as the time of its realization. Though, the miniaturization inevitably results in both decreasing the DNA-biosensor output signal value and increasing the noise signal level. That is why the studies devoted to the influence of different factors, particularly ligands on the output signal value and noise level of DNA-biosensors become actual tasks.
Objectives: To theoretically calculate the dependence of DNA-biosensor output signal on the concentration of ligands in the solution. To study the characteristic peculiarities of DNA-biosensor output signal.
Theory: The model, in the frame of which the theoretical calculations were carried out, is described here. There is an underlayer, on which the single-stranded molecules of DNA-targets are immobilized. The underlayer borders on the solution, where there are both single-stranded DNA molecules complementary to DNA-targets and ligands able to be adsorbed on DNA duplexes. The value of output signal DNA-biosensor is proportional to the number of DNA duplexes. Adsorption of ligands on DNA duplexes results in changing the output signal of DNA-biosensor. It is accepted that the adsorbed ligand enhances DNA-biosensor output signal. Taking into account that the formation and decomposition of the complex of ligands with DNA duplex occur in a random way, the number of bound ligands to DNA duplexes will change randomly as well, which will inevitably result in DNA-biosensor output signal fluctuations.
Results: It has been shown that along with increasing the concentration of ligands in the solution the output signal of DNA-biosensors rises monotonously and the relaxation time of the output signal decreases. It was also shown that the output signal dispersion of DNA-biosensor increases at first with the concentration increase of ligands in the solution, then passing through the maximum decreases and tends to zero at the further concentration enhancement of ligands in the solution.
Conclusions: The obtained data can be applied practically in the preparation of micro DNA-biosensors and analysis of the measurement results.
Downloads
References
Mullen, W.H., & Evans, G.P. (1988). Biosensors in laboratory. Int. Labmate, 13, 15-17.
Turner, E., Carube, I., & Wilson, J. (1992). Biosensory, osnovy i prilozhenija. Moskow: Mir. (In Russian).
Drummond, T.G., Hill, M.G., & Barton, J. (2003). Electrochemical DNA sensors. Nat. biotechnol., 21(10), 1192-1199.
Domany, E. (2005). Analysis of DNA-chip and antigen-chip data: studies of cancer, stem cells and autoimmune diseases. Comp. Phys. Commun., 169, 183-187.
Yevdokimov, Y.M. (1998). Biosenors Based on Single-and Double-Stranded Linear DNA Molecules. Sensory systems, 12(1), 1-13.
Vardevanyan, P.O., Antonyan, A.P., Parsadanyan, M.A., Shahinyan, M.A., & Melkonyan, G.A. (2015). Behavior of ethidium bromide-Hoechst 33258-DNA and ethidium bromide-methylene blue-DNA triple systems by means of UV melting. International Journal of Spectroscopy, 2015, 1-5. doi: 10.1155/2015/586231.
Karapetian, A.T., Grigoryan, Z.A., Mаmasakhlisov, Y.S., Minasyants, M.V., & Vardevanyan, P.O. (2016). Theoretical treatment of helix-coil transition of complexes DNA with two different ligands having different binding parameters. J. Biomol. Struct. Dyn., 34(1), 201-205.
Vardevanyan, P.O., Antonyan, A.P., Parsadanyan, M.A., Torosyan, M.A., & Karapetian, A.T. (2016). Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters. J. Biomol. Struct. Dyn., 34(7), 1377-1382.
Vardevanyan, P.O., Antonyan, A.P., Parsadanyan, M.A., Shahinyan, M.A., & Sahakyan, V.G. (2017). Peculiarities of interaction of synthetic polyribonucleotide poly(rA)-poly(rU) with some intercalators. J. Biomol. Struct. Dyn., 36(14), 3607-3613. doi: 10.1080/07391102.2017.1402708
Mamasakhlisov, Y., Sngryan, H., Tonoyan, Sh., Hakobyan, A., & Vardevanyan, P. (2018). The double-stranded DNA stability in presence of a flexible polymer. J. Biomol. Struct. Dyn., Published online: 23 Apr 2018. DOI: 10.1080/07391102.2018.1459320.
Tonoyan, Sh.A., Hakobyan, A.A., Andreassian, A.K., Morozov, V.F., & Mamasakhlisov, Y.Sh. (2018). Sensitivity of DNA sensors in the presence of charged ligands. Journal of Contemporary Physics, 53(2), 179-186.
Evtjugin, G.A., Budnikov, G.K., Porfir'eva, A.V. (2008). Jelektrohimicheskie DNK-sensory dlja opredelenija biologicheski aktivnyh nizkomolekuljarnyh soedinenij. Rossijskij himicheskij zhurnal (Zhurnal rossijskogo himicheskogo obshhestva im. D.I. Mendeleeva), LII(2), 66-79. (In Russian)
Cai, H., Cao, X., Jiang, Y., He, P., & Fang Y. (2003). Carbon nanotube-ehanced electrochemical DNA biosensor for DNA hybridization detection. Anal. Bioanal. Chem., 375(2), 287-235.
R. Kubo. (1967). Statisticheskaja mehanika. M.: Mir. (In Russian)
Arakelyan, V., Babayan, Yu., & Potikyan, G. (2000). Determination of constant rates of adsorption of ligand on DNA by analysis of correlation functions. J. Biomol. Struct. Dyn., 18(2), 231-235.
Arakelyan, V.B., Babayan, S.Yu., Tairyan, V.I., Arakelyan, A.V., Parsadanyan, M.A., & Vardevanyan, P.O. (2006). Kinetics of Ligand Binding to Nucleic Acids. J. Biomol. Struct. Dyn., 23(4), 479-483.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
