Experimental and computational studies of thiolation of oligonucleotide towards its stabilizing on the surface of silver nanoparticles

Document Type : Research Article


Qaemshahr Branch, Islamic Azad University, Qaemshahr, I.R. IRAN


In this study, a specific sequence of oligonucleotides was attached to silver nanoparticles after thiolization in a saline medium. Investigation of this bond was performed using ultraviolet-visible spectroscopy (UV_Vis spectroscopy) by changing the silver nanoparticles' wavelength and thiol oligonucleotide attached to silver nanoparticles. Also, by bond transfer in polyacrylamide gel electrophoresis (PAGE) due to the increase in molecular weight after binding silver nanoparticles to a thiolated oligonucleotide, this bond's accuracy has been investigated. To find the bonds' electronic structure and stability, DFT studies have been performed using the Gaussian 09 program, aiming to see the optimal conditions for the binding of thiolated oligonucleotides to silver nanoparticles. In general, the binding of silver nanoparticles to thiolated oligonucleotides makes the specific adsorption of the sequence to the cell more targeted. Also, it increases the accuracy, precision, and specificity of adsorption. Calculations showed the absorption energy of -54.4 kJ / mol, the transfer of electric charge of 0.129 e after binding the thiolated oligonucleotide to silver nanoparticles, indicating a useful connection between them.


Main Subjects

[1]  Lundin K. E.,  Gissberg O., Smith C. I. E.,  Oligonucleotide Therapies: The Past and the Present, Hum. Gene. Ther., 26: 475-485 (2015).
[2] Yang J., Stolee J. A., Jiang H., Xiao L., Kiesman W. F., Antia F. D., Fillon Y. A., Ng A., Shi X., Solid-Phase Synthesis of Phosphorothioate Oligonucleotides Using Sulfurization Byproducts for in Situ Capping, J. Org. Chem., 83: 11577–11585 (2018).
[3] Condon D. E., Kennedy S. D., Mort B. C., Kierzek R., Yildirim I., Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics, J. Chem. Theory Comput., 11: 2729-2742 (2015).
[4]  Becke T. D.,  Ness  S.,   Sudhop S.,  Gaub H.  E.,  Hilleringmann  M., Schilling A. F., Clausen-Schaumann H., Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy, J. Vis. Exp., 138: p, 58167 (2018).
[5] Cardenas M., Barauskas J., Schillen K., Brennan J. L., Brust M., Nylander T., Thiol-Specific and Nonspecific Interactions between DNA and Gold Nanoparticles, Langmuir, 22: 3294-3299 (2006).
[6] Dougan J. A., Karlsson C., Smith W. E., Graham D., Enhanced Oligonucleotide–Nanoparticle Conjugate Stability using Thioctic Acid Modified Oligonucleotides, Nucleic Acids Res.,  35: 3668–3675 (2007).
[9] Pérez-Rentero S., Grijalvo S., Ferreira R., Eritja R., Synthesis of Oligonucleotides Carrying Thiol Groups Using a Simple Reagent Derived from Threonine, Molecules, 17:  10026-10045 (2012).
[10]  Shukla M. K., Dubey M., Zakar E., Leszczynski J., DFT Investigation of the Interaction of Gold Nanoclusters with Nucleic Acid Base Guanine and the Watson-Crick Guanine-Cytosine Base Pair, J. Phys. Chem. C., 113: 3960–3966 (2009).
[11]   de Freitas L. F.,  Varca G. H. C.,  Batista J. G. d. S., Lugão A. B.,  An Overview of the Synthesis of Gold Nanoparticles Using Radiation Technologies, J. Nanomater., 8: 939 (2018).
[12] Pramanik S., Chatterjee S., Saha A., Devi,  P. S., Kumar, G. S., Unraveling the Interaction of Silver Nanoparticles with Mammalia and Bacterial DNA, J. Phys. Chem. B., 120:  15313-5324 (2016).
[13] Rahban M., Divsalar A., Saboury A. A., Golestani A., Nanotoxicity and Spectroscopy Studies of Silver Nanoparticle: Calf Thymus DNA and K562 as Targets, J. Phys. Chem. C., 114:  5798-5803 (2010).
[14] Goodman C. M., Chari N. S., Han G., Hong R., Ghosh P., Rotello V. M., DNA-Binding by Functionalized Gold Nanoparticles: Mechanism and Structural Requirements, Chem. Biol. Drug Des., 67: 297-304 (2006).
[15] Sato K., Hosokawa K., Maeda M., Rapid Aggregation of Gold Nanoparticles Induced by Non-Cross-Linking DNA Hybridization, J. Am. Chem. Soc., 125: 8102–8103 (2003).
[16] Sato K., Hosokawa K., Maeda M., Non-Cross-Linking Gold Nanoparticle Aggregation as a Detection Method for Single-Base Substitutions, Nucleic Acids Res., 33:  e4 (2005).
[17] Sato K., Onoguchi M., Sato Y., Hosokawa K., Maeda M., Noncross-Linking Gold Nanoparticle Aggregation for Sensitive Detection of Single-Nucleotide Polymorphisms: Optimization of the Particle Diameter, Anal. Biochem., 350: 162–164 (2006).
[18] A.Shokuhi. Rad, S. M. Aghaei, E. Aali, M. Peyravi, A DFT Study of O2 and Cl2 Adsorption onto Al12N12 Fullerene- Like NanoclusterDiam. Relat. Mater, 77: 116-123 (2017).
[19] A. Shokuhi Rad, Y.  Modanlou Jouibary,  V. P.  Foukolaei, E. Binaeian, Study on the Surface Interaction of Furan with X12Y12 (X = B, Al, and Y = N, P) Semiconductors: DFT Calculations, Curr. Appl. Phys., 27: 316–322 (2016).
[20] Cardenas M., Barauskas J., Schillen K., Brennan J. L., Brust M., Nylander T., Thiol-Specific and Nonspecific Interactions between DNA and Gold Nanoparticles, Langmuir, 22: 3294-3299 (2006).
[23] Efcavitch J. W., “The Electrophoresis of Synthetic Oligonucleotide: In Gel Electrophoresis of Nucleic A CIDS- a Practical Approach”, Rickwood D. and Hames B. D., Eds. Oxford University Press: Oxford, (1990).
[24] Bischoff R., Coull J. M., Regnier F. E., Introduction of 5'-terminal Functional Groups into Synthetic Oligonucleotides for Selective Immobilization, Anal. Biochem., 164: 336-344 (1987).
[26] Shokuhi Rad A., Abedini E., Chemisorption of NO on Pt-Decorated Graphene as Modified Nanostructure Media: a First Principles Study, Appl. Surf. Sci., 360: 1041–1046 (2016).
[27] Shokuhi Rad A., Adsorption of C2H2 and C2H4 on Pt-Decorated Graphene Nanostructure: Ab-Initio Study, Synth. Met., 21: 115–120 (2016).
[28] Shokuhi Rad A., DFT Study of Nitrous Oxide Adsorption on the Surface of Pt-Decorated Graphene, Phys. Chem. Res., 4: 619-626 (2016).
[29] Gan W., Gonella G., Zhang M., Dai H. L., Communication: Reactions and Adsorption at the Surface of Silver Nanoparticles Probed by Second Harmonic Generation, J. Phys. Chem. B., 134: 3456-3465 (2011).
[30] Li S. S., “Semiconductor Physical Electronics”, 2nd ed., Springer, Berlin, (2006).
[31] Liu Y., Chen D., Zhang W., Zhang Y., Mobile DNA Tetrahedron on Ultra-Low Adsorption Lipid Membrane for Directional Control of Cell Sensing, Sensor. Actuat. B-Chem., 307: 127570 (2020).
[32] González-López A., Abedul M. T. F., “Laboratory Methods in Dynamic Electroanalysis, ELSEVIER, (2020).
[33] Mobed A., Hasanzadeh M., Shadjou N., Hassanpour S., Saadati A., Agazadeh M., Immobilization of ssDNA on the Surface of Silver Nanoparticles-Graphene Quantum Dots Modified by Gold Nanoparticles towards Bio Sensing of Microorganism, Microchem. J., 152: 104286 (2020).