The Effect of Carbon Nanotube on Improving Catalytic G-quadruplex Sensing Properties

محورهای موضوعی : پلیمر

Fahimeh Otovat ¹ , Mohammad Reza Bozorgmehr ² , Ali Mahmoudi ³ , Ali Morsali ⁴

1 - Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
2 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
3 - Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
4 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

تاریخ دریافت : 1402/09/22 تاریخ پذیرش : 1402/09/22 تاریخ انتشار : 1402/07/09

کلید واژه:

چکیده مقاله :

In the use of G-quadruplex as DNAzyme, the background signal corresponding to Hemin is high.Therefore, it limits the application of DNAzyme. If carbon nanotubes are added to the system containing G-quadruplex and Hemin, this problem will be solved. However, the mechanism of the nanotube effect on DNAzyme is not known. In this work, molecular dynamics simulation was used to clarify this mechanism. The interaction between G-quadruplex and Hemin was simulated in the presence and absence of carbon nanotubes. The calculated distance between the center of mass ofG-quadruplex and Hemin during the simulation time shows that the nanotube increases the affinity of hemin to G-quadruplex. Also, the calculation of the conformational factor of the G-quadruplex residues shows that Hemin is bonded to the G-quadruplex from the top and side. The obtained results are in good agreement with the available experimental evidence.

منابع و مأخذ:

1. Torabi S, Jamshidi M, Amooshahi P, Mehrdadian M, Khazalpour S. Transition metal-catalyzed electrochemical processes for C–C bond formation. New Journal of Chemistry. 2020;44(36):15321-36.


2. Parshall GW, Putscher RE. Organometallic chemistry and catalysis in industry. Journal of Chemical Education. 1986;63(3):189.


3. Keatinge-Clay AT, Shelat AA, Savage DF, Tsai S-C, Miercke LJ, O'Connell III JD, et al. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA: ACP transacylase. Structure. 2003;11(2):147-54.


4. Hughes G, Lewis JC. Introduction: biocatalysis in industry. 2018;118(1):1-3.


5. Pyser JB, Chakrabarty S, Romero EO, Narayan AR. State-of-the-art biocatalysis. ACS Central Science. 2021;7(7):1105-16.


6. Souza PMd, Magalhães PdO. Application of microbial α-amylase in industry-A review. Brazilian journal of microbiology. 2010;41:850-61.


7. Ray A. Application of lipase in industry. Asian Journal of Pharmacy and technology. 2012;2(2):33-7.


8. Kirk O, Borchert TV, Fuglsang CC. Industrial enzyme applications. Current opinion in biotechnology. 2002;13(4):345-51.


9. Bell EL, Finnigan W, France SP, Green AP, Hayes MA, Hepworth LJ, et al. Biocatalysis. Nature Reviews Methods Primers. 2021;1(1):1-21.


10. Kazlauskas RJ. Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. Current opinion in chemical biology. 2000;4(1):81-8.


11. Sheldon RA, Brady D. The limits to biocatalysis: pushing the envelope. Chemical Communications. 2018;54(48):6088-104.


12. Morshed MN, Behary N, Bouazizi N, Guan J, Nierstrasz VA. An overview on biocatalysts immobilization on textiles: Preparation, progress and application in wastewater treatment. Chemosphere. 2021;279:130481.


13. Willner I, Shlyahovsky B, Zayats M, Willner B. DNAzymes for sensing, nanobiotechnology and logic gate applications. Chemical Society Reviews. 2008;37(6):1153-65.


14. McConnell EM, Cozma I, Mou Q, Brennan JD, Lu Y, Li Y. Biosensing with DNAzymes. Chemical Society Reviews. 2021.


15. Zhao M, Wang M, Zhang X, Zhu Y, Cao J, She Y, et al. Recognition elements based on the molecular biological techniques for detecting pesticides in food: a review. Critical Reviews in Food Science and Nutrition. 2021:1-24.


16. Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chemical Society Reviews. 2022.


17. Yang H, Zhou Y, Liu J. G-quadruplex DNA for construction of biosensors. TrAC Trends in Analytical Chemistry. 2020;132:116060.


18. Liu J, Cao Z, Lu Y. Functional nucleic acid sensors. Chemical reviews. 2009;109(5):1948-98.


19. Kong D-M, Xu J, Shen H-X. Positive effects of ATP on G-quadruplex-hemin DNAzyme-mediated reactions. Analytical chemistry. 2010;82(14):6148-53.


20. Stadlbauer P, Islam B, Otyepka M, Chen J, Monchaud D, Zhou J, et al. Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding. Journal of Chemical Theory and Computation. 2021;17(3):1883-99.


21. Li D, Ling S, Cheng X, Yang Z, Lv B. Development of a DNAzyme-based colorimetric biosensor assay for dual detection of Cd2+ and Hg2+. Analytical and Bioanalytical Chemistry. 2021;413(28):7081-91.


22. Britz DA, Khlobystov AN. Noncovalent interactions of molecules with single walled carbon nanotubes. Chemical Society Reviews. 2006;35(7):637-59.


23. Khan S, Burciu B, Filipe CD, Li Y, Dellinger K, Didar TF. DNAzyme-based biosensors: Immobilization strategies, applications, and future prospective. Acs Nano. 2021;15(9):13943-69.


24. Wang H, Zhang F, Wang Y, Shi F, Luo Q, Zheng S, et al. DNAzyme-Amplified Electrochemical Biosensor Coupled with pH Meter for Ca2+ Determination at Variable pH Environments. Nanomaterials. 2021;12(1):4.


25. Parkinson GN, Lee MP, Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 2002;417(6891):876-80.


26. Price DJ, Brooks III CL. A modified TIP3P water potential for simulation with Ewald summation. The Journal of chemical physics. 2004;121(20):10096-103.


27. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. Journal of computational chemistry. 2005;26(16):1701-18.


28. Macke TJ, Svrcek-Seiler W, Brown RA, Kolossváry I, Bomble YJ, Case DA, et al. AmberTools Users’ Manual. Ver; 2010.


29. Bazoobandi M, Bozorgmehr MR, Mahmoudi A, Morsali A. The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint. Combinatorial Chemistry & High Throughput Screening. 2019;22(8):546-54.


30. Gordon MS, Schmidt MW. Advances in electronic structure theory: GAMESS a decade later. Theory and applications of computational chemistry: Elsevier; 2005. p. 1167-89.


31. Imbalzano G, Zhuang Y, Kapil V, Rossi K, Engel EA, Grasselli F, et al. Uncertainty estimation for molecular dynamics and sampling. The Journal of Chemical Physics. 2021;154(7):074102.


32. Hess B, Bekker H, Berendsen HJ, Fraaije JG. LINCS: a linear constraint solver for molecular simulations. Journal of computational chemistry. 1997;18(12):1463-72.


33. Nabavi M, Housaindokht MR, Bozorgmehr MR, Sadeghi A. Theoretical design and experimental study of new aptamers with the enhanced binding affinity relying on colorimetric assay for tetracycline detection. Journal of Molecular Liquids. 2022;349:118196.


34. Miyamoto S, Kollman PA. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of computational chemistry. 1992;13(8):952-62.


35. Sargsyan K, Grauffel C, Lim C. How molecular size impacts RMSD applications in molecular dynamics simulations. Journal of chemical theory and computation. 2017;13(4):1518-24.


36. Housaindokht MR, Bozorgmehr MR, Bahrololoom M. Analysis of ligand binding to proteins using molecular dynamics simulations. Journal of theoretical biology. 2008;254(2):294-300.


37. Zhang Y, Li B. Reducing background signal of G-quadruplex–hemin DNAzyme sensing platform by single-walled carbon nanotubes. Biosensors and Bioelectronics. 2011;27(1):137-40.


38. Li D, Li C, Liang A, Jiang Z. SERS and fluorescence dual-mode sensing trace hemin and K+ based on G-quarplex/hemin DNAzyme catalytic amplification. Sensors and Actuators B: Chemical. 2019;297:126799.


39. Selvaraj C, BTV S, Xiong H. Developing Trends in DNA Biosensor and Their Applications. Metal, Metal-Oxides and Metal Sulfides for Batteries, Fuel Cells, Solar Cells, Photocatalysis and Health Sensors: Springer; 2021. p. 245-84.