Computer aided aptamer selection for fabrication of electrochemical sensor to detect Aflatoxin B₁

References

• Alonso, H., Bliznyuk, A. A., & Gready, J. E. (2006). Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews, 26(5), 531–568. https://doi.org/10.1002/med.20067
   PubMed Web of Science ®Google Scholar
• Anderson, A. C. (2003). The process of structure-based drug design. Chemistry & Biology, 10(9), 787–797. https://doi.org/10.1016/j.chembiol.2003.09.002
   PubMed Web of Science ®Google Scholar
• Antczak, M., Popenda, M., Zok, T., Sarzynska, J., Ratajczak, T., Tomczyk, K., Adamiak, R. W., & Szachniuk, M. (2016). New functionality of RNAComposer: Application to shape the axis of miR160 precursor structure. Acta Biochimica Polonica, 63(4), 737–744. https://doi.org/10.18388/abp.2016_1329
   PubMed Web of Science ®Google Scholar
• Bayat, P., Nosrati, R., Alibolandi, M., Rafatpanah, H., Abnous, K., Khedri, M., & Ramezani, M. (2018). SELEX Methods on the road to protein targeting with nucleic acid aptamers. Biochimie, 154, 132–155. https://doi.org/10.1016/j.biochi.2018.09.001
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J., P. M., Van Gunsteren, W. F., Di Nola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Cappel, D., Hall, M. L., Lenselink, E. B., Beuming, T., Qi, J., Bradner, J., & Sherman, W. (2016). Relative binding free energy calculations applied to protein homology models. Journal of Chemical Information and Modeling, 56(12), 2388–2400. https://doi.org/10.1021/acs.jcim.6b00362
   PubMed Web of Science ®Google Scholar
• Discovery Studio. (2008). Discovery studio. Accelrys [2.1].
   Google Scholar
• Dai, H., Wu, X., Duan, S., Li, Z., Zhang, Q., Shen, Y., Bi, J., Shu, Z., Xiao, A., Pi, F., Liu, X., & Wang, J. (2023). An electrochemical sensor based on curcumin-encapsulated zeolitic imidazolate framework-8 for the sensitive determination of aflatoxin B1 in grain products. Microchemical Journal, 191, 108852. https://doi.org/10.1016/j.microc.2023.108852
   Web of Science ®Google Scholar
• Davis, A. M., Teague, S. J., & Kleywegt, G. J. (2003). Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angewandte Chemie (International ed. in English), 42(24), 2718–2736. https://doi.org/10.1002/anie.200200539
   PubMed Web of Science ®Google Scholar
• Ellis, W. O., Smith, J. P., Simpson, B. K., Oldham, J. H., & Scott, P. M. (1991). Aflatoxins in food: Occurrence, biosynthesis, effects on organisms, detection, and methods of control. Critical Reviews in Food Science and Nutrition, 30(4), 403–439. https://doi.org/10.1080/10408399109527551
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Gizachew, D., Chang, C.-H., Szonyi, B., De La Torre, S., & Ting, W. E. (2019). Aflatoxin B1 (AFB1) production by Aspergillus flavus and Aspergillus parasiticus on ground Nyjer seeds: The effect of water activity and temperature. International Journal of Food Microbiology, 296, 8–13. https://doi.org/10.1016/j.ijfoodmicro.2019.02.017
   PubMed Web of Science ®Google Scholar
• Hansson, T., Oostenbrink, C., & Van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196. https://doi.org/10.1016/s0959-440x(02)00308-1
   PubMed Web of Science ®Google Scholar
• Heredia, F. (2020). DNA/Aptamer dataset. Mendeley Data, V1, https://doi.org/10.17632/76jgjbgndr.1
   Google Scholar
• Hess, B., Bekker, H., Berendsen, H., J., C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2015). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Klug, S. J., & Famulok, M. (1994). All you wanted to know about SELEX. Molecular Biology Reports, 20(2), 97–107. https://doi.org/10.1007/bf00996358
   PubMed Web of Science ®Google Scholar
• Kucukcakan, B., & Hayrulai-Musliu, Z. (2015). Challenging role of dietary aflatoxin B1 exposure and hepatitis B infection on risk of hepatocellular carcinoma. Open Access Macedonian Journal of Medical Sciences, 3(2), 363–369. https://doi.org/10.3889/oamjms.2015.032
   PubMedGoogle Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Kurita, T. (2019). Principal component analysis (PCA). Computer Vision: A Reference Guide, 1–4.
   Google Scholar
• Law, S. M. (2020). Modevectors. https://pymolwiki.org/index.php/Modevectors.
   Google Scholar
• Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
   PubMed Web of Science ®Google Scholar
• M., James, A., Teemu, M., Roland, S., Szilard, P., Jeremy, C. S., Berk, H., & Erik, L. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Markov, K., Pleadin, J., Bevardi, M., Vahčić, N., Sokolić-Mihalak, D., & Frece, J. (2013). Natural occurrence of aflatoxin B1, ochratoxin A and citrinin in croatian fermented meat products. Food Control. 34(2), 312–317. https://doi.org/10.1016/j.foodcont.2013.05.002
   Web of Science ®Google Scholar
• Mayer, G. (2009). The chemical biology of aptamers. Angewandte Chemie (International ed. in English), 48(15), 2672–2689. https://doi.org/10.1002/anie.200804643
   PubMed Web of Science ®Google Scholar
• Meng, H.-M., Liu, H., Kuai, H., Peng, R., Mo, L., & Zhang, X. B. (2016). Aptamer-integrated DNA nanostructures for biosensing, bioimaging and cancer therapy. Chemical Society Reviews, 45(9), 2583–2602. https://doi.org/10.1039/c5cs00645g
   PubMed Web of Science ®Google Scholar
• Musheev, M. U., & Krylov, S. N. (2006). Selection of aptamers by systematic evolution of ligands by exponential enrichment: Addressing the polymerase chain reaction issue. Analytica Chimica Acta, 564(1), 91–96. https://doi.org/10.1016/j.aca.2005.09.069
   PubMed Web of Science ®Google Scholar
• Neme, K., & Mohammed, A. (2017). Mycotoxin occurrence in grains and the role of postharvest management as a mitigation strategies. A review. Food Control. 78, 412–425. https://doi.org/10.1016/j.foodcont.2017.03.012
   Web of Science ®Google Scholar
• Ou, G., Zhao, A., Liao, H., Zhang, Z., & Xiao, F. (2023). Au nanopartics decorated urchin-like Bi2S3 on graphene wrapped carbon fiber microelectrode: towards electrochemical immunosensor for sensitive determination of aflatoxin B1. Journal of Electroanalytical Chemistry, 929, 117124. https://doi.org/10.1016/j.jelechem.2022.117124
   Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A., & Orozco, M. (2007). Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophysical Journal, 92(11), 3817–3829. https://doi.org/10.1529/biophysj.106.097782
   PubMed Web of Science ®Google Scholar
• Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E. K., Blazewicz, J., & Adamiak, R. W. (2010). RNA FRABASE 2.0: An advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 11(1), 1-12. https://doi.org/10.1186/1471-2105-11-231
   PubMedGoogle Scholar
• Rostkowski, M., Olsson, M. H., Søndergaard, C. R., & Jensen, J. H. (2011). Graphical analysis of pH-dependent properties of proteins predicted Using PROPKA. BMC Structural Biology, 11(1), 1-6. https://doi.org/10.1186/1472-6807-11-6
   PubMedGoogle Scholar
• Schrödinger Release. (2019). 4: LigPrep. Schrödinger, LLC, New York, NY.
   Google Scholar
• Schrödinger SiteMap. (2019). LLC. New York, NY.
   Google Scholar
• Serrano, A. F. R., & Hsing, I. M. (2022). Prediction of aptamer–small-molecule interactions using metastable states from multiple independent molecular dynamics simulations. Journal of Chemical Information and Modeling, 62(19), 4799–4809. https://doi.org/10.1021/acs.jcim.2c00734
   PubMed Web of Science ®Google Scholar
• Sharma, M., Bulusu, G., & Mitra, A. (2009). MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA (New York, N.Y.), 15(9), 1673–1692. https://doi.org/10.1261/rna.1675809
   PubMed Web of Science ®Google Scholar
• Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: A software program for pK a prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/s10822-007-9133-z
   PubMed Web of Science ®Google Scholar
• Singh, A. K., Dhiman, T. K., V S, L. G. B., & Solanki, P. R. (2021). Dimanganese trioxide (Mn2O3) based label-free electrochemical biosensor for detection of aflatoxin-B1. Bioelectrochemistry (Amsterdam, Netherlands), 137, 107684. https://doi.org/10.1016/j.bioelechem.2020.107684
   PubMed Web of Science ®Google Scholar
• Sousa da Silva, A., & W., Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Sun, X., Sun, J., Ye, Y., Ji, J., Sheng, L., Yang, D., & Sun, X. (2023). Metabolic pathway-based self-assembled Au@MXene liver microsome electrochemical biosensor for rapid screening of aflatoxin B1. Bioelectrochemistry (Amsterdam, Netherlands), 151, 108378. https://doi.org/10.1016/j.bioelechem.2023.108378
   PubMed Web of Science ®Google Scholar
• Ulrich, E., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Van Egmond, H. P., Schothorst, R. C., & Jonker, M. A. (2007). regulations relating to mycotoxins in food. Analytical and Bioanalytical Chemistry, 389(1), 147–157. https://doi.org/10.1007/s00216-007-1317-9
   PubMed Web of Science ®Google Scholar
• Wang, T., Chen, C., Larcher, L. M., Barrero, R. A., & Veedu, R. N. (2019). Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnology Advances, 37(1), 28–50. https://doi.org/10.1016/j.biotechadv.2018.11.001
   PubMed Web of Science ®Google Scholar
• Wang, C., Li, Y., & Zhao, Q. (2020). A competitive electrochemical aptamer-based method for aflatoxin B1 detection with signal-off response. Analytical Methods, 12(5), 646–650. https://doi.org/10.1039/C9AY02276G
   Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. W., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Xie, M., Zhao, F., Zhang, Y., Xiong, Y., & Han, S. (2022). Recent advances in aptamer-based optical and electrochemical biosensors for detection of pesticides and veterinary drugs. Food Control. 131, 108399. https://doi.org/10.1016/j.foodcont.2021.108399
   Web of Science ®Google Scholar
• Yan, J., Xiong, H., Cai, S., Wen, N., He, Q., Liu, Y., Peng, D., & Liu, Z. (2019). Advances in aptamer screening technologies. Talanta, 200, 124–144. https://doi.org/10.1016/j.talanta.2019.03.015
   PubMed Web of Science ®Google Scholar
• Yüce, M., Ullah, N., & Budak, H. (2015). Trends in Aptamer selection methods and applications. The Analyst, 140(16), 5379–5399. https://doi.org/10.1039/c5an00954e
   PubMed Web of Science ®Google Scholar
• Zhang, J., Gao, L., Chai, B., Zhao, J., Yang, Z., & Yang, K. (2022). Electrochemical aptasensor for aflatoxin B1 detection using cerium dioxide nanoparticle supported on iron-porphyrinic metal–organic framework as signal probes. Microchemical Journal, 181, 107716. https://doi.org/10.1016/j.microc.2022.107716
   Web of Science ®Google Scholar
• Zhang, H., Ye, S., Huang, L., Fan, S., Mao, W., Hu, Y., Yu, Y., & Fu, F. (2023). An electrochemical biosensor for the detection of aflatoxin b1 based on the specific aptamer and HCR biological magnification. Analytical Methods: Advancing Methods and Applications, 15(1), 99–108. https://doi.org/10.1039/d2ay01682f
   Web of Science ®Google Scholar
• Zhao, J., Cao, Y., & Zhang, L. (2020). Exploring the computational methods for protein-ligand binding site prediction. Computational and Structural Biotechnology Journal, 18, 417–426. https://doi.org/10.1016/j.csbj.2020.02.008
   PubMed Web of Science ®Google Scholar
• Zhong, T., Li, S., Li, X., JiYe, Y., Mo, Y., Chen, L., Zhang, Z., Wu, H., Li, M., & Luo, Q. (2022). A label-free electrochemical aptasensor based on aunps-loaded zeolitic imidazolate framework-8 for sensitive determination of Aflatoxin B1. Food Chemistry, 384, 132495. https://doi.org/10.1016/j.foodchem.2022.132495
   PubMed Web of Science ®Google Scholar
• Zuker, M. (2000). Calculating nucleic acid secondary structure. Current Opinion in Structural Biology, 10(3), 303–310. https://doi.org/10.1016/s0959-440x(00)00088-9
   PubMed Web of Science ®Google Scholar
• Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31(13), 3406–3415. https://doi.org/10.1093/nar/gkg595
   PubMed Web of Science ®Google Scholar