Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach

References

• Ahmad, N. A., Zulkifli, R. M., Hussin, H., & Nadri, M. H. (2021). In silico approach for Post-SELEX DNA aptamers: A mini-review. Journal of Molecular Graphics & Modelling, 105, 107872. https://doi.org/10.1016/j.jmgm.2021.107872
   PubMed Web of Science ®Google Scholar
• Alhadrami, H. A., Chinnappan, R., Eissa, S., Rahamn, A. A., & Zourob, M. (2017). High affinity truncated DNA aptamers for the development of fluorescence based progesterone biosensors. Analytical Biochemistry, 525, 78–84. https://doi.org/10.1016/j.ab.2017.02.014
   PubMed Web of Science ®Google Scholar
• Aubin-Tam, M.-E., Appleyard, D. C., Ferrari, E., Garbin, V., Fadiran, O. O., Kunkel, J., & Lang, M. J. (2011). Adhesion through single peptide aptamers. The Journal of Physical Chemistry. A, 115(16), 3657–3664. https://doi.org/10.1021/jp1031493
   PubMed Web of Science ®Google Scholar
• Baptista, L. A., & Netz, P. A. (2019). Single molecule force spectroscopy of a streptomycin-binding RNA aptamer: An out-of-equilibrium molecular dynamics study. The Journal of Chemical Physics, 151(19), 195102.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., Postma, Jv., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Blank, M., & Blind, M. (2005). Aptamers as tools for target validation. Current Opinion in Chemical Biology, 9(4), 336–342. https://doi.org/10.1016/j.cbpa.2005.06.011
   PubMed Web of Science ®Google Scholar
• Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., & Toole, J. J. (1992). Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355(6360), 564–566. https://doi.org/10.1038/355564a0
   PubMed Web of Science ®Google Scholar
• Bunka, D. H., & Stockley, P. G. (2006). Aptamers come of age - at last. Nature Reviews. Microbiology, 4(8), 588–596. https://doi.org/10.1038/nrmicro1458
   PubMed Web of Science ®Google Scholar
• Case, D. A., Belfon, K., Ben-Shalom, I., Brozell, S. R., Cerutti, D., Cheatham, T., Cruzeiro, V. W. D., Darden, T., Duke, R. E., & Giambasu, G., Amber 2020 (2020).
   Google Scholar
• Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr, Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Chen, Z., Hu, L., Zhang, B.-T., Lu, A., Wang, Y., Yu, Y., & Zhang, G. (2021). Artificial intelligence in aptamer–target binding prediction. International Journal of Molecular Sciences, 22(7), 3605. https://doi.org/10.3390/ijms22073605
   PubMed Web of Science ®Google Scholar
• Da Silva, A. W. S., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC Reearch Notes, 5, 1–8.
   PubMedGoogle Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• de Oliveira, R. C., Paschoal, J. A. R., Sismotto, M., da Silva Airoldi, F. P., & Reyes Reyes, F. G. (2009). Development and validation of an LC-APCI-MS-MS analytical method for the determination of streptomycin and dihydrostreptomycin residues in milk. Journal of Chromatographic Science, 47(9), 756–761. https://doi.org/10.1093/chromsci/47.9.756
   PubMed Web of Science ®Google Scholar
• Dua, P., Kim, S., & Lee, D-k. (2011). Nucleic acid aptamers targeting cell-surface proteins. Methods (San Diego, Calif.), 54(2), 215–225. https://doi.org/10.1016/j.ymeth.2011.02.002
   PubMed Web of Science ®Google Scholar
• Ellington, A. D., & Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature, 346(6287), 818–822. https://doi.org/10.1038/346818a0
   PubMed Web of Science ®Google Scholar
• Emrani, A. S., Danesh, N. M., Lavaee, P., Ramezani, M., Abnous, K., & Taghdisi, S. M. (2016). Colorimetric and fluorescence quenching aptasensors for detection of streptomycin in blood serum and milk based on double-stranded DNA and gold nanoparticles. Food Chemistry, 190, 115–121. https://doi.org/10.1016/j.foodchem.2015.05.079
   PubMed Web of Science ®Google Scholar
• Flores, S. C., Sherman, M., Bruns, C. M., Eastman, P., & Altman, R. B. (2011). Fast flexible modeling of RNA structure using internal coordinates. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(5), 1247–1257. https://doi.org/10.1109/TCBB.2010.104
   PubMed Web of Science ®Google Scholar
• Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. (2009). GAUSSIAN09. Gaussian Inc.
   Google Scholar
• Ghanbari, K., & Roushani, M. (2018). A novel electrochemical aptasensor for highly sensitive and quantitative detection of the streptomycin antibiotic. Bioelectrochemistry (Amsterdam, Netherlands), 120, 43–48. https://doi.org/10.1016/j.bioelechem.2017.11.006
   PubMed Web of Science ®Google Scholar
• Granja, R. H., Niño, A. M. M., Zucchetti, R. A., Niño, R. E. M., Patel, R., & Salerno, A. G. (2009). Determination of streptomycin residues in honey by liquid chromatography-tandem mass spectrometry. Analytica Chimica Acta, 637(1–2), 64–67. https://doi.org/10.1016/j.aca.2009.01.006
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (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
• Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jayasena, S. D. (1999). Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry, 45(9), 1628–1650. https://doi.org/10.1093/clinchem/45.9.1628
   PubMed Web of Science ®Google Scholar
• Kaur, H., & Yung, L.-Y. L. (2012). Probing high affinity sequences of DNA aptamer against VEGF165. PloS One, 7(2), e31196. https://doi.org/10.1371/journal.pone.0031196
   PubMed Web of Science ®Google Scholar
• Keefe, A. D., Pai, S., & Ellington, A. (2010). Aptamers as therapeutics. Nature Reviews. Drug Discovery, 9(7), 537–550. https://doi.org/10.1038/nrd3141
   PubMed Web of Science ®Google Scholar
• Krieger, R. (2001). Handbook of pesticide toxicology: Principles and agents. Academic press.
   Google Scholar
• Kumari, R., Kumar, R., & Lynn, A., Open Source Drug Discovery Consortium. (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
• Le, T. T., Chumphukam, O., & Cass, A. E. (2014). Determination of minimal sequence for binding of an aptamer. A comparison of truncation and hybridization inhibition methods. RSC Advances., 4(88), 47227–47233. https://doi.org/10.1039/C4RA08243E
   Web of Science ®Google Scholar
• Liu, J., Cao, Z., & Lu, Y. (2009). Functional nucleic acid sensors. Chemical Reviews, 109(5), 1948–1998.
   PubMed Web of Science ®Google Scholar
• Nick, T. A., de Oliveira, T. E., Pilat, D. W., Spenkuch, F., Butt, H-Jr., Helm, M., Netz, P. A., & Berger, Rd. (2016). Stability of a split streptomycin binding aptamer. The Journal of Physical Chemistry. B, 120(27), 6479–6489. https://doi.org/10.1021/acs.jpcb.6b02440
   PubMed Web of Science ®Google Scholar
• Robertson, D. L., & Joyce, G. F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 344(6265), 467–468. https://doi.org/10.1038/344467a0
   PubMed Web of Science ®Google Scholar
• Roushani, M., Ghanbari, K., & Hoseini, S. J. (2018). Designing an electrochemical aptasensor based on immobilization of the aptamer onto nanocomposite for detection of the streptomycin antibiotic. Microchemical Journal, 141, 96–103. https://doi.org/10.1016/j.microc.2018.05.016
   Web of Science ®Google Scholar
• Stefanucci, A., Amato, J., Brancaccio, D., Pagano, B., Randazzo, A., Santoro, F., Mayol, L., Learte-Aymamí, S., Rodriguez, J., Mascareñas, J. L., Novellino, E., Carotenuto, A., & Mollica, A. (2021). A novel β-hairpin peptide derived from the ARC repressor selectively interacts with the major groove of B-DNA. Bioorganic Chemistry, 112, 104836. https://doi.org/10.1016/j.bioorg.2021.104836
   PubMed Web of Science ®Google Scholar
• Stefanucci, A., Mosquera, J., Vázquez, E., Mascareñas, J. L., Novellino, E., & Mollica, A. (2015). Synthesis, characterization, and DNA binding profile of a macrocyclic β-sheet analogue of ARC protein. ACS Medicinal Chemistry Letters, 6(12), 1220–1224. https://doi.org/10.1021/acsmedchemlett.5b00363
   PubMed Web of Science ®Google Scholar
• Sussman, D., Nix, J. C., & Wilson, C. (2000). The structural basis for molecular recognition by the vitamin B 12 RNA aptamer. Nature Structural Biology, 7(1), 53–57. https://doi.org/10.1038/71253
   PubMedGoogle Scholar
• Taghdisi, S. M., Danesh, N. M., Nameghi, M. A., Ramezani, M., & Abnous, K. (2016). A label-free fluorescent aptasensor for selective and sensitive detection of streptomycin in milk and blood serum. Food Chemistry, 203, 145–149. https://doi.org/10.1016/j.foodchem.2016.02.017
   PubMed Web of Science ®Google Scholar
• Tereshko, V., Skripkin, E., & Patel, D. J. (2003). Encapsulating streptomycin within a small 40-mer RNA. Chemistry & Biology, 10(2), 175–187. https://doi.org/10.1016/S1074-5521(03)00024-3
   PubMedGoogle Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Wegener, H. C. (2003). Antibiotics in animal feed and their role in resistance development. Current Opinion in Microbiology, 6(5), 439–445. https://doi.org/10.1016/j.mib.2003.09.009
   PubMed Web of Science ®Google Scholar
• Winkler, W., Nahvi, A., & Breaker, R. R. (2002). Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature, 419(6910), 952–956. https://doi.org/10.1038/nature01145
   PubMed Web of Science ®Google Scholar
• Yin, J., Guo, W., Qin, X., Pei, M., Wang, L., & Ding, F. (2016a). A regular “signal attenuation” electrochemical aptasensor for highly sensitive detection of streptomycin. New Journal of Chemistry, 40(11), 9711–9718. https://doi.org/10.1039/C6NJ02209J
   Web of Science ®Google Scholar
• Yin, J., Guo, W., Qin, X., Zhao, J., Pei, M., & Ding, F. (2017). A sensitive electrochemical aptasensor for highly specific detection of streptomycin based on the porous carbon nanorods and multifunctional graphene nanocomposites for signal amplification. Sensors and Actuators B: Chemical, 241, 151–159. https://doi.org/10.1016/j.snb.2016.10.062
   Web of Science ®Google Scholar
• Yin, Y., Qin, X., Wang, Q., & Yin, Y. (2016b). A novel electrochemical aptasensor for sensitive detection of streptomycin based on gold nanoparticle-functionalized magnetic multi-walled carbon nanotubes and nanoporous PtTi alloy. RSC Advances, 6(45), 39401–39408. https://doi.org/10.1039/C6RA02029A
   Web of Science ®Google Scholar
• Zhao, J., Wu, Y., Tao, H., Chen, H., Yang, W., & Qiu, S. (2017). Colorimetric detection of streptomycin in milk based on peroxidase-mimicking catalytic activity of gold nanoparticles. RSC Advances, 7(61), 38471–38478. https://doi.org/10.1039/C7RA06434A
   Web of Science ®Google Scholar
• Zhou, N., Wang, J., Zhang, J., Li, C., Tian, Y., & Wang, J. (2013). Selection and identification of streptomycin-specific single-stranded DNA aptamers and the application in the detection of streptomycin in honey. Talanta, 108, 109–116. https://doi.org/10.1016/j.talanta.2013.01.064
   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