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Research Article

Molecular dynamics simulation as a promising approach for computational study of liquid crystal-based aptasensors

, , , &
Received 04 Jan 2024, Accepted 01 Feb 2024, Published online: 12 Feb 2024

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Aho, N., Buslaev, P., Jansen, A., Bauer, P., Groenhof, G., & Hess, B. (2022). Scalable constant pH molecular dynamics in GROMACS. Journal of Chemical Theory and Computation, 18(10), 6148–6160. https://doi.org/10.1021/acs.jctc.2c00516-
  • An, J. E., Kim, K. H., Park, S. J., Seo, S. E., Kim, J., Ha, S., Bae, J., & Kwon, O. S. (2022). Wearable cortisol aptasensor for simple and rapid real-time monitoring. ACS Sensors, 7(1), 99–108. https://doi.org/10.1021/acssensors.1c01734
  • Azzouz, A., Hejji, L., Kim, K.-H., Kukkar, D., Souhail, B., Bhardwaj, N., Brown, R. J. C., & Zhang, W. (2022). Advances in surface plasmon resonance-based biosensor technologies for cancer biomarker detection. Biosensors & Bioelectronics, 197, 113767. https://doi.org/10.1016/j.bios.2021.113767
  • Bini, A., Mascini, M., Mascini, M., & Turner, A. P. (2011). Selection of thrombin-binding aptamers by using computational approach for aptasensor application. Biosensors & Bioelectronics, 26(11), 4411–4416. https://doi.org/10.1016/j.bios.2011.04.053
  • Blanchaert, B., Huang, S., Wach, K., Adams, E., & Van Schepdael, A. (2017). Assay development for aminoglycosides by HPLC with direct UV detection. Journal of Chromatographic Science, 55(3), 197–204. https://doi.org/10.1093/chromsci/bmw169
  • Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614. https://doi.org/10.1002/jcc.21287
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
  • Cao, L.-R., Zhang, C.-Y., Zhang, D.-L., Chu, H.-Y., Zhang, Y.-B., & Li, G.-H, (2017). Recent developments in using molecular dynamics simulation techniques to study biomolecules. Acta Physico-Chimica Sinica, 33(7), 1354–1365. https://doi.org/10.3866/PKU.WHXB201704144
  • Chakraborty, K., Khatua, P., & Bandyopadhyay, S. (2016). Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies. Physical Chemistry Chemical Physics, 18(23), 15899–15910. https://doi.org/10.1039/c6cp00663a
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Darmostuk, M., Rimpelova, S., Gbelcova, H., & Ruml, T. (2015). Current approaches in SELEX: an update to aptamer selection technology. Biotechnology Advances, 33(6 Pt 2), 1141–1161. https://doi.org/10.1016/j.biotechadv.2015.02.008
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr, 40(1), 82–92.
  • Devi, M., Pani, I., & Pal, S. K. (2022). Liquid crystals as signal transducers for sensing of analytes using aptamer as recognition probe. Liquid Crystals Reviews, 9(2), 65–84. https://doi.org/10.1080/21680396.2022.2053597
  • DiCicco, M., Duong, T., Chu, A., & Jansen, S. A. (2003). Tobramycin and gentamycin elution analysis between two in situ polymerizable orthopedic composites. Journal of Biomedical Materials Research. Part B, Applied Biomaterials, 65(1), 137–149. https://doi.org/10.1002/jbm.b.10528
  • Du, Y., & Dong, S. (2017). Nucleic acid biosensors: Recent advances and perspectives. Analytical Chemistry, 89(1), 189–215. https://doi.org/10.1021/acs.analchem.6b04190
  • 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
  • Fletcher, R., & Powell, M. J. (1963). A rapidly convergent descent method for minimization. The Computer Journal, 6(2), 163–168. https://doi.org/10.1093/comjnl/6.2.163
  • Frisch, A. (2009). gaussian 09W Reference. 25p, 470
  • Gao, S., Hu, B., Zheng, X., Liu, D., Sun, M., Qin, J., Zhou, H., Jiao, B., & Wang, L. (2016). Study of the binding mechanism between aptamer GO18-Td and gonyautoxin 1/4 by molecular simulation. Physical Chemistry Chemical Physics: PCCP, 18(34), 23458–23461. https://doi.org/10.1039/c6cp00777e
  • Hussain, A., Pina, A. S., & Roque, A. C. (2009). Bio-recognition and detection using liquid crystals. Biosensors & Bioelectronics, 25(1), 1–8. https://doi.org/10.1016/j.bios.2009.04.038
  • Jang, C. H., Tingey, M. L., Korpi, N. L., Wiepz, G. J., Schiller, J. H., Bertics, P. J., & Abbott, N. L. (2005). Using liquid crystals to report membrane proteins captured by affinity microcontact printing from cell lysates and membrane extracts. Journal of the American Chemical Society, 127(25), 8912–8913. https://doi.org/10.1021/ja051079g
  • Johnson, R. R., Kohlmeyer, A., Johnson, A. T., & Klein, M. L. (2009). Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics. Nano Letters, 9(2), 537–541. https://doi.org/10.1021/nl802645d
  • 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
  • Khanniche, S., Mathieu, D., Pereira, F., Frenois, C., Colin, D., Barthet, C., & Hairault, L. (2017). Quantitative evaluation of the responses of a gravimetric gas sensor based on mesoporous functionalized silica: Application to 2, 4-DNT and TNT detection. Sensors and Actuators B: Chemical, 248, 470–480. https://doi.org/10.1016/j.snb.2017.03.137
  • Khoshbin, Z., Abnous, K., Taghdisi, S. M., & Verdian, A. (2021). Liquid crystal-based biosensors as lab-on-chip tools: Promising for future on-site detection test kits. TrAC Trends in Analytical Chemistry, 142, 116325. https://doi.org/10.1016/j.trac.2021.116325
  • Khoshbin, Z., Abnous, K., Taghdisi, S. M., & Verdian, A. (2021). A novel liquid crystal-based aptasensor for ultra-low detection of ochratoxin a using a pi-shaped DNA structure: Promising for future on-site detection test strips. Biosensors & Bioelectronics, 191, 113457. https://doi.org/10.1016/j.bios.2021.113457
  • Khoshbin, Z., Verdian, A., Housaindokht, M. R., Izadyar, M., & Rouhbakhsh, Z. (2018). Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection. Biosensors & Bioelectronics, 122, 263–283. https://doi.org/10.1016/j.bios.2018.09.060
  • Khoshbin, Z., Zahraee, H., Ramezani, M., Alibolandi, M., Verdian, A., Abnous, K., & Taghdisi, S. M. (2023). Surfactant-regularized liquid crystal aptasensor for optical monitoring of prostate-specific antigen: Appropriate for health care monitoring. Microchemical Journal, 193, 109002. https://doi.org/10.1016/j.microc.2023.109002
  • Kim, H. W., Rhee, Y. M., & Shin, S. K. (2018). Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Physical Chemistry Chemical Physics, 20(32), 21068–21074. https://doi.org/10.1039/c8cp03050b
  • Kissell, R., & Poserina, J. (2017). Advanced math and statistics. In R. Kissell & J. Poserina (Eds.), Optimal Sports Math, Statistics, and Fantasy. (pp. 103–135): Academic Press.
  • Krieger, E., & Vriend, G. (2014). YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics , 30(20), 2981–2982. https://doi.org/10.1093/bioinformatics/btu426
  • Kutnowski, N., Shmuely, H., Dahan, I., Shmulevich, F., Davidov, G., Shahar, A., Eichler, J., Zarivach, R., & Shaanan, B. (2018). The 3-D structure of VNG0258H/RosR–A haloarchaeal DNA-binding protein in its ionic shell. Journal of Structural Biology, 204(2), 191–198. https://doi.org/10.1016/j.jsb.2018.08.008
  • Law, W. S., Kubán, P., Yuan, L. L., Zhao, J. H., Li, S. F. Y., & Hauser, P. C. (2006). Determination of tobramycin in human serum by capillary electrophoresis with contactless conductivity detection. Electrophoresis, 27(10), 1932–1938. https://doi.org/10.1002/elps.200500819
  • Li, D., Ling, S., Meng, D., Zhou, B., Liang, P., & Lv, B. (2022). Sensitive fluorescent aptasensing of tobramycin on graphene oxide coupling strand displacement amplification and hybridization chain reaction. International Journal of Biological Macromolecules, 220, 1287–1293. https://doi.org/10.1016/j.ijbiomac.2022.08.158
  • Li, M.-R., Zhang, N., & Zhang, F.-S. (2018). Computational investigation of the conformation transitions of DNA in modified water models. Journal of Molecular Liquids, 271, 175–181. https://doi.org/10.1016/j.molliq.2018.08.129
  • Li, M., Shoemaker, B. A., Thangudu, R. R., Ferraris, J. D., Burg, M. B., & Panchenko, A. R. (2013). Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics. The Journal of Physical Chemistry. B, 117(42), 13226–13234. https://doi.org/10.1021/jp403310a
  • Li, Z., Wan, H., Shi, Y., & Ouyang, P. (2004). Personal experience with four kinds of chemical structure drawing software: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. Journal of Chemical Information and Computer Sciences, 44(5), 1886–1890. https://doi.org/10.1021/ci049794h
  • Luo, D., & Mu, Y. (2016). Computational insights into the stability and folding pathways of human telomeric DNA G-quadruplexes. The Journal of Physical Chemistry. B, 120(22), 4912–4926. https://doi.org/10.1021/acs.jpcb.6b01919
  • Ma, Q., Wang, Y., Jia, J., & Xiang, Y. (2018). Colorimetric aptasensors for determination of tobramycin in milk and chicken eggs based on DNA and gold nanoparticles. Food Chemistry, 249, 98–103. https://doi.org/10.1016/j.foodchem.2018.01.022
  • Mary, V., Haris, P., Varghese, M. K., Aparna, P., & Sudarsanakumar, C. (2017). Experimental probing and molecular dynamics simulation of the molecular recognition of DNA duplexes by the flavonoid luteolin. Journal of Chemical Information and Modeling, 57(9), 2237–2249. https://doi.org/10.1021/acs.jcim.6b00747
  • Meng, T., Kosmider, L., Chai, G., Moothedathu Raynold, A. A., Pearcy, A. C., Qin, B., Wang, Y., Lu, X., Halquist, M. S., & Xu, Q. (2021). LC-MS/MS method for simultaneous quantification of dexamethasone and tobramycin in rabbit ocular biofluids. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, 1170, 122610. https://doi.org/10.1016/j.jchromb.2021.122610
  • Monti, S., Cappelli, C., Bronco, S., Giusti, P., & Ciardelli, G. (2006). Towards the design of highly selective recognition sites into molecular imprinting polymers: A computational approach. Biosensors & Bioelectronics, 22(1), 153–163. https://doi.org/10.1016/j.bios.2006.05.017
  • Moradi, S., Shareghi, B., Saboury, A. A., & Farhadian, S. (2020). Investigation on the interaction of acid phosphatase with putrescine using docking, simulations methods and multispectroscopic techniques. International Journal of Biological Macromolecules, 150, 90–101. https://doi.org/10.1016/j.ijbiomac.2020.02.057
  • Mukhtar, N. H., Mamat, N. A., & See, H. H. (2018). Monitoring of tobramycin in human plasma via mixed matrix membrane extraction prior to capillary electrophoresis with contactless conductivity detection. Journal of Pharmaceutical and Biomedical Analysis, 158, 184–188. https://doi.org/10.1016/j.jpba.2018.05.044
  • Nada, H., & Furukawa, Y. (2012). Antifreeze proteins: Computer simulation studies on the mechanism of ice growth inhibition. Polymer Journal, 44(7), 690–698. https://doi.org/10.1038/pj.2012.13
  • Nicholls, I. A., Andersson, H. S., Charlton, C., Henschel, H., Karlsson, B. C. G., Karlsson, J. G., O'Mahony, J., Rosengren, A. M., Rosengren, K. J., & Wikman, S. (2009). Theoretical and computational strategies for rational molecularly imprinted polymer design. Biosensors & Bioelectronics, 25(3), 543–552. https://doi.org/10.1016/j.bios.2009.03.038
  • O'Neill, M., & Kelly, S. M. (2003). Liquid crystals for charge transport, luminescence, and photonics. Advanced Materials, 15(14), 1135–1146. https://doi.org/10.1002/adma.200300009
  • Pagano-Stauffer, L. A., Johnson, K. M., Clark, N., & Handschy, M. (1986). Optical logic gates using ferroelectric liquid crystals liquid crystals and spatial light modulator materials (Vol. 684 [Paper presentation]. pp. 88–95): SPIE. https://doi.org/10.1117/12.936484
  • Pal, P., Aich, R., Chakraborty, S., & Jana, B. (2022). Molecular factors of ice growth inhibition for hyperactive and globular antifreeze proteins: Insights from molecular dynamics simulation. Langmuir: The ACS Journal of Surfaces and Colloids, 38(49), 15132–15144. https://doi.org/10.1021/acs.langmuir.2c02149
  • Pani, I., Sil, S., & Pal, S. K. (2023). Liquid crystal biosensors: A new therapeutic window to point-of-care diagnostics. Langmuir: The ACS Journal of Surfaces and Colloids, 39(3), 909–917. https://doi.org/10.1021/acs.langmuir.2c02959
  • 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
  • Patel, S., Mackerell, A. D., Jr., & Brooks, C. L. 3rd (2004). CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. Journal of Computational Chemistry, 25(12), 1504–1514. https://doi.org/10.1002/jcc.20077
  • Phanchai, W., Srikulwong, U., Chompoosor, A., Sakonsinsiri, C., & Puangmali, T. (2018). Insight into the molecular mechanisms of AuNP-based aptasensor for colorimetric detection: A molecular dynamics approach. Langmuir: The ACS Journal of Surfaces and Colloids, 34(21), 6161–6169. https://doi.org/10.1021/acs.langmuir.8b00701
  • Pilz da Cunha, M., Debije, M. G., & Schenning, A. (2020). Bioinspired light-driven soft robots based on liquid crystal polymers. Chemical Society Reviews, 49(18), 6568–6578. https://doi.org/10.1039/d0cs00363h
  • Plattner, N., Doerr, S., De Fabritiis, G., & Noé, F. (2017). Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry, 9(10), 1005–1011. https://doi.org/10.1038/nchem.2785
  • Rigoldi, F., Spero, L., Dalle Vedove, A., Redaelli, A., Parisini, E., & Gautieri, A. (2016). Molecular dynamics simulations provide insights into the substrate specificity of FAOX family members. Molecular bioSystems, 12(8), 2622–2633. https://doi.org/10.1039/c6mb00405a
  • Rosalia, M., Chiesa, E., Tottoli, E. M., Dorati, R., Genta, I., Conti, B., & Pisani, S. (2022). Tobramycin nanoantibiotics and their advantages: A minireview. International Journal of Molecular Sciences, 23(22), 14080. https://doi.org/10.3390/ijms232214080
  • Rouhbakhsh, Z., Verdian, A., & Rajabzadeh, G. (2020). Design of a liquid crystal-based aptasensing platform for ultrasensitive detection of tetracycline. Talanta, 206, 120246. https://doi.org/10.1016/j.talanta.2019.120246
  • Shang, M., Zhang, J., Qi, H., Gao, Y., Yan, J., & Song, W. (2019). All-electrodeposited amorphous MoS(x)@ZnO core-shell nanorod arrays for self-powered visible-light-activated photoelectrochemical tobramycin aptasensing. Biosensors & Bioelectronics, 136, 53–59. https://doi.org/10.1016/j.bios.2019.04.019
  • Shao, Z., Sun, J., Wang, J., Lv, K., Liao, B., Wang, R., & Jiang, H. (2021). Effects of modified cellulose on methane hydrate decomposition: Experiments and molecular dynamics simulations. ACS Sustainable Chemistry & Engineering, 9(29), 9689–9697. https://doi.org/10.1021/acssuschemeng.1c01495
  • Verdian, A., Rouhbakhsh, Z., & Fooladi, E. (2021). An ultrasensitive platform for PCB77 detection: New strategy for liquid crystal-based aptasensor fabrication. Journal of Hazardous Materials, 402, 123531. https://doi.org/10.1016/j.jhazmat.2020.123531
  • Vicens, Q., & Westhof, E. (2002). Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chemistry & Biology, 9(6), 747–755. https://doi.org/10.1016/s1074-5521(02)00153-9
  • Wang, J., Qian, Y., Li, L., & Qiu, X. (2020). Atomic force microscopy and molecular dynamics simulations for study of lignin solution self-assembly mechanisms in organic-aqueous solvent mixtures. ChemSusChem. 13(17), 4420–4427. https://doi.org/10.1002/cssc.201903132
  • Wang, S., Li, Z., Duan, F., Hu, B., He, L., Wang, M., Zhou, N., Jia, Q., & Zhang, Z. (2019). Bimetallic cerium/copper organic framework-derived cerium and copper oxides embedded by mesoporous carbon: Label-free aptasensor for ultrasensitive tobramycin detection. Analytica Chimica Acta, 1047, 150–162. https://doi.org/10.1016/j.aca.2018.09.064
  • Wang, Y., Hu, Q., Tian, T., Gao, Y., & Yu, L. (2016). A liquid crystal-based sensor for the simple and sensitive detection of cellulase and cysteine. Colloids and Surfaces. B, Biointerfaces, 147, 100–105. https://doi.org/10.1016/j.colsurfb.2016.07.059
  • Wang, Y., Killian, J., Hamasaki, K., & Rando, R. R. (1996). RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry, 35(38), 12338–12346. https://doi.org/10.1021/bi960878w
  • Zahraee, H., Arab, S. S., Khoshbin, Z., & Bozorgmehr, M. R. (2023a). A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer’s disease insignia. Journal of Biomolecular Structure & Dynamics, 41(20), 10830–10839. https://doi.org/10.1080/07391102.2022.2158939
  • Zahraee, H., Khoshbin, Z., Mohammadi, F., Mashreghi, M., Abnous, K., & Taghdisi, S. M. (2023b). Three-way junction skeleton biosensors based on aptamers, DNAzymes, and DNA hybridization probes. TrAC Trends in Analytical Chemistry, 165, 117160. https://doi.org/10.1016/j.trac.2023.117160
  • Zahraee, H., Mehrzad, A., Abnous, K., Chen, C.-H., Khoshbin, Z., & Verdian, A. (2023c). Recent Advances in aptasensing strategies for monitoring phycotoxins: Promising for food safety. Biosensors, 13(1), 56. https://doi.org/10.3390/bios13010056
  • Zahraee, H., Mohammadi, F., Parvaee, E., Khoshbin, Z., & Arab, S. S. (2023d). Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: Molecular dynamics simulation exploration. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2023.2247086
  • Zavvar, T. S., Khoshbin, Z., Ramezani, M., Alibolandi, M., Abnous, K., & Taghdisi, S. M. (2022). CRISPR/Cas-engineered technology: Innovative approach for biosensor development. Biosensors & Bioelectronics, 214, 114501. https://doi.org/10.1016/j.bios.2022.114501
  • Zeng, X., Zhang, L., Xiao, X., Jiang, Y., Guo, Y., Yu, X., Pu, X., & Li, M. (2016). Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model. Scientific Reports, 6(1), 24065. https://doi.org/10.1038/srep24065
  • Zhang, H. W., Li, H. K., Han, Z. Y., Yuan, R., & He, H. (2022). Incorporating Fullerenes in nanoscale metal-organic matrixes: An ultrasensitive platform for impedimetric aptasensing of tobramycin. ACS Applied Materials & Interfaces, 14(5), 7350–7357. https://doi.org/10.1021/acsami.1c23320
  • Zhu, L., Liang, G., Guo, C., Xu, M., Wang, M., Wang, C., Zhang, Z., & Du, M. (2022). A new strategy for the development of efficient impedimetric tobramycin aptasensors with metallo-covalent organic frameworks (MCOFs). Food Chemistry, 366, 130575. https://doi.org/10.1016/j.foodchem.2021.130575
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/10.1002/jcc.21816

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