Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein

References

• Adasme, M. F., Linnemann, K. L., Bolz, S. N., Kaiser, F., Salentin, S., Haupt, V. J., & Schroeder, M. (2021). PLIP 2021: Expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Research, 49(W1), W530–W534. https://doi.org/10.1093/NAR/GKAB294
   PubMed Web of Science ®Google Scholar
• Ahmad, B., Ashfaq, U. A., Rahman, M. U., Masoud, M. S., & Yousaf, M. Z. (2019). Conserved B and T cell epitopes prediction of Ebola virus glycoprotein for vaccine development: An immuno-informatics approach. Microbial Pathogenesis, 132, 243–253. https://doi.org/10.1016/J.MICPATH.2019.05.010
   PubMed Web of Science ®Google Scholar
• Ali, M. T., & Islam, M. O. (2015). A highly conserved GEQYQQLR epitope has been identified in the nucleoprotein of Ebola virus by using an in silico approach. Advances in Bioinformatics, 2015, 278197–278198. https://doi.org/10.1155/2015/278197
   PubMedGoogle 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
• Bai, Y., Li, Y., Zhang, D., Wang, H., & Zhao, Q. (2017). Enhancing the affinity of anti-human α-thrombin 15-Mer DNA aptamer and anti-immunoglobulin e aptamer by PolyT extension. Analytical Chemistry, 89(17), 9467–9473. https://doi.org/10.1021/ACS.ANALCHEM.7B02313/SUPPL_FILE/AC7B02313_SI_001PDF.
   PubMed Web of Science ®Google Scholar
• Behrens, C., Binotti, B., Schmidt, C., Robinson, C. V., Chua, J. J. E., & Kühnel, K. (2013). Crystal structure of the human short coiled coil protein and insights into SCOC-FEZ1 complex formation. PLoS One, 8(10), e76355. https://doi.org/10.1371/JOURNAL.PONE.0076355
   PubMed Web of Science ®Google Scholar
• Biesiada, M., Pachulska-Wieczorek, K., Adamiak, R. W., & Purzycka, K. J. (2016). RNAComposer and RNA 3D structure prediction for nanotechnology. Methods, 103, 120–127. https://doi.org/10.1016/j.ymeth.2016.03.010
   PubMed Web of Science ®Google Scholar
• Biesiada, M., Purzycka, K. J., Szachniuk, M., Blazewicz, J., & Adamiak, R. W. (2016). Automated RNA 3D structure prediction with RNA composer. In Methods in molecular biology (Vol. 1490, pp. 199–215). Humana Press.
   Google Scholar
• Bloom, D. E., & Cadarette, D. (2019). Infectious disease threats in the twenty-first century: Strengthening the global response. Frontiers in Immunology, 10, 549. https://doi.org/10.3389/FIMMU.2019.00549
   PubMed Web of Science ®Google Scholar
• Bradshaw, R. T., Patel, B. H., Tate, E. W., Leatherbarrow, R. J., & Gould, I. R. (2011). Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction. Protein Engineering, Design & Selection: PEDS, 24(1-2), 197–207. https://doi.org/10.1093/PROTEIN/GZQ047
   PubMed Web of Science ®Google Scholar
• Broadhurst, M. J., Brooks, T. J. G., & Pollock, N. R. (2016). Diagnosis of Ebola virus disease: Past, present, and future. Clinical Microbiology Reviews, 29(4), 773–793. https://doi.org/10.1128/CMR.00003-16
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Brown, J. H., Yang, Y., Reshetnikova, L., Gourinath, S., Süveges, D., Kardos, J., Hóbor, F., Reutzel, R., Nyitray, L., & Cohen, C. (2008). An unstable head-rod junction may promote folding into the compact off-state conformation of regulated myosins. Journal of Molecular Biology, 375(5), 1434–1443. https://doi.org/10.1016/j.jmb.2007.11.071
   PubMed Web of Science ®Google Scholar
• Brown, S. P., & Muchmore, S. W. (2009). Large-scale application of high-throughput molecular mechanics with Poisson-Boltzmann surface area for routine physics-based scoring of protein-ligand complexes. Journal of Medicinal Chemistry, 52(10), 3159–3165. https://doi.org/10.1021/JM801444X
   PubMed Web of Science ®Google Scholar
• Cao, C., Li, P., Liao, H., Wang, J., Tang, X., & Yang, L. (2020). Cys-functionalized AuNP substrates for improved sensing of the marine toxin STX by dynamic surface-enhanced Raman spectroscopy. Analytical and Bioanalytical Chemistry, 412(19), 4609–4617. https://doi.org/10.1007/S00216-020-02710-9
   PubMed Web of Science ®Google Scholar
• Cataldo, R., Ciriaco, F., & Alfinito, E. (2018). A validation strategy for in silico generated aptamers. Computational Biology and Chemistry, 77, 123–130. https://doi.org/10.1016/J.COMPBIOLCHEM.2018.09.014
   PubMed Web of Science ®Google Scholar
• CDC. (2022). CDC Transmission | Ebola Hemorrhagic Fever | CDC. https://www.cdc.gov/vhf/ebola/transmission/index.html
   Google Scholar
• Changula, K., Yoshida, R., Noyori, O., Marzi, A., Miyamoto, H., Ishijima, M., Yokoyama, A., Kajihara, M., Feldmann, H., Mweene, A. S., & Takada, A. (2013). Mapping of conserved and species-specific antibody epitopes on the Ebola virus nucleoprotein. Virus Research, 176(1-2), 83–90. https://doi.org/10.1016/J.VIRUSRES.2013.05.004
   PubMed Web of Science ®Google Scholar
• Choi, S. J., & Ban, C. (2016). Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition. Scientific Reports, 6(1), 34998. https://doi.org/10.1038/srep34998
   PubMedGoogle Scholar
• Chou, S. H., Chin, K. H., & Wang, A. H. J. (2005). DNA aptamers as potential anti-HIV agents. Trends in Biochemical Sciences, 30(5), 231–234. https://doi.org/10.1016/J.TIBS.2005.03.004
   PubMed Web of Science ®Google Scholar
• Cleri, F., Lensink, M. F., & Blossey, R. (2021). DNA aptamers block the receptor binding domain at the spike protein of SARS-CoV-2. Frontiers in Molecular Biosciences, 8, 713003. https://doi.org/10.3389/FMOLB.2021.713003/FULL
   PubMed Web of Science ®Google Scholar
• Cuesta-López, S., Menoni, H., Angelov, D., & Peyrard, M. (2011). Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions. Nucleic Acids Research, 39(12), 5276–5283. https://doi.org/10.1093/NAR/GKR096
   PubMed Web of Science ®Google 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, 5648. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W. F., Mark, A. E., Rigault, A., Siegel, J., Harrowfield, J., & Chevrier, B. (1998). Peptide folding: When simulation meets experiment. Angewandte Chemie International Edition in English, 31, 1387–1404. https://doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2
   Google Scholar
• Deng, B., Lin, Y., Wang, C., Li, F., Wang, Z., Zhang, H., Li, X. F., & Le, X. C. (2014). Aptamer binding assays for proteins: The thrombin example—A review. Analytica Chimica Acta, 837, 1–15. https://doi.org/10.1016/J.ACA.2014.04.055
   PubMed Web of Science ®Google Scholar
• De Vries, S. J., Van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. https://doi.org/10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Devi, A., & Chaitanya, N. S. N. (2021). Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: An in silico study. Molecular Diversity, 26(1), 157–169. https://doi.org/10.1007/s11030-020-10171-6
   PubMed Web of Science ®Google Scholar
• Dong, S., Yang, P., Li, G., Liu, B., Wang, W., Liu, X., Xia, B., Yang, C., Lou, Z., Guo, Y., & Rao, Z. (2015). Insight into the Ebola virus nucleocapsid assembly mechanism: Crystal structure of Ebola virus nucleoprotein core domain at 1.8 Å resolution. Protein & Cell, 6(5), 351–362. https://doi.org/10.1007/S13238-015-0163-3/FIGURES/5
   PubMed Web of Science ®Google Scholar
• Dunker, A. K., Babu, M. M., Barbar, E., Blackledge, M., Bondos, S. E., Dosztányi, Z., Dyson, H. J., Forman-Kay, J., Fuxreiter, M., Gsponer, J., Han, K.-H., Jones, D. T., Longhi, S., Metallo, S. J., Nishikawa, K., Nussinov, R., Obradovic, Z., Pappu, R. V., Rost, B., … Uversky, V. N. (2013). What’s in a name? Why these proteins are intrinsically disordered. Intrinsically Disordered Proteins, 1(1), e24157. https://doi.org/10.4161/idp.24157
   PubMedGoogle Scholar
• Ebola Detection Using Rapid Tests and ELISA Kits for Humans and Animals. (2022). https://www.prnewswire.com/news-releases/eboladetection-using-rapid-tests-and-elisa-kits-forhumans-and-animals-369183957.html
   Google Scholar
• Elskens, J. P., Elskens, J. M., & Madder, A. (2020). Chemical modification of aptamers for increased binding affinity in diagnostic applications: Current status and future prospects. International Journal of Molecular Sciences, 21(12), 4522. https://doi.org/10.3390/IJMS21124522
   PubMed Web of Science ®Google Scholar
• Emami, N., Pakchin, P. S., & Ferdousi, R. (2020). Computational predictive approaches for interaction and structure of aptamers. Journal of Theoretical Biology, 497, 110268. https://doi.org/10.1016/J.JTBI.2020.110268
   PubMed Web of Science ®Google Scholar
• Gall, T., Le; Romero, P. R., Cortese, M. S., Uversky, V. N., & Dunker, A. K. (2012). Intrinsic disorder in the protein data bank. Journal of Biomolecular Structure & Dynamics, 24(4), 325–342. https://doi.org/10.1080/07391102.2007.10507123
   Google Scholar
• Gao, J., Chen, Z., Mao, L., Zhang, W., Wen, W., Zhang, X., & Wang, S. (2019). Electrochemiluminescent aptasensor based on resonance energy transfer system between CdTe quantum dots and cyanine dyes for the sensitive detection of ochratoxin A. Talanta, 199, 178–183. https://doi.org/10.1016/J.TALANTA.2019.02.044
   PubMed Web of Science ®Google Scholar
• Gao, S., Hu, B., Zheng, X., Cao, Y., Liu, D., Sun, M., Jiao, B., & Wang, L. (2016). Gonyautoxin 1/4 aptamers with high-affinity and high-specificity: From efficient selection to aptasensor application. Biosensors & Bioelectronics, 79, 938–944. https://doi.org/10.1016/J.BIOS.2016.01.032
   PubMed Web of Science ®Google Scholar
• Gao, S., Hu, W., Zheng, X., Cai, S., & Wu, J. (2019). Functionalized aptamer with an antiparallel G-quadruplex: Structural remodeling, recognition mechanism, and diagnostic applications targeting CTGF. Biosensors & Bioelectronics, 142, 111475. https://doi.org/10.1016/j.bios.2019.111475
   PubMed Web of Science ®Google Scholar
• Gelinas, A. D., Davies, D. R., & Janjic, N. (2016). Embracing proteins: Structural themes in aptamer–protein complexes. Current Opinion in Structural Biology, 36, 122–132. https://doi.org/10.1016/J.SBI.2016.01.009
   PubMed Web of Science ®Google Scholar
• Gilson, M. K., & Zhou, H. X. (2007). Calculation of protein-ligand binding affinities. Annual Review of Biophysics and Biomolecular Structure, 36(1), 21–42. https://doi.org/10.1146/ANNUREV.BIOPHYS.36.040306.132550
   PubMedGoogle Scholar
• Goda, T., & Miyahara, Y. (2020). Label-free monitoring of histone acetylation using aptamer-functionalized field-effect transistor and quartz crystal microbalance sensors. Micromachines, 11(9), 820. https://doi.org/10.3390/MI11090820
   PubMed Web of Science ®Google Scholar
• Goudarzi, M., Fazeli, M., Azad, M., & Seyedjavadi, S. S. (2015). Survey of clinical features, pathogenesis and therapeutic options for Ebola haemorrhagic fever. Archives of Advances in Biosciences, 6, 145–152. https://doi.org/10.22037/JPS.V6I3.9788
   Google Scholar
• GROMACS Gmx Hbond—GROMACS. (2019). 1 Documentation. https://manual.gromacs.org/2019.1/onlinehelp/gmx-hbond.html
   Google Scholar
• Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R., & Hofacker, I. L. (2008). The Vienna RNA Websuite. Nucleic Acids Research, 36(Web Server issue), W70–W74. https://doi.org/10.1093/NAR/GKN188
   PubMed 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
• Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., & Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie Chemical Monthly, 125(2), 167–188. https://doi.org/10.1007/BF00818163
   Google Scholar
• Hong, S. L., Xiang, M. Q., Tang, M., Pang, D. W., & Zhang, Z. L. (2019). Ebola virus aptamers: From highly efficient selection to application on magnetism-controlled chips. Analytical Chemistry, 91(5), 3367–3373. https://doi.org/10.1021/ACS.ANALCHEM.8B04623/ASSET/IMAGES/LARGE/AC-2018-04623F_0006.JPEG
   PubMed Web of Science ®Google Scholar
• Hooft, R. W. W., Sander, C., & Vriend, G. (1996). Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins: Structure, Function, and Genetics, 26(4), 363–376. https://doi.org/10.1002/(SICI)1097-0134(199612)26:4
   PubMed Web of Science ®Google Scholar
• Hooft, R. W. W., Vriend, G., Sander, C., & Abola, E. E. (1996). Errors in protein structures. Nature, 381(6580), 272–272. https://doi.org/10.1038/381272a0.
   PubMed Web of Science ®Google Scholar
• Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., De Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/NMETH.4067
   PubMed Web of Science ®Google Scholar
• Huang, Y., Xu, L., Sun, Y., & Nabel, G. J. (2002). The assembly of Ebola virus nucleocapsid requires virion-associated proteins 35 and 24 and posttranslational modification of nucleoprotein. Molecular Cell, 10(2), 307–316. https://doi.org/10.1016/S1097-2765(02)00588-9
   PubMed Web of Science ®Google Scholar
• Huo, S., Massova, I., & Kollman, P. A. (2002). Computational alanine scanning of the 1:1 human growth hormone-receptor complex. Journal of Computational Chemistry, 23(1), 15–27. https://doi.org/10.1002/JCC.1153
   PubMed Web of Science ®Google Scholar
• Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008). CHARMM-GUI: A web-based graphical user interface for CHARMM. Journal of Computational Chemistry, 29(11), 1859–1865. https://doi.org/10.1002/JCC.20945
   PubMed Web of Science ®Google Scholar
• Judson, S., Prescott, J., & Munster, V. (2015). Understanding Ebola virus transmission. Viruses, 7(2), 511–521. https://doi.org/10.3390/V7020511
   PubMed Web of Science ®Google Scholar
• Kaur, H., Bruno, J. G., Kumar, A., & Sharma, T. K. (2018). Aptamers in the therapeutics and diagnostics pipelines. Theranostics, 8(15), 4016–4032. https://doi.org/10.7150/THNO.25958
   PubMed Web of Science ®Google Scholar
• Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. https://doi.org/10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar
• Kiley, M. P., Regnery, R. L., & Johnson, K. M. (1980). Ebola virus: Identification of virion structural proteins. The Journal of General Virology, 49(2), 333–341. https://doi.org/10.1099/0022-1317-49-2-333/CITE/REFWORKS
   PubMedGoogle Scholar
• Kilgour, M., Liu, T., Walker, B. D., Ren, P., & Simine, L. (2021). E2EDNA: Simulation protocol for DNA aptamers with ligands. Journal of Chemical Information and Modeling, 61(9), 4139–4144. https://doi.org/10.1021/ACS.JCIM.1C00696
   PubMed Web of Science ®Google Scholar
• Kirchdoerfer, R. N., Saphire, E. O., & Ward, A. B. (2019). Cryo-EM structure of the Ebola virus nucleoprotein–RNA comple. Acta Crystallographica. Section F, Structural Biology Communications, 75(Pt 5), 340–347. https://doi.org/10.1107/S2053230X19004424
   PubMedGoogle Scholar
• Ksiazek, T. G., West, C. P., Rollin, P. E., Jahrling, P. B., & Peters, C. J. (1999). ELISA for the detection of antibodies to Ebola viruses. The Journal of Infectious Diseases, 179 Suppl 1(s1), S192–S198. https://doi.org/10.1086/514313
   PubMedGoogle Scholar
• Kuo, T. C., Lee, P. C., Tsai, C. W., & Chen, W. Y. (2013). Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer – Thermodynamics and spectroscopic evidences. Journal of Molecular Recognition: JMR, 26(3), 149–159. https://doi.org/10.1002/JMR.2260
   PubMed Web of Science ®Google Scholar
• Lam, S. D., Das, S., Sillitoe, I., & Orengo, C. (2017). An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallographica. Section D, Structural Biology, 73(Pt 8), 628–640. https://doi.org/10.1107/S2059798317008920
   PubMedGoogle Scholar
• Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/ACS.JCTC.5B00935
   PubMed Web of Science ®Google Scholar
• Li, J., Zhu, J., Li, Y., Huang, T., & Li, Y. (2020). L-cysteine-modified magnetic microspheres for extraction and quantification of saxitoxin in rat plasma with liquid chromatography and tandem mass spectrometry. Journal of Separation Science, 43(12), 2429–2435. https://doi.org/10.1002/JSSC.202000070
   PubMed Web of Science ®Google Scholar
• Liao, X., Fu, H., Yan, T., & Lei, J. (2019). Electroactive metal–organic framework composites: Design and biosensing application. Biosensors & Bioelectronics, 146, 111743. https://doi.org/10.1016/J.BIOS.2019.111743
   PubMed Web of Science ®Google Scholar
• Lobanov, M. I., Bogatyreva, N. S., & Galzitskaia, O. V. (2008). Radius of gyration is indicator of compactness of protein structure. Molecular Biology, 42, 701–706.
   PubMed Web of Science ®Google Scholar
• Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011). ViennaRNA package 2.0. Algorithms for Molecular Biology: AMB, 6(1), 26. https://doi.org/10.1186/1748-7188-6-26/TABLES/2
   PubMed Web of Science ®Google Scholar
• Mairal, T., Ozalp, V. C., Lozano Sánchez, P., Mir, M., Katakis, I., & O'Sullivan, C. K. (2008). Aptamers: Molecular tools for analytical applications. Analytical and Bioanalytical Chemistry, 390(4), 989–1007. https://doi.org/10.1007/S00216-007-1346-4/FIGURES/5
   PubMed Web of Science ®Google Scholar
• Makiala, S., Mukadi, D., De Weggheleire, A., Muramatsu, S., Kato, D., Inano, K., Gondaira, F., Kajihara, M., Yoshida, R., Changula, K., Mweene, A., Mbala-Kingebeni, P., Muyembe-Tamfum, J.-J., Masumu, J., Ahuka, S., & Takada, A. (2019). Clinical Evaluation of Quicknavitm-Ebola in the 2018 outbreak of Ebola virus disease in the Democratic Republic of the Congo. Viruses, 11(7), 589. https://doi.org/10.3390/v11070589.
   PubMed Web of Science ®Google Scholar
• Martin, D. R., Sibuyi, N. R., Dube, P., Fadaka, A. O., Cloete, R., Onani, M., Madiehe, A. M., & Meyer, M. (2021). Aptamer-based diagnostic systems for the rapid screening of TB at the point-of-care. Diagnostics, 11(8), 1352. https://doi.org/10.3390/DIAGNOSTICS11081352
   Web of Science ®Google Scholar
• Massova, I., & Kollman, P. A. (1999). Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. Journal of the American Chemical Society, 121(36), 8133–8143. https://doi.org/10.1021/JA990935J/SUPPL_FILE/JA990935J_S.PDF
   Web of Science ®Google Scholar
• Maszota-Zieleniak, M., Zsila, F., & Samsonov, S. A. (2021). Computational insights into heparin-small molecule interactions: Evaluation of the balance between stacking and non-stacking binding modes. Carbohydrate Research, 507, 108390. https://doi.org/10.1016/J.CARRES.2021.108390
   PubMed Web of Science ®Google Scholar
• Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., & Turner, D. H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America, 101(19), 7287–7292. https://doi.org/10.1073/PNAS.0401799101
   PubMed Web of Science ®Google Scholar
• Moran, Z., Rodriguez, W., Ahmadou, D., Soropogui, B., Magassouba, N. F., Kelly-Cirino, C., & Ben Amor, Y. (2020). Comparative performance study of three Ebola rapid diagnostic tests in Guinea. BMC Infectious Diseases, 20(1), 670. https://doi.org/10.1186/S12879-020-05339-2
   PubMed Web of Science ®Google Scholar
• Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2010). Protein-protein docking dealing with the unknown. Journal of Computational Chemistry, 31(2), 317–342. https://doi.org/10.1002/JCC.21276
   PubMed Web of Science ®Google Scholar
• Musyoka, T., & Bishop, Ö. T. (2019). South African Abietane diterpenoids and their analogs as potential antimalarials: Novel insights from hybrid computational approaches. Molecules, 24(22), 4036. https://doi.org/10.3390/MOLECULES24224036
   PubMed Web of Science ®Google Scholar
• Nagatoishi, S., Isono, N., Tsumoto, K., & Sugimoto, N. (2011). Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding. Biochimie, 93(8), 1231–1238. https://doi.org/10.1016/J.BIOCHI.2011.03.013
   PubMed Web of Science ®Google Scholar
• Ni, S., Yao, H., Wang, L., Lu, J., Jiang, F., Lu, A., & Zhang, G. (2017). Chemical modifications of nucleic acid aptamers for therapeutic purposes. International Journal of Molecular Sciences, 18(8), 1683. https://doi.org/10.3390/IJMS18081683
   PubMed Web of Science ®Google Scholar
• Niikura, M., Ikegami, T., Saijo, M., Kurane, I., Miranda, M. E., & Morikawa, S. (2001). Detection of Ebola viral antigen by enzyme-linked immunosorbent assay using a novel monoclonal antibody to nucleoprotein. Journal of Clinical Microbiology, 39(9), 3267–3271. https://doi.org/10.1128/JCM.39.9.3267-3271.2001/ASSET/2863C2CC-44F0-422C-9DD2-7155EB44E166/ASSETS/GRAPHIC/JM0911453004.JPEG
   PubMed Web of Science ®Google Scholar
• Noda, T., Hagiwara, K., Sagara, H., & Kawaoka, Y. (2010). Characterization of the Ebola virus nucleoprotein-RNA complex. The Journal of General Virology, 91(Pt 6), 1478–1483. https://doi.org/10.1099/VIR.0.019794-0/CITE/REFWORKS
   PubMedGoogle Scholar
• Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2015). GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Computer Physics Communications, 186, 105–107. https://doi.org/10.1016/j.cpc.2014.09.010
   Google Scholar
• PyMOL Setting:H_bond. (2022). [PyMOL documentation]. https://pymol.org/dokuwiki/doku.php?id=setting:h_bond
   Google Scholar
• Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7(1), 95–99. https://doi.org/10.1016/S0022-2836(63)80023-6
   PubMed Web of Science ®Google Scholar
• Reddy, M., Reddy, C., Rathore, R., Erion, M., Aparoy, P., Reddy, R., & Reddanna, P. (2014). Free energy calculations to estimate ligand-binding affinities in structure-based drug design. Current Pharmaceutical Design, 20(20), 3323–3337. https://doi.org/10.2174/13816128113199990604.
   PubMed Web of Science ®Google Scholar
• Reusken, C., Niedrig, M., Pas, S., Anda, P., Baize, S., Charrel, R., Di Caro, A., Drosten, C., Fernandez-Garcia, M. D., Franco, L., Gunther, S., Leparc-Goffart, I., Martina, B., Pannetier, D., Papa, A., Sanchez-Seco, M. P., Vapalahti, O., & Koopmans, M. (2015). Identification of essential outstanding questions for an adequate European laboratory response to Ebolavirus Zaire West Africa 2014. Journal of Clinical Virology, 62, 124–134. https://doi.org/10.1016/J.JCV.2014.11.007
   PubMed Web of Science ®Google Scholar
• Rhinehardt, K. L., Mohan, R. V., & Srinivas, G. (2015). Computational modeling of peptide–aptamer binding. Methods in Molecular Biology, 1268, 313–333. https://doi.org/10.1007/978-1-4939-2285-7_14
   PubMedGoogle Scholar
• Riccitelli, N. J., & Lupták, A. (2010). Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods, 52(2), 133–140. https://doi.org/10.1016/J.YMETH.2010.06.005
   PubMed Web of Science ®Google Scholar
• Rifai, E. A., Van Dijk, M., Vermeulen, N. P. E., Yanuar, A., & Geerke, D. P. (2019). A Comparative linear interaction energy and MM/PBSA study on SIRT1-ligand binding free energy calculation. Journal of Chemical Information and Modeling, 59(9), 4018–4033. https://doi.org/10.1021/ACS.JCIM.9B00609/SUPPL_FILE/CI9B00609_SI_002.ZIP
   PubMed Web of Science ®Google Scholar
• Rohloff, J. C., Gelinas, A. D., Jarvis, T. C., Ochsner, U. A., Schneider, D. J., Gold, L., & Janjic, N. (2014). Nucleic acid ligands with protein-like side chains: Modified aptamers and their use as diagnostic and therapeutic agents. Molecular Therapy. Nucleic Acids, 3(10), e201. https://doi.org/10.1038/MTNA.2014.49
   PubMedGoogle Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/NAR/GKV315
   PubMed Web of Science ®Google Scholar
• Schubert, T., & Längst, G. (2015). Studying epigenetic interactions using microscale thermophoresis (MST). AIMS Biophysics, 2(3), 370–380. https://doi.org/10.3934/biophy.2015.3.370
   Google Scholar
• Semper, A. E., Broadhurst, M. J., Richards, J., Foster, G. M., Simpson, A. J. H., Logue, C. H., Kelly, J. D., Miller, A., Brooks, T. J. G., Murray, M., & Pollock, N. R. (2016). Performance of the GeneXpert Ebola assay for diagnosis of Ebola virus disease in Sierra Leone: A field evaluation study. PLoS Medicine, 13(3), e1001980. https://doi.org/10.1371/JOURNAL.PMED.1001980
   PubMed Web of Science ®Google Scholar
• Shangguan, D., Tang, Z., Mallikaratchy, P., Xiao, Z., & Tan, W. (2007). Optimization and modifications of aptamers selected from live cancer cell lines. Chembiochem: A European Journal of Chemical Biology, 8(6), 603–606. https://doi.org/10.1002/cbic.200600532
   PubMed Web of Science ®Google Scholar
• Sharawy, M., & Consta, S. (2018). Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K Ions. The Journal of Chemical Physics, 149(22), 225102. https://doi.org/10.1063/1.5050534
   PubMed Web of Science ®Google Scholar
• Shubham, S., Hoinka, J., Banerjee, S., Swanson, E., Dillard, J. A., Lennemann, N. J., Przytycka, T. M., Maury, W., & Nilsen-Hamilton, M. (2018). A 2’FY-RNA motif defines an aptamer for Ebolavirus secreted protein. Scientific Reports, 8(1), 12373. https://doi.org/10.1038/S41598-018-30590-8
   PubMedGoogle Scholar
• Sino Biological Inc. (2022). ELISA test (Elisa for Ebola). SinoBiological ELISA for Ebola Virus Disease (EVD) Available online: http://www.elisa-antibody.com/ELISA-test/elisa-for-ebola-hf.html
   Google Scholar
• Sugita, Y., Matsunami, H., Kawaoka, Y., Noda, T., & Wolf, M. (2018). Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution. Nature, 563(7729), 137–140. https://doi.org/10.1038/s41586-018-0630-0
   PubMed Web of Science ®Google Scholar
• Sykes, J., Holland, B., & Charleston, M. (2022). Unattained geometric configurations of secondary structure elements in protein structural space. Journal of Structural Biology, 214, 107870. https://doi.org/10.1016/j.jsb.2022.107870
   Google Scholar
• Tan, S. Y., Acquah, C., Sidhu, A., Ongkudon, C. M., Yon, L. S., & Danquah, M. K. (2016). SELEX modifications and bioanalytical techniques for aptamer–target binding characterization. Critical Reviews in Analytical Chemistry, 46(6), 521–537. https://doi.org/10.1080/10408347.2016.1157014
   PubMed Web of Science ®Google Scholar
• Tao, X., Wang, X., Liu, B., & Liu, J. (2020). Conjugation of antibodies and aptamers on nanozymes for developing biosensors. Biosensors & Bioelectronics, 168, 112537. https://doi.org/10.1016/J.BIOS.2020.112537
   PubMed Web of Science ®Google Scholar
• Uversky, V. N. (2017). How to predict disorder in a protein of interest. Methods in Molecular Biology, 1484, 137–158. https://doi.org/10.1007/978-1-4939-6406-2_11
   PubMedGoogle Scholar
• Vainer, R., Cohen, S., Shahar, A., Zarivach, R., & Arbely, E. (2016). Structural basis for P53 Lys120-acetylation-dependent DNA-binding mode. Journal of Molecular Biology, 428(15), 3013–3025. https://doi.org/10.1016/J.JMB.2016.06.009
   PubMed Web of Science ®Google Scholar
• Vajda, T., & Perczel, A. (2016). The clear and dark sides of water: Influence on the coiled coil folding domain. Biomolecular Concepts, 7(3), 189–195. https://doi.org/10.1515/BMC-2016-0005/MACHINEREADABLECITATION/RIS
   PubMedGoogle Scholar
• Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). Gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/ACS.JCTC.1C00645/SUPPL_FILE/CT1C00645_SI_001.PDF
   PubMed Web of Science ®Google Scholar
• Van Vuren, P. J., Grobbelaar, A., Storm, N., Conteh, O., Konneh, K., Kamara, A., Sanne, I., & Paweska, J. T. (2015). Comparative evaluation of the diagnostic performance of the prototype cepheid GeneXpert Ebola assay. Journal of Clinical Microbiology, 54(2), 359–367. https://doi.org/10.1128/JCM.02724-15
   PubMed Web of Science ®Google Scholar
• Van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., Van Dijk, M., De Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/J.JMB.2015.09.014
   PubMed Web of Science ®Google Scholar
• Vriend, G. (1990). WHAT IF: A molecular modeling and drug design program. Journal of Molecular Graphics, 8(1), 52–56, 29. https://doi.org/10.1016/0263-7855(90)80070-V
   PubMedGoogle Scholar
• Waddad, A. Y., Ramharack, P., Soliman, M. E. S., & Govender, T. (2019). Grafted hyaluronic acid N-acetyl-l-methionine for targeting of LAT1 receptor: In-silico, synthesis and microscale thermophoresis studies. International Journal of Biological Macromolecules, 125, 767–777. https://doi.org/10.1016/J.IJBIOMAC.2018.12.104
   PubMed Web of Science ®Google Scholar
• Wang, C., Greene, D., Xiao, L., Qi, R., & Luo, R. (2017). Recent developments and applications of the MMPBSA method. Frontiers in Molecular Biosciences, 4, 87. https://doi.org/10.3389/FMOLB.2017.00087/BIBTEX
   PubMed Web of Science ®Google Scholar
• Wang, T., Chen, L., Chikkanna, A., Chen, S., Brusius, I., Sbuh, N., & Veedu, R. N. (2021). Development of nucleic acid aptamer-based lateral flow assays: A robust platform for cost-effective point-of-care diagnosis. Theranostics, 11(11), 5174–5196. https://doi.org/10.7150/thno.56471
   PubMed Web of Science ®Google Scholar
• Wang, X., Gao, X., He, J., Hu, X., Li, Y., Li, X., Fan, L., & Yu, H. Z. (2019). Systematic truncating of aptamers to create high-performance graphene oxide (GO)-based aptasensors for the multiplex detection of mycotoxins. The Analyst, 144(12), 3826–3835. https://doi.org/10.1039/C9AN00624A
   PubMed Web of Science ®Google Scholar
• WHO Ebola Outbreak. (2021). North Kivu. https://www.who.int/emergencies/situations/ebola-2021-north-kivu
   Google Scholar
• WHO. (2022). Ebola Virus Disease. https://www.who.int/news-room/fact-sheets/detail/ebola-virus-disease
   Google Scholar
• WHO Laboratory Diagnosis of Ebola Virus Disease. (2022). https://apps.who.int/iris/bitstream/handle/10665/134009/WHO_EVD_GUIDANCE_L%20AB_14.1;jsessionid=A139094B4D95C076BB7FBC7032AD1F1D?sequence=1> 2014 (accessed on 19 January 2022)
   Google Scholar
• Xie, Y. C., Eriksson, L. A., & Zhang, R. B. (2020). Molecular dynamics study of the recognition of ATP by nucleic acid aptamers. Nucleic Acids Research, 48(12), 6471–6480. https://doi.org/10.1093/NAR/GKAA428
   PubMed Web of Science ®Google Scholar
• Yan, A. C., & Levy, M. (2018). Aptamer-mediated delivery and cell-targeting aptamers: Room for improvement. Nucleic Acid Therapeutics, 28(3), 194–199. https://doi.org/10.1089/NAT.2018.0732
   PubMed Web of Science ®Google Scholar
• Zhang, H., Zhang, C., Li, Z., Li, C., Wei, X., Zhang, B., & Liu, Y. (2019). A new method of RNA secondary structure prediction based on convolutional neural network and dynamic programming. Frontiers in Genetics, 10, 467. https://doi.org/10.3389/FGENE.2019.00467/BIBTEX
   PubMed Web of Science ®Google Scholar
• Zhao, L., Wang, J., Su, D., Zhang, Y., Lu, H., Yan, X., Bai, J., Gao, Y., & Lu, G. (2020). The DNA controllable peroxidase mimetic activity of MoS2 nanosheets for constructing a robust colorimetric biosensor. Nanoscale, 12(37), 19420–19428. https://doi.org/10.1039/D0NR05649A
   PubMed Web of Science ®Google Scholar
• Zhu, G., Zhang, H., Jacobson, O., Wang, Z., Chen, H., Yang, X., Niu, G., & Chen, X. (2017). Combinatorial screening of DNA aptamers for molecular imaging of HER2 in cancer. Bioconjugate Chemistry, 28(4), 1068–1075. https://doi.org/10.1021/ACS.BIOCONJCHEM.6B00746
   PubMed Web of Science ®Google Scholar
• Zhu, X., Zhang, Y., Liu, M., & Liu, Y. (2021). 2D titanium carbide MXenes as emerging optical biosensing platforms. Biosensors & Bioelectronics, 171, 112730. https://doi.org/10.1016/J.BIOS.2020.112730
   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