References
-
Jolles, A. et al. Endemic persistence of a highly contagious pathogen: Foot-and-mouth disease in its wildlife host. Sci. (New York N Y). 374, 104–109. https://doi.org/10.1126/science.abd2475 (2021).
-
Tang, H. et al. Immunogenicity analysis of the E. coli expressed structural protein VP1 of persistent infection foot-and-mouth disease virus. Virology 579, 111–118. https://doi.org/10.1016/j.virol.2023.01.004 (2023).
-
Ranjitha, H. B. et al. Thermostable negative-marker foot-and-mouth disease virus serotype O induces protective immunity in Guinea pigs. Appl. Microbiol. Biotechnol. 107, 1285–1297. https://doi.org/10.1007/s00253-023-12359-w (2023).
-
Beck-Johnson, L. M. et al. An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study. Epidemics 42, 100668. https://doi.org/10.1016/j.epidem.2023.100668 (2023).
-
Wang, Y. et al. Development and evaluation of multiplex real-time RT-PCR assays for the detection and differentiation of foot-and-mouth disease virus and Seneca Valley virus 1. Transbound. Emerg. Dis. 67, 604–616. https://doi.org/10.1111/tbed.13373 (2020).
-
Reeve, R. et al. Tracking the antigenic evolution of Foot-and-Mouth disease virus. PLoS One. 11, e0159360. https://doi.org/10.1371/journal.pone.0159360 (2016).
-
Jamal, S. M. & Belsham, G. J. Foot-and-mouth disease: past, present and future. Vet. Res. 44, 116. https://doi.org/10.1186/1297-9716-44-116 (2013).
-
Jara, M., Frias-De-Diego, A., Dellicour, S., Baele, G. & Machado, G. Tracing foot-and-mouth disease virus phylogeographical patterns and transmission dynamics. bioRxiv, 590612 https://doi.org/10.1101/590612 (2019).
-
Chathuranga, W. A. G. et al. Efficacy of a novel multiepitope vaccine candidate against Foot-and-Mouth disease virus serotype O and A. Vaccines (Basel). 10. https://doi.org/10.3390/vaccines10122181 (2022).
-
Wong, C. L., Yong, C. Y., Ong, H. K., Ho, K. L. & Tan, W. S. Advances in the diagnosis of Foot-and-Mouth disease. Front. Vet. Sci. 7, 477. https://doi.org/10.3389/fvets.2020.00477 (2020).
-
Park, K. S. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens. Bioelectron. 102, 179–188. https://doi.org/10.1016/j.bios.2017.11.028 (2018).
-
Wang, T. et al. Development of nucleic acid aptamer-based lateral flow assays: A robust platform for cost-effective point-of-care diagnosis. Theranostics 11, 5174–5196. https://doi.org/10.7150/thno.56471 (2021).
-
Tang, L. et al. De Novo evolution of an Antibody-Mimicking multivalent aptamer via a DNA framework. Small Methods. 7, e2300327. https://doi.org/10.1002/smtd.202300327 (2023).
-
Wang, T., Rahimizadeh, K. & Veedu, R. N. Development of a novel DNA oligonucleotide targeting Low-Density lipoprotein receptor. Mol. Ther. Nucleic Acids. 19, 190–198. https://doi.org/10.1016/j.omtn.2019.11.004 (2020).
-
Navien, T. N., Thevendran, R., Hamdani, H. Y., Tang, T. H. & Citartan, M. In Silico molecular Docking in DNA aptamer development. Biochimie 180, 54–67. https://doi.org/10.1016/j.biochi.2020.10.005 (2021).
-
Andronescu, M. et al. Algorithms for testing that sets of DNA words concatenate without secondary structure. Nat. Comput. 2, 391–415. https://doi.org/10.1023/B:NACO.0000006770.91995.ec (2003).
-
Lu, J. S., Bindewald, E., Kasprzak, W. K. & Shapiro, B. A. RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinformatics 34, 4297–4299. https://doi.org/10.1093/bioinformatics/bty468 (2018).
-
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865. https://doi.org/10.1002/jcc.20945 (2008).
-
Yan, Y., Zhang, D., Zhou, P., Li, B. & Huang, S. Y. HDOCK: a web server for protein-protein and protein-DNA/RNA Docking based on a hybrid strategy. Nucleic Acids Res. 45, W365–W373. https://doi.org/10.1093/nar/gkx407 (2017).
-
Tan, S. Y. et al. SELEX modifications and bioanalytical techniques for Aptamer-Target binding characterization. Crit. Rev. Anal. Chem. 46, 521–537. https://doi.org/10.1080/10408347.2016.1157014 (2016).
-
Oliveira, R. et al. Modelling aptamers with nucleic acid mimics (NAM): from sequence to three-dimensional Docking. PLoS One. 17, e0264701. https://doi.org/10.1371/journal.pone.0264701 (2022).
-
Parisien, M., Cruz, J. A., Westhof, E. & Major, F. New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA 15, 1875–1885. https://doi.org/10.1261/rna.1700409 (2009).
-
Vivekananda, J. & Kiel, J. L. Anti-Francisella tularensis DNA aptamers detect tularemia antigen from different subspecies by Aptamer-Linked immobilized sorbent assay. Lab. Invest. 86, 610–618. https://doi.org/10.1038/labinvest.3700417 (2006).
-
McKeague, M. et al. Selection and characterization of a novel DNA aptamer for label-free fluorescence biosensing of Ochratoxin A. Toxins (Basel). 6, 2435–2452. https://doi.org/10.3390/toxins6082435 (2014).
-
de Lacerda, S., Almeida, C. M., Santos, N. B. F. D., Plentz, V. C. F., de Andrade, A. S. R. & F. & Foot-and-mouth disease virus: DNA aptamer selection for the 3ABC protein. Virus Res. 323, 199008. https://doi.org/10.1016/j.virusres.2022.199008 (2023).
-
Nordin, N. A. et al. Aptamer-Based detection of Foot-and-Mouth disease virus using Single-Stranded DNA probe. Appl. Biochem. Biotechnol. 197, 1760–1772. https://doi.org/10.1007/s12010-024-05093-0 (2025).
-
Tolle, F., Wilke, J., Wengel, J. & Mayer, G. Byproduct formation in repetitive PCR amplification of DNA libraries during SELEX. PLoS One. 9, e114693. https://doi.org/10.1371/journal.pone.0114693 (2014).
-
Quintela, I. A. et al. Elucidating the molecular Docking and binding dynamics of aptamers with Spike proteins across SARS-CoV-2 variants of concern. Front. Microbiol. 16, 1503890. https://doi.org/10.3389/fmicb.2025.1503890 (2025).
-
Reuss, A. J., Vogel, M., Weigand, J. E., Suess, B. & Wachtveitl, J. Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations. Biophys. J. 107, 2962–2971. https://doi.org/10.1016/j.bpj.2014.11.001 (2014).
-
Sun, D. et al. Computational tools for aptamer identification and optimization. TRAC Trends Anal. Chem. 157 https://doi.org/10.1016/j.trac.2022.116767 (2022).
-
Patel, D. J. et al. Structure, recognition and adaptive binding in RNA aptamer complexes. J. Mol. Biol. 272, 645–664. https://doi.org/10.1006/jmbi.1997.1281 (1997).
-
Curtale, G. & Citarella, F. Dynamic nature of noncoding RNA regulation of adaptive immune response. Int. J. Mol. Sci. 14, 17347–17377. https://doi.org/10.3390/ijms140917347 (2013).
-
Laing, C. & Schlick, T. Computational approaches to RNA structure prediction, analysis, and design. Curr. Opin. Struct. Biol. 21, 306–318. https://doi.org/10.1016/j.sbi.2011.03.015 (2011).
-
Wang, T. et al. A detailed Protein-SELEX protocol allowing visual assessments of individual steps for a high success rate. Hum. Gene Therapy Methods. 30, 1–16. https://doi.org/10.1089/hgtb.2018.237 (2019).
-
Hu, B. et al. Study of the binding mechanism of aptamer to palytoxin bydocking and molecular simulation. Sci. Rep. 9, 15494. https://doi.org/10.1038/s41598-019-52066-z (2019).
