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Peer-reviewedCC BY 4.0Molecular Therapy: Nucleic Acids

Selection and characterization of ssDNA aptamers targeting tick-borne encephalitis virus particles

  • Yuji Fujii1
  • Tomohiro Shinozaki2
  • Minato Hirano3
  • Mizuki Fukuta3
  • Taiichi Sakamoto2
  • Kentaro Yoshii4
4 affiliations
  1. 1Department of Viral Ecology, Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; Experimental Animal Research Division, Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
  2. 2Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
  3. 3Department of Viral Ecology, Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan
  4. 4Department of Viral Ecology, Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; Corresponding author: Kentaro Yoshii, Department of Viral Ecology, Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan.
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Abstract

Aptamers are single-stranded nucleic acids that bind to target molecules with high affinity, serving as versatile molecular tools for diagnostic and therapeutic applications. Although several aptamers against the envelope (E) protein of tick-borne encephalitis virus (TBEV) have been reported, their recognition of native viral particles remain insufficiently characterized. We identified novel ssDNA aptamers against TBEV through systematic evolution of ligands by exponential enrichment (SELEX) using a recombinant E protein that preserved the major antigenic properties of viral particles. The four major aptamer candidates showed binding activity not only to TBEV E proteins but also to TBEV-derived subviral particles. Additionally, these aptamers recognized TBEV-infected cells and retained their binding activity under serum conditions mimicking the in vivo environment. Some aptamers also exhibited inhibitory effects against TBEV infection in vitro . Furthermore, sequence truncation yielded optimized variants that retained high target affinity, demonstrated enhanced serum stability over 24 h, and neutralized viral infection. These findings provide crucial functional validation of ssDNA aptamers targeting TBEV particles and support their development as antibody-independent platforms for diagnostic, antiviral, and targeted delivery strategies for TBEV and related flaviviruses.

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Cite

BibTeXRIS
BibTeX
@article{fujii2026selection,
  title = {{Selection and characterization of ssDNA aptamers targeting tick-borne encephalitis virus particles}},
  author = {Yuji Fujii and Tomohiro Shinozaki and Minato Hirano and Mizuki Fukuta and Taiichi Sakamoto and Kentaro Yoshii},
  journal = {Molecular Therapy: Nucleic Acids},
  year = {2026},
  month = oct,
  doi = {10.1016/j.omtn.2026.103138},
  url = {https://doi.org/10.1016/j.omtn.2026.103138},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Selection and characterization of ssDNA aptamers targeting tick-borne encephalitis virus particles
AU  - Yuji Fujii
AU  - Tomohiro Shinozaki
AU  - Minato Hirano
AU  - Mizuki Fukuta
AU  - Taiichi Sakamoto
AU  - Kentaro Yoshii
PY  - 2026
DA  - 2026/10/12
JO  - Molecular Therapy: Nucleic Acids
DO  - 10.1016/j.omtn.2026.103138
UR  - https://doi.org/10.1016/j.omtn.2026.103138
AB  - Aptamers are single-stranded nucleic acids that bind to target molecules with high affinity, serving as versatile molecular tools for diagnostic and therapeutic applications. Although several aptamers against the envelope (E) protein of tick-borne encephalitis virus (TBEV) have been reported, their recognition of native viral particles remain insufficiently characterized. We identified novel ssDNA aptamers against TBEV through systematic evolution of ligands by exponential enrichment (SELEX) using a recombinant E protein that preserved the major antigenic properties of viral particles. The four major aptamer candidates showed binding activity not only to TBEV E proteins but also to TBEV-derived subviral particles. Additionally, these aptamers recognized TBEV-infected cells and retained their binding activity under serum conditions mimicking the in vivo environment. Some aptamers also exhibited inhibitory effects against TBEV infection in vitro . Furthermore, sequence truncation yielded optimized variants that retained high target affinity, demonstrated enhanced serum stability over 24 h, and neutralized viral infection. These findings provide crucial functional validation of ssDNA aptamers targeting TBEV particles and support their development as antibody-independent platforms for diagnostic, antiviral, and targeted delivery strategies for TBEV and related flaviviruses.
SN  - 2162-2531
ER  -