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Background <p>Despite the increasing prominence of small extracellular vesicles (sEVs) and liquid biopsies for early cancer diagnosis, the development of high-performance molecular probes specifically targeting sEVs remains limited. In this study, we present a novel enzymatic digestion sEV-systematic evolution of ligands by exponential enrichment (EDGE-SELEX) strategy that eliminates the need for sEV immobilization, thereby preserving the native structural and biochemical characteristics of sEVs and better mimicking their clinical environment.</p> Results <p>Using the EDGE-SELEX approach combined with a post-selection optimization process, we successfully identified two novel aptamers, H7F-3 and H15F, exhibiting high affinity for colorectal cancer (CRC)-derived sEVs, with dissociation constants of 8.149 and 3.347 nM, respectively. Structural analysis suggested that the G6 motif plays an important role in aptamer-sEV binding. This motif also demonstrated potential for incorporation into split and blocking aptamer designs. Furthermore, we developed an aptamer-based loop-mediated isothermal amplification for sEV detection (ABLE) system, which achieved detection limit of 20 particles/µL for CRC-derived sEVs.</p> Conclusions <p>Our findings demonstrate the applicability of SELEX technology to native sEVs and highlight the diagnostic potential of the identified aptamers for sEV-based cancer detection. The EDGE-SELEX method and the G6 motif may serve as valuable tools for future clinical applications in non-invasive cancer diagnostics and aptamer engineering, although further validation with clinical samples is warranted.</p> Graphical abstract <p></p>

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Immobilization-free SELEX for aptamer discovery targeting colorectal cancer-derived small extracellular vesicles

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月25日

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  • Eun Sung Lee,
  • Byung Seok Cha,
  • Junhyeong Kim,
  • Seung Hyeon Reo,
  • Jinseo Son,
  • Ki Soo Park

摘要

Background

Despite the increasing prominence of small extracellular vesicles (sEVs) and liquid biopsies for early cancer diagnosis, the development of high-performance molecular probes specifically targeting sEVs remains limited. In this study, we present a novel enzymatic digestion sEV-systematic evolution of ligands by exponential enrichment (EDGE-SELEX) strategy that eliminates the need for sEV immobilization, thereby preserving the native structural and biochemical characteristics of sEVs and better mimicking their clinical environment.

Results

Using the EDGE-SELEX approach combined with a post-selection optimization process, we successfully identified two novel aptamers, H7F-3 and H15F, exhibiting high affinity for colorectal cancer (CRC)-derived sEVs, with dissociation constants of 8.149 and 3.347 nM, respectively. Structural analysis suggested that the G6 motif plays an important role in aptamer-sEV binding. This motif also demonstrated potential for incorporation into split and blocking aptamer designs. Furthermore, we developed an aptamer-based loop-mediated isothermal amplification for sEV detection (ABLE) system, which achieved detection limit of 20 particles/µL for CRC-derived sEVs.

Conclusions

Our findings demonstrate the applicability of SELEX technology to native sEVs and highlight the diagnostic potential of the identified aptamers for sEV-based cancer detection. The EDGE-SELEX method and the G6 motif may serve as valuable tools for future clinical applications in non-invasive cancer diagnostics and aptamer engineering, although further validation with clinical samples is warranted.

Graphical abstract