De Novo Development of Fluorogenic RNA-Based Biosensors Using Capture-SELEX in Tandem with Droplet Microfluidics

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Abstract
The detection of small molecules (e.g., pesticides, pollutants, antibiotics, drug residues) is critical for human health and environmental surveys as well as for many industrial applications. Fluorogenic RNA-based biosensors (FRBs) are aptamer-based tools specifically reporting on the presence of such targets by converting a specific binding event into fluorescence emission, thus making them of particular interest for on-site sensing applications. However, new sensor aptamers suited for FRB development are tedious to develop. In this study, we show that Capture-SELEX used in tandem with our microfluidic-assisted screening technology (μIVC) accelerates de novo FRB development by reprogramming the specificity of an existing sensor aptamer, followed by fluorescence-based functional selection. Furthermore, we show that these new sensor aptamers can be repurposed into functional biotechnological tools, such as gene-regulating aptazymes, thus demonstrating the versatility of our pipeline for the development of sensor aptamers adapted for various applications.
Funding Information
  • Agence Nationale de la Recherche (ANR-10-IDEX-0002)
  • Agence Nationale de la Recherche (ANR-17-EURE-0023)
  • Agence Nationale de la Recherche (ANR-20- SFRI0012)
  • Fondation pour la Recherche M?dicale (FDT202304016628)
  • Fondation pour la Recherche M?dicale (FDT202504020198)
  • Centre National de la Recherche Scientifique
  • Laboratoire d'Excellence NetRNA (ANR-10-LABX-0036)

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