A method for selecting structure-switching aptamers applied to a colorimetric gold nanoparticle assay

Area of Science:

• Biochemistry
• Molecular Biology
• Nanotechnology

Background:

• Small molecules are crucial biomarkers for human health and performance, making them ideal targets for biosensing.
• Nucleic acid aptamers are effective recognition elements in biosensors, but selecting them for small molecules presents unique challenges.
• Existing aptamer selection methods often require target immobilization or suffer from low partitioning efficiency.

Purpose of the Study:

• To describe a modified method for selecting structure-switching aptamers specifically for small molecule targets.
• To address limitations in partitioning efficiency and background sequence removal in aptamer selection.
• To develop a robust aptamer-based biosensor with a rapid, colorimetric readout for small molecule detection.

Main Methods:

• Utilized DNA aptamer libraries hybridized to complementary DNA capture probes on magnetic beads.
• Employed target-induced conformational changes for separating binding sequences from non-binders.
• Incorporated negative selection steps, simplified enrichment monitoring, and extended capture probe length for enhanced stringency.
• Developed a gold nanoparticle assay for colorimetric detection based on aptamer conformational changes.

Main Results:

• The modified selection method demonstrated improved stringency and efficiency in isolating aptamers against small molecules.
• Selected structure-switching aptamers successfully reported target presence through conformational changes.
• The gold nanoparticle assay provided a simple, rapid colorimetric readout suitable for clinical applications.
• Proof-of-principle experiments in buffer established a foundation for biosensing in physiological fluids.

Conclusions:

• The developed method offers an advantageous approach for selecting aptamers against small molecules without target immobilization.
• The structure-switching aptamers and gold nanoparticle assay provide a promising platform for sensitive and rapid small molecule biosensing.
• Further optimization holds potential for real-world applications in clinical diagnostics and health monitoring.