title: More DNA-Aptamers for Small Drugs: A Capture-SELEX Coupled with Surface Plasmon Resonance and High-Throughput Sequencing.
abstract: To address limitations in the production of DNA aptamers against small molecules, we introduce a DNA-based capture-SELEX (systematic evolution of ligands by exponential enrichment) protocol with long and continuous randomized library for more flexibility, coupled with in-stream direct-specificity monitoring via SPR and high throughput sequencing (HTS). Applying this capture-SELEX on tobramycin shows that target-specificity arises at cycle number 8, which is confirmed by sequence convergence in HTS analysis. Interestingly, HTS also shows that the most enriched sequences are already visible after only two capture-SELEX cycles. The best aptamers displayed K(D) of approximately 200 nM, similar to RNA and DNA-based aptamers previously selected for tobramycin. The lowest concentration of tobramycin detected on label-free SPR experiments with the selected aptamers is 20-fold smaller than the clinical range limit, demonstrating suitability for small-drug biosensing.
authors: †Institute of Bioengineering, Ecole Polytechnique Féderale De Lausanne (EPFL), Lausanne, Vaud, 1015, Switzerland.
authors: Fabio M
authors: FM
authors: Spiga
authors: ‡Structural Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.
authors: Paolo
authors: P
authors: Maietta
authors: †Institute of Bioengineering, Ecole Polytechnique Féderale De Lausanne (EPFL), Lausanne, Vaud, 1015, Switzerland.
authors: Carlotta
authors: C
authors: Guiducci
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D057166:High-Throughput Screening Assays; D008024:Ligands; D008969:Molecular Sequence Data; D052156:SELEX Aptamer Technique; D016415:Sequence Alignment; D020349:Surface Plasmon Resonance
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D004247:DNA
keywords: SELEX; aptamer; small molecules; surface plasmon resonance