High-Affinity Anti-nivolumab DNA Aptamer: A Novel Capture Reagent for Its Bioanalysis by an Enzyme-Linked Aptamer Assay

Bioanalysis of the immune checkpoint inhibitor nivolumab is crucial for pharmacokinetic studies. However, conventional ligand-binding assays (LBAs) often suffer from the lot-to-lot variability of capture antibodies. Here, we developed a high-affinity anti-nivolumab DNA aptamer as a robust alternative reagent. An integrated strategy combining Fast Protein Liquid Chromatography-based screening, next-generation sequencing, aptamer search algorithm, and computational modeling enabled rapid aptamer identification and optimization. The anti-nivolumab aptamer, mutant 2-3, discovered through in silico modification exhibited a dissociation constant (KD) of 33 nM. Using this aptamer, an enzyme-linked aptamer assay (ELAA) successfully quantified nivolumab in 400-fold diluted plasma samples over a range of 0.02–5.0 µg/mL, demonstrating good precision with a coefficient of variation less than 11.9%. This novel analytical method provides a sufficient quantitative range for the bioanalysis of nivolumab, thus offering a robust, specific, and cost-effective alternative for future pharmacokinetic studies.