Validation of Aptamer–Protein Interactions by Biolayer Interferometry: A Study of 88 Candidate Molecules

Abstract

An aptamer’s low mass confines the label-free response to hundredths of a nanometer, where artifacts mimic binding yet yield computable dissociation constants. To define and test a priori criteria distinguishing binding from artifact, 88 computationally designed aptamers against seven human proteins were studied by biolayer interferometry in two orthogonal configurations, with control antibodies. Six criteria, fixed in advance, are reported as a priori decision rules, not validated requirements. Control antibodies validated 6 of 8 preparations; for the other 68 pairs, the maximum response was 0.019–0.219 nm, bounding KD at ≥8.6 µM, 120-fold above the 70 nM threshold. Two of three signals clearing it gave exponents far above the 1:1 expectation (1.04 vs. 0.31; 0.85 vs. 0.41); the third failed parameter consistency (KD scatter ×28). Rankings on two PCSK9 preparations did not correlate (ρ = −0.26); predicted and experimental KD differed by 3–7 orders of magnitude (ρ = 0.497, n = 25). No aptamer reached the predefined affinity under the conditions tested. Local fitting returns internally consistent KD for data incompatible with a 1:1 model; we propose isotherm verification and antibody validation of every preparation as minimal requirements. No positive-control aptamer was available, limiting interpretation.