Validation of Aptamer-Protein Interactions by Biolayer Interferometry: A Study of 88 Candidate Molecules.
- 1Petrovsky National Research Center of Surgery, Institute of Biology of Ageing and Healthy Longevity Medicine with Clinic of Predictive Medicine, 119435 Moscow, Russia.
- 2SistemaBioTech, LLC, 1-ya Kuryanovskaya Str. 34, 109235 Moscow, Russia.
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.
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BibTeX
@article{ershova2026validation,
title = {{Validation of Aptamer-Protein Interactions by Biolayer Interferometry: A Study of 88 Candidate Molecules.}},
author = {Elizaveta S Ershova and Natalia V Pozdnyakova and Aleksandra Yu Egorshina and Elena V Yakushenko and Igor V Dobrokhotov and Nadezhda P Lyamina and Bella B Gagulaeva and Alexey Moskalev},
journal = {International journal of molecular sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198469},
url = {https://europepmc.org/article/MED/42883724},
note = {CC BY},
}
RIS
TY - JOUR
TI - Validation of Aptamer-Protein Interactions by Biolayer Interferometry: A Study of 88 Candidate Molecules.
AU - Elizaveta S Ershova
AU - Natalia V Pozdnyakova
AU - Aleksandra Yu Egorshina
AU - Elena V Yakushenko
AU - Igor V Dobrokhotov
AU - Nadezhda P Lyamina
AU - Bella B Gagulaeva
AU - Alexey Moskalev
PY - 2026
DA - 2026/09/23
JO - International journal of molecular sciences
DO - 10.3390/ijms27198469
UR - https://europepmc.org/article/MED/42883724
AB - 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.
SN - 1422-0067
ER -