ArticleProceedings of the National Academy of Sciences of the United States of America2016
Controlling uncertainty in aptamer selection.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Nucleic acid aptamers: new methods for selection, target validation, molecular diagnostics and therapeutics.Signal transduction and targeted therapy · 2026Review
- A novel DNA aptamer for Vibrio cholerae O139 detection: a whole-cell SELEX approach.Molecular biology reports · 2025Article
- Article
- New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers.International journal of molecular sciences · 2024Review
- In vitro selection of aptamers and their applications.Nature reviews. Methods primers · 2023Article
- Discrete stochastic models of SELEX: Aptamer capture probabilities and protocol optimization.The Journal of chemical physics · 2022Article
- Albumin-Binding Aptamer Chimeras for Improved siRNA Bioavailability.Cellular and molecular bioengineering · 2022Article
- A system for multiplexed selection of aptamers with exquisite specificity without counterselection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development.Angewandte Chemie (International ed. in English) · 2021Review
- A bispecific circular aptamer tethering a built-in universal molecular tag for functional protein delivery.Chemical science · 2020Article
- High-efficiency enrichment enables identification of aptamers to circulating Plasmodium falciparum-infected erythrocytes.Scientific reports · 2020Article
- Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers.Molecular therapy. Nucleic acids · 2018Article
- In vitro selection of an XNA aptamer capable of small-molecule recognition.Nucleic acids research · 2018Article
- Time-lapse imaging of molecular evolution by high-throughput sequencing.Nucleic acids research · 2018Article
- Single-round isolation of diverse RNA aptamers from a random sequence pool.Biology methods & protocols · 2018Article
- Aptamer Bioinformatics.International journal of molecular sciences · 2017Review
- Emerging cancer-specific therapeutic aptamers.Current opinion in oncology · 2017Review
- A statistical framework for analyzing deep mutational scanning data.Genome biology · 2017Article
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Authors and funding
6 authors.
Funding
Abstract
The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these aptamers through evolutionary selection of high-affinity candidates from a highly diverse random pool. This randomness dictates an unknown population distribution of fitness parameters, encoded by the binding affinities, toward SELEX targets. Adding to this uncertainty, repeating SELEX under identical conditions may lead to variable outcomes. These uncertainties pose a challenge when tuning selection pressures to isolate high-affinity ligands. Here, we present a stochastic hybrid model that describes the evolutionary selection of aptamers to explore the impact of these unknowns. To our surprise, we find that even single copies of high-affinity ligands in a pool of billions can strongly influence population dynamics, yet their survival is highly dependent on chance. We perform Monte Carlo simulations to explore the impact of environmental parameters, such as the target concentration, on selection efficiency in SELEX and identify strategies to control these uncertainties to ultimately improve the outcome and speed of this time- and resource-intensive process.
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Registered trials
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