ArticleJournal of the American Chemical Society2006
Aptamers selected for higher-affinity binding are not more specific for the target ligand.
Article in Journal of the American Chemical Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 125 citations in OpenAlex.
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- Biomarker-targeted functionalized magnetic nanoparticles: synthesis and aptamer conjugation optimization toward Alzheimer's disease biosensing.Nanoscale advances · 2026Article
- Probing the Specificity of Fluorescent Deoxyribozymes Using Single-Step Selections and Machine Learning.ACS chemical biology · 2026Article
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- How Binding Affinity and Binding Specificity Map to Sequence Space.Journal of molecular evolution · 2026Article
- Enriching Higher Affinity Aptamers by Addressing the Kinetic Aspect of the DNA Strand-Displacement Reaction.Angewandte Chemie (International ed. in English) · 2026Article
- Aptamers and aptamer-drug conjugates as synthetic immune modulators for cancer immunotherapy.Frontiers in immunology · 2026Review
- Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.Nucleic acids research · 2025Article
- The Diagnostic and Therapeutic Potential of Oligonucleotide Aptamers in Alzheimer's Disease.Cells · 2025Review
- Exploring the relationship between aptamer binding thermodynamics, affinity, and specificity.Nucleic acids research · 2025Article
- Therapeutic Applications of Aptamers.International journal of molecular sciences · 2024Review
- A Prebiotic Genetic Nucleotide as an Early Darwinian Ancestor for Pre-RNA Evolution.ACS omega · 2024Article
- Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine.JACS Au · 2024Article
- Minimizing amplification bias during reverse transcription for in vitro selections.RNA (New York, N.Y.) · 2023Article
- Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer.Journal of the American Chemical Society · 2023Article
- Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting.ACS omega · 2023Article
- The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.PloS one · 2023Article
- Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes.Nature communications · 2022Article
- Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA-binding site.The Journal of biological chemistry · 2022Article
- High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification.Nucleic acids research · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Previous study of eleven different in vitro-selected RNA aptamers that bind guanosine triphosphate (GTP) with K(d)s ranging from 8 microM to 9 nM showed that more information is required to specify the structures of the higher-affinity aptamers. We are interested in understanding how the more complex aptamers achieve higher affinities for the ligand. In vitro selection produces structural solutions to a functional problem that are are as simple as possible in terms of the information content needed to define them. It has long been assumed that the simplest way to improve the affinity of an aptamer is to increase the shape and functional group complementarity of the RNA binding pocket for the ligand. This argument underlies the hypothesis that selection for higher-affinity aptamers automatically leads to structures that bind more specifically to the target molecule. Here, we examined the binding specificities of the eleven GTP aptamers by carrying out competition binding studies with sixteen different chemical analogues of GTP. The aptamers have distinct patterns of specificity, implying that each RNA is a structurally unique solution to the problem of GTP binding. However, these experiments failed to provide evidence that higher-affinity aptamers bind more specifically to GTP. We suggest that the simplest way to improve aptamer K(d)s may be to increase the stability of the RNA tertiary structure with additional intramolecular RNA-RNA interactions; increasingly specific ligand binding may emerge only in response to direct selection for specificity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.