ArticleBioconjugate chemistry2014
Rationally manipulating aptamer binding affinities in a stem-loop molecular beacon.
Article in Bioconjugate chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Stability modification of therapeutic aptamers: from biostability bottlenecks to nuclease-resistant construct design.RSC chemical biology · 2026Review
- From Powder to Pathogen: A Systematic Review of Detection, Pathogenicity, and Mitigation ofInternational journal of microbiology · 2026Review
- Development of a Molecular Beacon-Based Genosensor for Detection of Human Rotavirus A.Molecular biotechnology · 2025Article
- Harnessing in Silico Design for Electrochemical Aptasensor Optimization: Detection of Okadaic Acid (OA).Biosensors · 2025Article
- Establishing Detection Methods for Okadaic Acid Aptamer-Target Interactions: Insights from Computational and Experimental Approaches.Foods (Basel, Switzerland) · 2025Article
- Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets.Biosensors · 2022Review
- Selection and Characterization of Vimentin-Binding Aptamer Motifs for Ovarian Cancer.Molecules (Basel, Switzerland) · 2021Article
- Article
- DNA aptamer-based rolling circle amplification product as a novel immunological adjuvant.Scientific reports · 2020Article
- Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism.Scientific reports · 2020Article
- Combinatorial Inhibition of Cell Surface Receptors Using Dual Aptamer-Functionalized Nanoconstructs for Cancer Treatment.Pharmaceutics · 2020Article
- Article
- Independent control of the thermodynamic and kinetic properties of aptamer switches.Nature communications · 2019Article
- Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics.Small (Weinheim an der Bergstrasse, Germany) · 2019Review
- Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing.Science (New York, N.Y.) · 2018Article
- No Structure-Switching Required: A Generalizable Exonuclease-Mediated Aptamer-Based Assay for Small-Molecule Detection.Journal of the American Chemical Society · 2018Article
- Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation.Nucleic acids research · 2018Article
- New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection.Nucleic acids research · 2017Article
- Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers.Chemical science · 2017Article
- Bioprobes Based on Aptamer and Silica Fluorescent Nanoparticles for Bacteria Salmonella typhimurium Detection.Nanoscale research letters · 2016Article
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Authors and funding
2 authors.
Funding
Abstract
Single-stranded DNA sequences that are highly specific for a target ligand are called aptamers. While the incorporation of aptamer sequences into stem-loop molecular beacons has become an essential tool in optical biosensors, the design principles that determine the magnitude of binding affinity and its relationship to placement of the aptamer sequence in the stem-loop architecture are not well defined. By controlled placement of the aptamer along the loop region of the molecular beacon, it is observed that the binding affinity can be tuned over 4 orders of magnitude (1.3 nM - 203 μM) for the Huizenga and Szostak ATP DNA aptamer sequence. It is observed that the Kd is enhanced for the fully exposed sequence, with reduced binding affinity when the aptamer is part of the stem region of the beacon. Analysis of the ΔG values indicate a clear correlation between the aptamer hybridized length in the stem and its observed Kd. The use of a nanometal surface energy transfer probe method for monitoring ATP binding to the aptamer sequence allows the observation of negative cooperativity between the two ATP binding events. Maintenance of the high binding affinity of this ATP aptamer and the observation of two separate Kd's for ATP binding indicate NSET as an effective, nonmanipulative, optical method for tracking biomolecular changes.
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