ArticleNucleic acids research2010
Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 96 citations in OpenAlex.
- Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation.Nucleic acids research · 2025Article
- Investigating the Conformational Diversity of the TMR-3 Aptamer.Journal of the American Chemical Society · 2025Article
- Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target.ACS central science · 2024Article
- Aptamer and Electrochemical Aptasensor towards Selenate Ions (SeOInternational journal of molecular sciences · 2024Article
- Paired Capture and FISH Detection of Individual Virions Enable Cell-Free Determination of Infectious Titers.ACS sensors · 2023Article
- The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Article
- Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development.Angewandte Chemie (International ed. in English) · 2021Review
- What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.Nucleic acids research · 2021Article
- Aptasensors for Point-of-Care Detection of Small Molecules.Biosensors · 2020Review
- Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.Nucleic acids research · 2020Article
- Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors.Nature chemical biology · 2017Article
- Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria.Frontiers in microbiology · 2017Review
- Opportunities in the design and application of RNA for gene expression control.Nucleic acids research · 2016Review
- Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae.PloS one · 2016Article
- Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers.Nucleic acids research · 2015Article
- Analysis of In Vitro Aptamer Selection Parameters.Journal of molecular evolution · 2015Review
- In Vitro Screening and in Silico Modeling of RNA-Based Gene Expression Control.ACS chemical biology · 2015Article
- Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.Biophysical journal · 2014Article
- Selection and characterization of a novel DNA aptamer for label-free fluorescence biosensing of ochratoxin A.Toxins · 2014Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ability to generate RNA aptamers for synthetic biology using in vitro selection depends on the informational complexity (IC) needed to specify functional structures that bind target ligands with desired affinities in physiological concentrations of magnesium. We investigate how selection for high-affinity aptamers is constrained by chemical properties of the ligand and the need to bind in low magnesium. We select two sets of RNA aptamers that bind planar ligands with dissociation constants (K(d)s) ranging from 65 nM to 100 microM in physiological buffer conditions. Aptamers selected to bind the non-proteinogenic amino acid, p-amino phenylalanine (pAF), are larger and more informationally complex (i.e., rarer in a pool of random sequences) than aptamers selected to bind a larger fluorescent dye, tetramethylrhodamine (TMR). Interestingly, tighter binding aptamers show less dependence on magnesium than weaker-binding aptamers. Thus, selection for high-affinity binding may automatically lead to structures that are functional in physiological conditions (1-2.5 mM Mg(2+)). We hypothesize that selection for high-affinity binding in physiological conditions is primarily constrained by ligand characteristics such as molecular weight (MW) and the number of rotatable bonds. We suggest that it may be possible to estimate aptamer-ligand affinities and predict whether a particular aptamer-based design goal is achievable before performing the selection.
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