ArticleNucleic acids research2003
Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 38 citations in OpenAlex.
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- Target-Directed Approaches for Screening Small Molecules against RNA Targets.SLAS discovery : advancing life sciences R & D · 2020Review
- Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States.Journal of molecular biology · 2020Article
- Small Molecule-Based Pattern Recognition To Classify RNA Structure.Journal of the American Chemical Society · 2017Article
- Utilizing Intrinsic Properties of Polyaniline to Detect Nucleic Acid Hybridization through UV-Enhanced Electrostatic Interaction.Biomacromolecules · 2015Article
- Electrostatic interactions in aminoglycoside-RNA complexes.Biophysical journal · 2015Article
- Direct observation of aminoglycoside-RNA binding by localized surface plasmon resonance spectroscopy.Analytical chemistry · 2013Article
- Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.Nature chemical biology · 2011Article
- Identification of neomycin B-binding site in T box antiterminator model RNA.Bioorganic & medicinal chemistry · 2008Article
- Article
- Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs.Tetrahedron · 2007Article
- Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde-hydrazine chemistry and protease-cleavable linkers.Nucleic acids research · 2007Article
- Fluorescence of covalently attached pyrene as a general RNA folding probe.Nucleic acids research · 2006Article
- Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA.RNA (New York, N.Y.) · 2004Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
To quantitatively understand the binding affinity and target selectivity of small-molecule RNA interactions, it is useful to have a rapid, highly reproducible binding assay that can be readily generalized to different RNA targets. To that end, an assay has been developed and validated for measuring the binding of low-molecular weight ligands to RNA by monitoring the fluorescence of a covalently incorporated fluorophore. As a test system, the fluorescence of a pyrene-derivatized HIV-1 TAR (transactivating response element) RNA was measured upon titration with aminoglycoside antibiotics. The binding isotherms thus obtained fit well with a model for a 1:1 interaction and yield an accurate measure of the equilibrium dissociation constant. Among a series of natural aminoglycosides, the binding affinity correlates with the number of amines, supporting an electrostatic compensation model for binding. Furthermore, the ionic strength dependence confirms that much of the binding energy is electrostatic. Finally, by measuring the binding affinity in the presence of nucleic acid competitors, we confirm that although aminoglycosides show high RNA to DNA selectivity, their selectivity among different RNA targets is sub- optimal. We conclude that this newly developed assay can be generalized to measure the binding affinities and selectivities of a variety of small molecules to a specific RNA target.
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Registered trials
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