ArticleBiochemistry2022
RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction.
Article in Biochemistry, 2022. 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, 28 citations in OpenAlex.
- Protocol for detecting in vitro riboswitch conformational switching using a fluorescence anisotropy single-stranded RNA-targeting approach.STAR protocols · 2026Article
- An orthogonal RNA aptamer for targeted RNA regulation in phase-separated subcellular compartments.Nature communications · 2026Article
- NMR-Based Fragment Screening for RNA-Targeted Drug Discovery.Molecules (Basel, Switzerland) · 2026Review
- Eight Triplex-Binding Molecules from Four Chemical Classes Broadly Recognize the MALAT1 Triple Helix.Molecules (Basel, Switzerland) · 2025Article
- Streamlined Fragment-Based Discovery Platform for Targeting Structured RNAs.ACS chemical biology · 2025Article
- Structure-informed design of an ultrabright RNA-activated fluorophore.Nature chemistry · 2025Article
- Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.Angewandte Chemie (International ed. in English) · 2025Article
- Everything's under Control: Maximizing Biosensor Performance through Negative Control Probe Selection.Analytical chemistry · 2025Article
- Article
- Development of Biolayer Interferometry (BLI)-Based Double-Stranded RNA Detection Method with Application in mRNA-Based Therapeutics and Vaccines.Pharmaceutics · 2024Article
- Article
- In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers.Bio-protocol · 2023Article
- Fragment-Based Approaches to Identify RNA Binders.Journal of medicinal chemistry · 2023Review
- Sequence- and structure-specific RNA oligonucleotide binding attenuates heterogeneous nuclear ribonucleoprotein A1 dysfunction.Frontiers in molecular biosciences · 2023Article
- Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness.RNA biology · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Registered trials
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.