ArticleCell reports methods2022
Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq.
Article in Cell reports methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 14 citations in OpenAlex.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities.bioRxiv : the preprint server for biology · 2026Article
- RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions.Genome biology · 2026Article
- Biochemical principles of miRNA targeting in flies.Nature communications · 2026Article
- A unifying model for microRNA-guided silencing of messenger RNAs.Nature communications · 2025Article
- Functional microRNA targeting without seed pairing.Nucleic acids research · 2025Article
- Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome.Nucleic acids research · 2025Article
- Modeling RNA duplex dynamics with Gibbs sampling enhances base-pair prediction accuracy and reveals structural activity profiles.NAR genomics and bioinformatics · 2025Article
- Endo-bind-n-seq: identifying RNA motifs of RNA binding proteins isolated from endogenous sources.Life science alliance · 2025Article
- Role of Natural Binding Proteins in Therapy and Diagnostics.Life (Basel, Switzerland) · 2024Article
- Article
- A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength.EMBO reports · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
RNA Bind-n-Seq (RBNS) is a cost-effective, high-throughput method capable of identifying the sequence preferences of RNA-binding proteins and of qualitatively defining relative dissociation constants. Although RBNS is often described as an unbiased method, several factors may influence the outcome of the analysis. Here, we discuss these biases and present an analytical strategy to estimate absolute binding affinities from RBNS data, extend RBNS to kinetic studies, and develop a framework to compute relative association and dissociation rate constants. As proof of principle, we measured the equilibrium binding properties of mammalian Argonaute2 (AGO2) guided by eight microRNAs (miRNAs) and kinetic parameters for let-7a. The miRNA-binding site repertoires, dissociation constants, and kinetic parameters calculated from RBNS data using our methods correlate well with values measured by traditional ensemble and single-molecule approaches. Our data provide additional quantitative measurements for Argonaute-bound miRNA binding that should facilitate development of quantitative targeting rules for individual miRNAs.
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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.