ArticleNucleic acids research2008
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 52 citations in OpenAlex.
- Accessory microRNA byproducts expand RNA interference via microprocessor-mediated cleavage activation.Science advances · 2026Article
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Programming ADAR-recruiting hairpin RNA sensor to detect endogenous molecules.Nucleic acids research · 2025Article
- Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers.Molecular therapy. Nucleic acids · 2023Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.PloS one · 2023Article
- Therapeutic Potential of Aptamer-Protein Interactions.ACS pharmacology & translational science · 2022Review
- A comparative analysis of cell surface targeting aptamers.Nature communications · 2021Article
- Structural Biology for the Molecular Insight between Aptamers and Target Proteins.International journal of molecular sciences · 2021Review
- Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.FEBS open bio · 2018Article
- Topology independent comparison of RNA 3D structures using the CLICK algorithm.Nucleic acids research · 2017Article
- RNA aptamer inhibitors of a restriction endonuclease.Nucleic acids research · 2015Article
- MYB elongation is regulated by the nucleic acid binding of NFκB p50 to the intronic stem-loop region.PloS one · 2015Article
- The structure, function and evolution of proteins that bind DNA and RNA.Nature reviews. Molecular cell biology · 2014Review
- An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates.RNA (New York, N.Y.) · 2014Article
- Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.Nucleic acids research · 2014Article
- Selection and characterization of a DNA aptamer that can discriminate between cJun/cJun and cJun/cFos.PloS one · 2014Article
- The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.RNA (New York, N.Y.) · 2013Article
- RNA recognition by the DNA end-binding Ku heterodimer.RNA (New York, N.Y.) · 2013Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The binding of RNA molecules to proteins or other ligands can require extensive RNA folding to create an induced fit. Understanding the generality of this principle involves comparing structures of RNA before and after complex formation. Here we report the NMR solution structure of a 29-nt RNA aptamer whose crystal structure had previously been determined in complex with its transcription factor target, the p50(2) form of NF-kappaB. The RNA aptamer internal loop structure has pre-organized features that are also found in the complex, including non-canonical base pairing and cross-strand base stacking. Remarkably, the free RNA aptamer structure possesses a major groove that more closely resembles B-form DNA than RNA. Upon protein binding, changes in RNA structure include the kinking of the internal loop and distortion of the terminal tetraloop. Thus, complex formation involves both pre-formed and induced fit binding interactions. The high affinity of the NF-kappaB transcription factor for this RNA aptamer may largely be due to the structural pre-organization of the RNA that results in its ability to mimic DNA.
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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.