ArticleRNA (New York, N.Y.)2013
Tertiary structure-based analysis of microRNA-target interactions.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- Tyrosine-Capped Pt Nanozyme Functionalized with cDNA: An Innovative Sensor Designed for One-Step Detection of the miRNA-21 Biomarker.ACS omega · 2025Article
- miRVim: Three-dimensional miRNA Structure Database.MicroRNA (Shariqah, United Arab Emirates) · 2025Article
- 3D Modeling of Non-coding RNA Interactions.Advances in experimental medicine and biology · 2022Article
- Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility.Journal of molecular biology · 2021Article
- Article
- IL1B Increases Intestinal Tight Junction Permeability by Up-regulation of MIR200C-3p, Which Degrades Occludin mRNA.Gastroenterology · 2020Article
- miRNA target identification and prediction as a function of time in gene expression data.RNA biology · 2020Article
- Effects of the PIWI/MID domain of Argonaute protein on the association of miRNAi's seed base with the target.RNA (New York, N.Y.) · 2019Article
- Recent Molecular Genetic Explorations ofGenetics · 2018Article
- A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing.Nucleic acids research · 2017Article
- TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.RNA biology · 2017Article
- A structural view of microRNA-target recognition.Nucleic acids research · 2016Article
- Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition.Nucleic acids research · 2015Article
- Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.Nucleic acids research · 2014Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Current computational analysis of microRNA interactions is based largely on primary and secondary structure analysis. Computationally efficient tertiary structure-based methods are needed to enable more realistic modeling of the molecular interactions underlying miRNA-mediated translational repression. We incorporate algorithms for predicting duplex RNA structures, ionic strength effects, duplex entropy and free energy, and docking of duplex-Argonaute protein complexes into a pipeline to model and predict miRNA-target duplex binding energies. To ensure modeling accuracy and computational efficiency, we use an all-atom description of RNA and a continuum description of ionic interactions using the Poisson-Boltzmann equation. Our method predicts the conformations of two constructs of Caenorhabditis elegans let-7 miRNA-target duplexes to an accuracy of ∼3.8 Å root mean square distance of their NMR structures. We also show that the computed duplex formation enthalpies, entropies, and free energies for eight miRNA-target duplexes agree with titration calorimetry data. Analysis of duplex-Argonaute docking shows that structural distortions arising from single-base-pair mismatches in the seed region influence the activity of the complex by destabilizing both duplex hybridization and its association with Argonaute. Collectively, these results demonstrate that tertiary structure-based modeling of miRNA interactions can reveal structural mechanisms not accessible with current secondary structure-based methods.
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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.