ArticleScientific reports2012
Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.
Article in Scientific reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 32 papers.
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32 citing papers in PubMed.
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- Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex.Communications biology · 2021Article
- Length-Dependent Structural Transformations of Huntingtin PolyQ Domain Upon Binding to 2D-Nanomaterials.Frontiers in chemistry · 2020Article
- Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities.Current opinion in biotechnology · 2019Review
- Mapping the Pax6 3' untranslated region microRNA regulatory landscape.BMC genomics · 2018Article
- Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex.Scientific reports · 2018Article
- Exploring PAZ/3'-overhang interaction to improve siRNA specificity. A combined experimental and modeling study.Chemical science · 2018Article
- Differential Pd-nanocrystal facets demonstrate distinct antibacterial activity against Gram-positive and Gram-negative bacteria.Nature communications · 2018Article
- Why Is a High Temperature Needed byFrontiers in chemistry · 2018Article
- Non-canonical targets destabilize microRNAs in human Argonautes.Nucleic acids research · 2017Article
- Graphene-Induced Pore Formation on Cell Membranes.Scientific reports · 2017Article
- Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity.Scientific reports · 2016Article
- A structural view of microRNA-target recognition.Nucleic acids research · 2016Article
- Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b.Frontiers in genetics · 2016Article
- Dysregulated co-stimulatory molecule expression in a Sjögren's syndrome mouse model with potential implications by microRNA-146a.Molecular immunology · 2015Article
- Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity.Nucleic acids research · 2015Article
Corrections and comments
- Erratum issuedRen, Pengyu [added]
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) 'seed' region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 'hinge' and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs.
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