ArticleBiochemistry2014
Substrate recognition and specificity of double-stranded RNA binding proteins.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Staufen dsRNA-binding domain as modules to design bifunctional antibodies for siRNA delivery.Nucleic acids research · 2026Article
- siRNA Interaction and Transfection Properties of Polycationic Phosphorus Dendrimers.Biomacromolecules · 2025Article
- Mechanistic studies of small molecule ligands selective to RNA single G bulges.Nucleic acids research · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- RNA-protein interaction prediction without high-throughput data: An overview and benchmark ofComputational and structural biotechnology journal · 2024Article
- Article
- Structural insights into double-stranded RNA recognition and transport by SID-1.Nature structural & molecular biology · 2024Article
- DNA and RNA Binding Proteins: From Motifs to Roles in Cancer.International journal of molecular sciences · 2022Review
- Dissecting protein domain variability in the core RNA interference machinery of five insect orders.RNA biology · 2021Article
- How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.Molecular cell · 2020Review
- Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?Nucleic acids research · 2018Article
- DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA.Nucleic acids research · 2017Article
- RNA Scanning of a Molecular Machine with a Built-in Ruler.Journal of the American Chemical Society · 2017Article
- Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine-purine inversion site of an RNA duplex.Nucleic acids research · 2016Article
- Dynamic profiling of double-stranded RNA binding proteins.Nucleic acids research · 2015Article
- Viral RNA intermediates as targets for detection and discovery of novel and emerging mosquito-borne viruses.PLoS neglected tropical diseases · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Recognition of double-stranded (ds) RNA is an important part of many cellular pathways, including RNA silencing, viral recognition, RNA editing, processing, and transport. dsRNA recognition is often achieved by dsRNA binding domains (dsRBDs). We use atomistic molecular dynamics simulations to examine the binding interface of the transactivation response RNA binding protein (TRBP) dsRBDs to dsRNA substrates. Our results explain the exclusive selectivity of dsRBDs toward dsRNA and against DNA-RNA hybrid and dsDNA duplexes. We also provide corresponding experimental evidence. The dsRNA duplex is recognized by dsRBDs through the A-form of three duplex grooves and by the chemical properties of RNA bases, which have 2'-hydroxyl groups on their sugar rings. Our simulations show that TRBP dsRBD discriminates dsRNA- from DNA-containing duplexes primarily through interactions at two duplex grooves. The simulations also reveal that the conformation of the DNA-RNA duplex can be altered by dsRBD proteins, resulting in a weak binding of dsRBDs to DNA-RNA hybrids. Our study reveals the structural and molecular basis of protein-RNA interaction that gives rise to the observed substrate specificity of dsRNA binding proteins.
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Registered trials
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