ArticleNucleic acids research2020
Double-stranded RNA bending by AU-tract sequences.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.Nature communications · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Binding of a Tricationic meso-Substituted Porphyrin to poly(A)⋅poly(U): an Experimental Study.Journal of fluorescence · 2025Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Structure of coxsackievirus cloverleaf RNA and 3CScience advances · 2025Article
- Structural basis for gene silencing by siRNAs in humans.bioRxiv : the preprint server for biology · 2024Article
- Inverse-Folding Design of Yeast Telomerase RNA Increases Activity In Vitro.Non-coding RNA · 2023Article
- Article
- RNAi as a Foliar Spray: Efficiency and Challenges to Field Applications.International journal of molecular sciences · 2022Review
- Structural basis of R-loop recognition by the S9.6 monoclonal antibody.Nature communications · 2022Article
- Role of helical structure and dynamics in oligoadenylate synthetase 1 (OAS1) mismatch tolerance and activation by short dsRNAs.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders.Frontiers in molecular biosciences · 2022Article
- Structural analyses of an RNA stability element interacting with poly(A).Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. However, in contrast to dsDNA, sequence-dependent structural features of dsRNA have received little attention. In this work, we demonstrate that the nucleotide sequence can induce a bend in a canonical Watson-Crick base-paired dsRNA helix. Using all-atom molecular dynamics simulations, we identified a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that strongly bend the RNA double-helix. This finding was experimentally validated using atomic force microscopy imaging of dsRNA molecules designed to display macroscopic curvature via repetitions of phased AU-tract motifs. At the atomic level, this novel phenomenon originates from a localized compression of the dsRNA major groove and a large propeller twist at the position of the AU-tract. Moreover, the magnitude of the bending can be modulated by changing the length of the AU-tract. Altogether, our results demonstrate the possibility of modifying the dsRNA curvature by means of its nucleotide sequence, which may be exploited in the emerging field of RNA nanotechnology and might also constitute a natural mechanism for proteins to achieve recognition of specific dsRNA sequences.
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