ArticleProceedings of the National Academy of Sciences of the United States of America2015
Absence of knots in known RNA structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- Knotted folds induced by homochiral all-parallel (or all-antiparallel) double-helices.PNAS nexus · 2026Article
- Advancing Topoisomerase Research Using DNA Nanotechnology.Small methods · 2025Review
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- RNAspider: a webserver to analyze entanglements in RNA 3D structures.Nucleic acids research · 2022Article
- Entanglements of structure elements revealed in RNA 3D models.Nucleic acids research · 2021Article
- Knot_pull-python package for biopolymer smoothing and knot detection.Bioinformatics (Oxford, England) · 2020Article
- RNApdbee 2.0: multifunctional tool for RNA structure annotation.Nucleic acids research · 2018Article
- KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.The European physical journal. E, Soft matter · 2018Article
- Molecular Knots.Angewandte Chemie (International ed. in English) · 2017Review
- Synthesizing topological structures containing RNA.Nature communications · 2017Article
- A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds.Molecular based mathematical biology · 2017Article
- Ensemble View of RNAs and Proteins: Loops, Knots, Territories, and Evolution.Biophysical journal · 2016Article
- Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.Biophysical journal · 2016Article
- The elusive quest for RNA knots.RNA biology · 2016Article
- Knotted proteins: A tangled tale of Structural Biology.Computational and structural biotechnology journal · 2015Review
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.
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