دورية أكاديمية
أعرض في EDS

Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology.

التفاصيل البيبلوغرافية
العنوان: Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology.
المؤلفون: Niemyska W; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland. Electronic address: wanda@mimuw.edu.pl., Mukherjee S; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland., Gren BA; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland., Niewieczerzal S; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland., Bujnicki JM; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland. Electronic address: janusz@iimcb.gov.pl., Sulkowska JI; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland. Electronic address: jsulkowska@cent.uw.edu.pl.
المصدر: Journal of molecular biology [J Mol Biol] 2024 Mar 15; Vol. 436 (6), pp. 168455. Date of Electronic Publication: 2024 Jan 23.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier
Original Publication: 1959- : London : Academic Press
مواضيع طبية MeSH: RNA*/chemistry , RNA*/genetics , RNA Folding*, Molecular Dynamics Simulation
مستخلص: Knots are very common in polymers, including DNA and protein molecules. Yet, no genuine knot has been identified in natural RNA molecules to date. Upon re-examining experimentally determined RNA 3D structures, we discovered a trefoil knot 3 1 , the most basic non-trivial knot, in the RydC RNA. This knotted RNA is a member of a small family of short bacterial RNAs, whose secondary structure is characterized by an H-type pseudoknot. Molecular dynamics simulations suggest a folding pathway of the RydC RNA that starts with a native twisted loop. Based on sequence analyses and computational RNA 3D structure predictions, we postulate that this trefoil knot is a conserved feature of all RydC-related RNAs. The first discovery of a knot in a natural RNA molecule introduces a novel perspective on RNA 3D structure formation and on fundamental research on the relationship between function and spatial structure of biopolymers.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)
فهرسة مساهمة: Keywords: Entanglement of biomolecules; Molecular dynamics; RNA 3D structure; RNA folding; Topology in soft matter
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20240125 Date Completed: 20240318 Latest Revision: 20240718
رمز التحديث: 20240718
DOI: 10.1016/j.jmb.2024.168455
PMID: 38272438
قاعدة البيانات: MEDLINE
الوصف
تدمد:1089-8638
DOI:10.1016/j.jmb.2024.168455