title: Absence of knots in known RNA structures.
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.
authors: Physics, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy; michelet@sissa.it.
authors: Cristian
authors: C
authors: Micheletti
authors: Physics, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy;
authors: Marco
authors: M
authors: Di Stefano
authors: Institut de Physique Théorique, Commissariat à l'énergie atomique-Saclay, CEA, 91191 Gif-sur-Yvette, France; and Beijing Computational Science Research Center, Haidian District Beijing, 100084, China.
authors: Henri
authors: H
authors: Orland
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: PDB-wide topological profiling; RNA knots; RNA structure; physical knots
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