title: The elusive quest for RNA knots.
abstract: Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have not yet been found, despite the expectation that they should exist in Nature. We conclude by singling out a number of RNA sequences that, based on the properties of their predicted secondary structures, are good candidates for knotted RNAs.
authors.affiliation: a NASA Johnson Space Center , Houston , TX , 77058 USA.
authors.forename: Aaron S
authors.initials: AS
authors.lastname: Burton
authors.affiliation: b SISSA , Via Bonomea 265, I-34014 Trieste , Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Di Stefano
authors.affiliation: c Department of Chemistry , Portland State University , Portland OR , 97207 USA.
authors.forename: Niles
authors.initials: N
authors.lastname: Lehman
authors.affiliation: d Institut de Physique Théorique, Commissariat à l'énergie atomique CEA, IPhT CNRS, UMR3681 , F-91191 Gif-sur-Yvette France.|e Beijing Computational Science Research Center , Haidian District Beijing , 100084 , China.
authors.forename: Henri
authors.initials: H
authors.lastname: Orland
authors.affiliation: b SISSA , Via Bonomea 265, I-34014 Trieste , Italy.
authors.forename: Cristian
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry* / Q000235:genetics
chemical_list: D004279:DNA, Viral; D011506:Proteins; D012313:RNA
keywords: Physical knots; RNA knots; RNA structure
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