title: The separation between the 5'-3' ends in long RNA molecules is short and nearly constant.
abstract: RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. Despite an ensemble of different structures, it has been theoretically proposed that the separation between the 5' and 3' ends of long single-stranded RNA molecules (ssRNA) remains constant, independent of their base content and length. Here, we present the first experimental measurements of the end-to-end separation in long ssRNA molecules. To determine this separation, we use single molecule Fluorescence Resonance Energy Transfer of fluorescently end-labeled ssRNA molecules ranging from 500 to 5500 nucleotides in length, obtained from two viruses and a fungus. We found that the end-to-end separation is indeed short, within 5-9 nm. It is remarkable that the separation of the ends of all RNA molecules studied remains small and similar, despite the origin, length and differences in their secondary structure. This implies that the ssRNA molecules are 'effectively circularized' something that might be a general feature of RNAs, and could result in fine-tuning for translation and gene expression regulation.
authors.affiliation: Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México.
authors.forename: Nehemías
authors.initials: N
authors.lastname: Leija-Martínez
authors.affiliation: División de Biología Molecular, IPICYT, Camino a la Presa San Jose s/n, San Luis Potosí, SLP 78216, México.
authors.forename: Sergio
authors.initials: S
authors.lastname: Casas-Flores
authors.affiliation: Center for Nanociences and Nanotechnology, Universidad Nacional Autónoma de México, Km. 107 Carretera Tijuana-Ensenada s/n, Baja California 22800, México.
authors.forename: Rubén D
authors.initials: RD
authors.lastname: Cadena-Nava
authors.affiliation: Centre de Desenvolupament de Sensors, Instrumentación i Sistemes, Universitat Politecnica de Catalunya, Rambla de Sant Nebridi 10, E-0822, Terrasa, España.
authors.forename: Joan A
authors.initials: JA
authors.lastname: Roca
authors.affiliation: Molecular Biophysics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, SLP 78290, México.
authors.forename: José A
authors.initials: JA
authors.lastname: Mendez-Cabañas
authors.affiliation: Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México egomez@ifisica.uaslp.mx.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Gomez
authors.affiliation: Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México jaime@ifisica.uaslp.mx.
authors.forename: Jaime
authors.initials: J
authors.lastname: Ruiz-Garcia
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D009690:Nucleic Acid Conformation; D012331:RNA, Fungal / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger; D012367:RNA, Viral