title: Analysis of RNA flexibility by scanning force spectroscopy.
abstract: Scanning force spectroscopy was used to measure the mechanical properties of double stranded RNA molecules in comparison with DNA. We find that, similar to the B-S transition in DNA, RNA molecules are stretched from the assumed A' conformation to a stretched conformation by applying a defined force (plateau force). The force depends on the G + C content of the RNA and is distinct from that required for the B-S transition of a homologous DNA molecule. After the conformational change, DNA can be further extended by a factor of 0.7 +/- 0.2 (S-factor) before melting occurs and the binding of the molecule to the cantilever is finally disrupted. For RNA, the S-factor was higher (1.0 +/- 0.2) and more variable. Experiments to measure secondary structures in single stranded RNA yielded a large number of different force-distance curves, suggesting disruption and stretching of various secondary structures. Oriented attachment of the molecules to the substrate, a defined pick-up point and an increased resolution of the instrument could provide the means to analyse RNA secondary structures by scanning force spectroscopy.
authors.affiliation: Abteilung Genetik, FB 19, Universität Kassel, Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Bonin
authors.forename: Rong
authors.initials: R
authors.lastname: Zhu
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Klaue
authors.forename: Jürgen
authors.initials: J
authors.lastname: Oberstrass
authors.forename: Egbert
authors.initials: E
authors.lastname: Oesterschulze
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Nellen
mesh_terms: D001482:Base Composition; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D018583:Pliability; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013057:Spectrum Analysis / Q000379:methods*
chemical_list: D012330:RNA, Double-Stranded; D004247:DNA