Analysis of RNA flexibility by scanning force spectroscopy

• Published in: Nucleic acids research Vol. 30; no. 16; p. e81
• Main Authors: Bonin, Michael, Zhu, Rong, Klaue, Yvonne, Oberstrass, Jürgen, Oesterschulze, Egbert, Nellen, Wolfgang
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.08.2002; Oxford Publishing Limited (England)
• Subjects: Base Composition; DNA - chemistry; DNA - genetics; DNA - metabolism; Microscopy, Atomic Force; NAR Methods Online; Nucleic Acid Conformation; Nucleic Acid Denaturation; Pliability; RNA, Double-Stranded - chemistry; RNA, Double-Stranded - genetics; RNA, Double-Stranded - metabolism; Spectrum Analysis - methods
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gnf080

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.