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Nucleic Acids Research, 2002, Vol. 30, No. 16 e81
© 2002 Oxford University Press

Analysis of RNA flexibility by scanning force spectroscopy

Michael Bonin, Rong Zhu1, Yvonne Klaue, Jürgen Oberstrass, Egbert Oesterschulze1 and Wolfgang Nellen*

Abteilung Genetik, FB 19 and 1 Abteilung Technische Physik, FB 18, Universität Kassel, Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Straße 40, D-34132 Kassel, Germany

*To whom correspondence should be addressed. Tel: +49 561 804 4805; Fax: +49 561 804 4800; Email: nellen{at}hrz.uni-kassel.de

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.


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