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Originally published as Biophys J. BioFAST on January 14, 2005.
doi:10.1529/biophysj.104.052811
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Biophysical Journal 88:2737-2744 (2005)
© 2005 The Biophysical Society

Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA

J. A. Abels, F. Moreno-Herrero, T. van der Heijden, C. Dekker and N. H. Dekker

Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands

Correspondence: Address reprint requests to Nynke H. Dekker, E-mail: nynke.dekker{at}mb.tn.tudelft.nl.

Over the past few years, it has become increasingly apparent that double-stranded RNA (dsRNA) plays a far greater role in the life cycle of a cell than previously expected. Numerous proteins, including helicases, polymerases, and nucleases interact specifically with the double helix of dsRNA. To understand the detailed nature of these dsRNA-protein interactions, the (bio)chemical, electrostatic, and mechanical properties of dsRNA need to be fully characterized. We present measurements of the persistence length of dsRNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce a mean persistence length for long dsRNA molecules of 63.8 ± 0.7 nm from force-extension measurements with the magnetic tweezers. We present atomic force microscopy images of dsRNA and demonstrate a new method for analyzing these, which yields an independent, yet consistent value of 62 ± 2 nm for the persistence length. The introduction of these single-molecule techniques for dsRNA analysis opens the way for real-time, quantitative analysis of dsRNA-protein interactions.




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