Single-molecule measurements of the persistence length of double- stranded RNA

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 specically 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 +/- 6 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.