  We study theoretically the denaturation of single RNA molecules by mechanical
stretching, focusing on signatures of the (un)folding pathway in molecular
fluctuations. Our model describes the interactions between nucleotides by
incorporating the experimentally determined free energy rules for RNA secondary
structure, while exterior single stranded regions are modeled as freely jointed
chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila
group I intron), we compute the quasi-equilibrium fluctuations in the
end-to-end distance as the molecule is unfolded by pulling on opposite ends.
Unlike the average quasi-equilibrium force-extension curves, these fluctuations
reveal clear signatures from the unfolding of individual structural elements.
We find that the resolution of these signatures depends on the spring constant
of the force-measuring device, with an optimal value intermediate between very
rigid and very soft. We compare and relate our results to recent experiments by
Liphardt et al. [Science 292, 733-737 (2001)].

Soft Condensed Matter;Biomolecules