Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2002-08-09
Biophys. J. 84 (2003) 2831-2840
Physics
Condensed Matter
Soft Condensed Matter
10 pages, 8 figures, revised version, to be published in Biophys. J
Scientific paper
10.1016/S0006-3495(03)70012-5
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)].
Bundschuh Ralf
Gerland Ulrich
Hwa Terence
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