Mechanical unfolding of RNA: From hairpins to structures with internal multiloops

Details Mechanical unfolding of RNA: From hairpins to structures with internal multiloops Mechanical unfolding of RNA: From hairpins to structures with internal multiloops

2006-09-20

arxiv.org/abs/q-bio/0609029v1

Biophys. J. vol 92 (2007) 731-743

Biology

Quantitative Biology

Biomolecules

26 pages, 6 figures, Biophys. J. (in press)

Scientific paper

10.1529/biophysj.106.093062

Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional experiments. Upon application of constant force ($f$), RNA hairpins undergo cooperative transitions from folded to unfolded states whereas subdomains of ribozymes unravel one at a time. Here, we use a self-organized polymer (SOP) model and Brownian dynamics simulations to probe mechanical unfolding at constant force and constant-loading rate of four RNA structures of varying complexity. Our work shows (i) the response of RNA to force is largely determined by the native structure; (ii) only by probing mechanical unfolding over a wide range of forces can the underlying energy landscape be fully explored.

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