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

Abstract

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.

arXiv comment26 pages, 6 figures, Biophys. J. (in press)

References in corpus (8)

• A nonequilibrium equality for free energy differences
• Mechanical unfolding of RNA hairpins
• Forced-unfolding and force-quench refolding of RNA hairpins
• Thermodynamic and kinetic aspects of RNA pulling experiments
• Force-induced denaturation of RNA
• Slow nucleic acid unzipping kinetics from sequence-defined barriers
• Force dependent fragility in RNA hairpins
• Mechanically probing the folding pathway of single RNA molecules

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