dorsal/arxiv
View SchemaMechanical unfolding of RNA: From hairpins to structures with internal multiloops
| Authors | Changbong Hyeon, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609029 |
| URL | https://arxiv.org/abs/q-bio/0609029 |
| DOI | 10.1529/biophysj.106.093062 |
| Journal | Biophys. J. vol 92 (2007) 731-743 |
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.
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"abstract": "Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes,\nusing laser optical tweezer (LOT) experiments have begun to reveal the features\nof the energy landscape that cannot be easily explored using conventional\nexperiments. Upon application of constant force ($f$), RNA hairpins undergo\ncooperative transitions from folded to unfolded states whereas subdomains of\nribozymes unravel one at a time. Here, we use a self-organized polymer (SOP)\nmodel and Brownian dynamics simulations to probe mechanical unfolding at\nconstant force and constant-loading rate of four RNA structures of varying\ncomplexity. Our work shows (i) the response of RNA to force is largely\ndetermined by the native structure; (ii) only by probing mechanical unfolding\nover a wide range of forces can the underlying energy landscape be fully\nexplored.",
"arxiv_id": "q-bio/0609029",
"authors": [
"Changbong Hyeon",
"D. Thirumalai"
],
"categories": [
"q-bio.BM",
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"physics.bio-ph",
"q-bio.QM"
],
"doi": "10.1529/biophysj.106.093062",
"journal_ref": "Biophys. J. vol 92 (2007) 731-743",
"title": "Mechanical unfolding of RNA: From hairpins to structures with internal multiloops",
"url": "https://arxiv.org/abs/q-bio/0609029"
},
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