dorsal/arxiv
View SchemaProbing complex RNA structures by mechanical force
| Authors | S. Harlepp, T. Marchal, J. Robert, J-F. Leger, A. Xayaphoummine, H. Isambert, D. Chatenay |
|---|---|
| Categories | |
| ArXiv ID | physics/0309063 |
| URL | https://arxiv.org/abs/physics/0309063 |
| DOI | 10.1140/epje/e2004-00033-4 |
| Journal | European Physical Journal E 12 (2003) 605-615 |
Abstract
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.
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"abstract": "RNA secondary structures of increasing complexity are probed combining single\nmolecule stretching experiments and stochastic unfolding/refolding simulations.\nWe find that force-induced unfolding pathways cannot usually be interpretated\nby solely invoking successive openings of native helices. Indeed, typical\nforce-extension responses of complex RNA molecules are largely shaped by\nstretching-induced, long-lived intermediates including non-native helices. This\nis first shown for a set of generic structural motifs found in larger RNA\nstructures, and then for Escherichia coli\u0027s 1540-base long 16S ribosomal RNA,\nwhich exhibits a surprisingly well-structured and reproducible unfolding\npathway under mechanical stretching. Using out-of-equilibrium stochastic\nsimulations, we demonstrate that these experimental results reflect the slow\nrelaxation of RNA structural rearrangements. Hence, micromanipulations of\nsingle RNA molecules probe both their native structures and long-lived\nintermediates, so-called \"kinetic traps\", thereby capturing -at the single\nmolecular level- the hallmark of RNA folding/unfolding dynamics.",
"arxiv_id": "physics/0309063",
"authors": [
"S. Harlepp",
"T. Marchal",
"J. Robert",
"J-F. Leger",
"A. Xayaphoummine",
"H. Isambert",
"D. Chatenay"
],
"categories": [
"physics.bio-ph",
"cond-mat.soft",
"q-bio.BM"
],
"doi": "10.1140/epje/e2004-00033-4",
"journal_ref": "European Physical Journal E 12 (2003) 605-615",
"title": "Probing complex RNA structures by mechanical force",
"url": "https://arxiv.org/abs/physics/0309063"
},
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