Probing complex RNA structures by mechanical force
Laboratoire de Dynamique des Fluides Complexes, CNRS-ULP, Institut de Physique, 3 rue de l’Université, 67000, Strasbourg, France
2 Physico-Chimie Curie, CNRS UMR168, Section de Recherche, Institut Curie, 11 rue P. & M. Curie, 75005, Paris, France
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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 interpreted 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.
© EDP Sciences, Società Italiana di Fisica, and Springer-Verlag, 2003