Probing complex RNA structures by mechanical force

S. Harlepp (1) , T. Marchal (1) , J. Robert (1) , J.-F. Leger (1) , A. Xayaphoummine (1) , H. Isambert (1) , D. Chatenay (1)

1 LDFC - Laboratoire de Dynamique des Fluides Complexes

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.

Mots clés: RNA folding/unfolding; Single molecule experiments; Stochastic simulations; Non-native helices and kinetic traps; 16S ribosomal RNA; 16S ribosomal RNA.

Domaines: Biophysique [physics.bio-ph]

S. Harlepp, T. Marchal, J. Robert, J.-F. Leger, A. Xayaphoummine, et al.. Probing complex RNA structures by mechanical force. European Physical Journal E: Soft matter and biological physics, 2003, 12, pp.605-615. ⟨hal-00000601⟩