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.Comment: 9 pages, 9 figure