Probing complex RNA structures by mechanical force.
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.
Laboratoire de Dynamique des Fluides Complexes, CNRS-ULP, Institut de Physique, 3 rue de l'Université, 67000, Strasbourg, France.
S
S
Harlepp
T
T
Marchal
J
J
Robert
J-F
JF
Léger
A
A
Xayaphoummine
H
H
Isambert
D
D
Chatenay
D003198:Computer Simulation; D004548:Elasticity; D004926:Escherichia coli / Q000737:chemistry; D008846:Micromanipulation / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010812:Physical Stimulation / Q000379:methods*; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013314:Stress, Mechanical
D012336:RNA, Ribosomal, 16S; D012313:RNA