Journal of Physical Chemistry B, Vol.121, No.10, 2220-2229, 2017
Direct Observation of Folding Energy Landscape of RNA Hairpin at Mechanical Loading Rates
By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long PSab RNA hairpin. We find that in the free-energy landscape the barrier height (G(double dagger)) and transition distance (x(double dagger)) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas Delta G(double dagger) reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (Delta G) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F <-> U) transitions for PSab. Herein, we report three intermediate states I-1 I, and I-2, located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in PSab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments measure the folding properties of biomolecules. that are increasingly being used to measure the folding properties of biomolecules.