University at Albnay, SUNY, Albany, NY, USA.
Non-equilibrium thermodynamics is indispensible in studying mechanical unfolding
of single RNA molecules. In a typical experiment, single RNA molecules
are pulled and relaxed at fast loading/unloading rate that structure
transitions occur under non-equilibrium. Work dissipation is reflected by hysteresis
between forward and reverse trajectories in force-extension curve. Ligand
and protein binding can stabilize a specific domain within a large RNA,
which further complicates work dissipation in mechanical unfolding. Using experiment
and simulation, we examined mechanical unfolding of large RNAs
containing secondary and tertiary folding. The RNAs follow hierarchical folding
pathways. Secondary structure forms before tertiary contacts, and tertiary
interaction is disrupted before unfolding of secondary structure. Factors that selectively
bind and stabilize tertiary structure lead to increased work dissipation
by protecting secondary structure from unfolding. Furthermore, work dissipation
is quantified as a function of pulling rate and factor binding