Single molecule force spectroscopy

Force dependent hopping rate of RNA hairpins can be estimated from accurate measurement of the folding landscapes (PNAS '08)

The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular  Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible  Using simulations and theory, we study the effect of the dynamics of the attached handles on the handle-free RNA free energy profile F^o_eq(z_m), where z_m  is the molecular extension of the hairpin.  Accurate measurements of F^o_eq(z_m) requires stiff polymers with small L/l_p, where L is the contour length of the handle, and l_p is the persistence length.  Paradoxically, reliable estimates of the hopping rates can only be made using flexible handles.  Nevertheless, we show that the equilibrium free energy profile F^o_eq(z_m) at an external tension f_m, the force (f) at which the folded and unfolded states are equally populated, in conjunction with Kramers' theory, can provide accurate estimates of the force-dependent hopping rates in the absence of handles at arbitrary values of f.  Our theoretical framework shows that z_m is a good reaction coordinate for nucleic acid hairpins under tension.