Single molecule force spectroscopy
dependent hopping rate of RNA hairpins can be estimated from accurate
measurement of the folding landscapes (PNAS '08)
sequence-dependent folding landscapes of nucleic acid hairpins reflect
the complexity of biomolecular
generated using single molecule force clamp experiments by attaching semiflexible
simulations and theory, we study
the effect of the dynamics of the
attached handles on the handle-free RNA free energy profile Foeq(zm)
, where zm
is the molecular extension of the hairpin.
Accurate measurements of Foeq(zm)
requires stiff polymers with small L/lp
is the contour length of the
handle, and lp
is the persistence length.
reliable estimates of the
hopping rates can only be made
using flexible handles.
show that the
equilibrium free energy profile Foeq(zm)
at an external tension fm
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
the absence of handles at arbitrary values of f
framework shows that zm
is a good reaction coordinate for nucleic acid hairpins under tension.