Single-molecule experiments provide new insights into biological processes
hitherto not accessible by measurements performed on bulk systems. We report on
a study of the kinetics of a triple-branch DNA molecule with four
conformational states by pulling experiments with optical tweezers and
theoretical modelling. Three distinct force rips associated with different
transitions between the conformational states are observed in the folding and
unfolding trajectories. By applying transition rate theory to a free energy
model of the molecule, probability distributions for the first rupture forces
of the different transitions are calculated. Good agreement of the theoretical
predictions with the experimental findings is achieved. Furthermore, due to our
specific design of the molecule, we found a useful method to identify
permanently frayed molecules by estimating the number of opened basepairs from
the measured force jump values.Comment: 17 pages, 12 figure
