  We suggest that the thermodynamic stability parameters (nearest neighbor
stacking and hydrogen bonding free energies) of double-stranded DNA molecules
can be inferred reliably from time series of the size fluctuations (breathing)
of local denaturation zones (bubbles). On the basis of the reconstructed bubble
size distribution, this is achieved through stochastic optimization of the free
energies in terms of Simulated Annealing. In particular, it is shown that even
noisy time series allow the identification of the stability parameters at
remarkable accuracy. This method will be useful to obtain the DNA stacking and
hydrogen bonding free energies from single bubble breathing assays rather than
equilibrium data.
