title: Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization.
abstract: 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.
authors: Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India.
authors: Srijeeta
authors: S
authors: Talukder
authors: Pinaki
authors: P
authors: Chaudhury
authors: Ralf
authors: R
authors: Metzler
authors: Suman K
authors: SK
authors: Banik
mesh_terms: D004247:DNA / Q000737:chemistry*; D008954:Models, Biological; D015233:Models, Statistical; D009691:Nucleic Acid Denaturation; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D004247:DNA