Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

Details Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

2011-09-30

arxiv.org/abs/1109.6903v1

J Chem Phys 135 (2011) 165103

Biology

Quantitative Biology

Biomolecules

6 pages, 4 figures

Scientific paper

10.1063/1.3654958

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.

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