Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization
arXiv:1109.6903 · doi:10.1063/1.3654958
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.
6 pages, 4 figures
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Cited by in corpus (10)
- Physics of base-pairing dynamics in DNA
- Helix untwisting and bubble formation in circular DNA
- J-factors of short DNA molecules
- Flexibility of short DNA helices under mechanical stretching
- Entropic Penalties in Circular DNA Assembly
- Base pair fluctuations in helical models for nucleic acids
- Twisting short dsDNA with applied tension
- Loop exponent in DNA bubble dynamics
- Stochastic Optimization Based Study of Dimerization Kinetics
- Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA