Stochastic approach to DNA breathing dynamics
نویسندگان
چکیده
منابع مشابه
Stochastic approach to DNA breathing dynamics
– We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse ...
متن کاملDynamic approach to DNA breathing.
Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic qu...
متن کاملBreathing dynamics in heteropolymer DNA.
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initia...
متن کاملDetermining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization.
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 energie...
متن کاملMaster equation approach to DNA breathing in heteropolymer DNA.
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few k(B)T. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, w...
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ژورنال
عنوان ژورنال: Europhysics Letters (EPL)
سال: 2005
ISSN: 0295-5075,1286-4854
DOI: 10.1209/epl/i2005-10144-9