Abstract
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 quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.
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Abbreviations
- DNA:
-
double-stranded DNA
- ssDNA:
-
single-stranded DNA
- SSB:
-
single-stranded DNA binding protein
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PACS: 87.15.-v, 82.37.-j, 87.14.G
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Metzler, R., Ambjörnsson, T. Dynamic Approach to DNA Breathing. J Biol Phys 31, 339–350 (2005). https://doi.org/10.1007/s10867-005-2410-y
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DOI: https://doi.org/10.1007/s10867-005-2410-y