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  • Title: Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA.
    Author: Ambjörnsson T, Metzler R.
    Journal: Phys Rev E Stat Nonlin Soft Matter Phys; 2005 Sep; 72(3 Pt 1):030901. PubMed ID: 16241404.
    Abstract:
    We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding-protein-induced denaturation. We determine the effective free-energy landscape of the DNA bubble and explore its relaxation modes.
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