Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins

Details Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins

2004-11-30

arxiv.org/abs/q-bio/0411053v2

Biology

Quantitative Biology

Biomolecules

REVTeX4, 4 pages, 5 figures, revised version

Scientific paper

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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