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

Tobias Ambjornsson; Ralf Metzler

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

Tobias Ambjornsson·Ralf Metzler

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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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BibTeX RIS

Tobias Ambjornsson, Ralf Metzler. 2005-06-17. Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins. https://arxiv.org/abs/q-bio/0411053

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