  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.
