2026-07-072026-07-07http://salesiana.dossiersoluciones.com/handle/123456789/88487We 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.REVTeX4, 4 pages, 5 figures, revised versionBiomoleculesStatistical Mechanicstext