title: Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA.
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.
authors.affiliation: NORDITA, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark. ambjorn@nordita.dk
authors.forename: Tobias
authors.initials: T
authors.lastname: Ambjörnsson
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004735:Energy Transfer; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D011485:Protein Binding; D011489:Protein Denaturation; D013314:Stress, Mechanical; D013696:Temperature
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA