title: Modeling DNA unzipping in the presence of bound proteins.
abstract: Unzipping force analysis of protein association is a technique to investigate protein-DNA interactions by mechanically unzipping DNA. We computationally investigate the limits of this technique under quasistatic conditions. We find the minimum binding energy of a protein for which the protein can be detected using this technique and the minimum distance between the binding sites of two proteins of varying binding energies that can be resolved unambiguously with this technique.
authors.affiliation: The Ohio State University, Department of Physics, 191 W Woodruff Ave, Columbus, Ohio 43210, USA. farhat@pacific.mps.ohio-state.edu
authors.forename: Farhat
authors.initials: F
authors.lastname: Habib
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011485:Protein Binding; D011487:Protein Conformation; D013314:Stress, Mechanical
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA