title: Nucleosome repositioning via loop formation.
abstract: Active (catalyzed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eukaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by earlier works. The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model-being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed, and compared to existing experimental findings.
authors.affiliation: Max-Planck-Institut für Polymerforschung, Theory Group, Ackermannweg 10, D-55128 Mainz, Germany. kulic@mpip-mainz.mpg.de
authors.forename: I M
authors.initials: IM
authors.lastname: Kulić
authors.forename: H
authors.initials: H
authors.lastname: Schiessel
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004735:Energy Transfer; D046911:Macromolecular Substances; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D046911:Macromolecular Substances; D009707:Nucleosomes; D004247:DNA