title: Apparent persistence length renormalization of bent DNA.
abstract: We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in quantum mechanical tunneling problems. The results reveal a remarkable feature of sliding loops--an apparent strong reduction of the persistence length. We generalize these results to several other experimentally interesting situations ranging from rigid DNA-protein loops to the problem of anchoring deflections in atomic force microscopy stretching of semiflexible polymers. Expressions relating the force-extension measurements to the underlying loop or boundary deflection geometry are provided and applied to the case of the gal repressor dimer protein. The theoretical predictions are complemented and quantitatively confirmed by molecular dynamics simulations.
authors.affiliation: Max-Planck-Institute for Polymer Research, Theory Group, PO Box 3148, D 55021 Mainz, Germany.
authors.forename: Igor M
authors.initials: IM
authors.lastname: Kulić
authors.forename: Hervé
authors.initials: H
authors.lastname: Mohrbach
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lobaskin
authors.forename: Rochish
authors.initials: R
authors.lastname: Thaokar
authors.forename: Helmut
authors.initials: H
authors.lastname: Schiessel
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical
chemical_list: D004247:DNA