title: Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments.
abstract: Tethered particle motion (TPM) has become an important tool for single-molecule studies of biomolecules; however, concerns remain that the method may alter the dynamics of the biophysical process under study. We investigate the effect of the attached microsphere on an illustrative biological example: the formation and breakdown of protein-mediated DNA loops in the lac repressor system. By comparing data from a conventional TPM experiment with 800 nm polystyrene beads and dark-field TPM using 50 nm Au nanoparticles, we found that the lifetimes of the looped and unlooped states are only weakly modified, less than two-fold, by the presence of the large bead. This is consistent with our expectation of weak excluded-volume effects and hydrodynamic surface interactions from the cover glass and microsphere.
authors.affiliation: Department of Physics, University of Michigan, Ann Arbor, MI 48103, USA. milsteij@umich.edu
authors.forename: J N
authors.initials: JN
authors.lastname: Milstein
authors.forename: Y F
authors.initials: YF
authors.lastname: Chen
authors.forename: J-C
authors.initials: JC
authors.lastname: Meiners
mesh_terms: D055592:Biophysical Phenomena; D004247:DNA / Q000737:chemistry*; D057446:Hydrodynamics; D066298:In Vitro Techniques; D007700:Kinetics; D056968:Lac Repressors / Q000737:chemistry; D053768:Metal Nanoparticles; D008863:Microspheres; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D010316:Particle Size; D011506:Proteins / Q000737:chemistry*
chemical_list: D056968:Lac Repressors; D011506:Proteins; D004247:DNA