Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments

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. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 144–150, 2011.