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.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78494/1/21547_ftp.pd

Many-particle hydrodynamic interactions in parallel-wall geometry: Cartesian-representation method

This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel algorithm for accurate evaluation of the many-particle friction matrix in this system--no such algorithm has been available so far. Our approach involves expanding the fluid velocity field into spherical and Cartesian fundamental sets of Stokes flows. The interaction of the fluid with the particles is described using the spherical basis fields; the flow scattered with the walls is expressed in terms of the Cartesian fundamental solutions. At the core of our method are transformation relations between the spherical and Cartesian basis sets. These transformations allow us to describe the flow field in a system that involves both the walls and particles. We used our accurate numerical results to test the single-wall superposition approximation for the hydrodynamic friction matrix. The approximation yields fair results for quantities dominated by single particle contributions, but it fails to describe collective phenomena, such as a large transverse resistance coefficient for linear arrays of spheres

A Theoretical Model of a Molecular-Motor-Powered Pump

The motion of a cylindrical bead in a fluid contained within a two-dimensional channel is investigated using the boundary element method as a model of a biomolecular-motor-powered microfluidics pump. The novelty of the pump lies in the use of motor proteins (kinesin) to power the bead motion and the few moving parts comprising the pump. The performance and feasibility of this pump design is investigated using two model geometries: a straight channel, and a curved channel with two concentric circular walls. In the straight channel geometry, it is shown that increasing the bead radius relative to the channel width, increases the flow rate at the expense of increasing the force the kinesins must generate in order to move the bead. Pump efficiency is generally higher for larger bead radii, and larger beads can support higher imposed loads. In the circular channel geometry, it is shown that bead rotation modifies the force required to move the bead and that shifting the bead inward slightly reduces the required force. Bead rotation has a minimal effect on flow rate. Recirculation regions, which can develop between the bead and the channel walls, influence the stresses and force on the bead. These results suggest this pump design is feasible, and the kinesin molecules provide sufficient force to deliver pico- to atto- l/s flows.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44478/1/10544_2005_Article_6168.pd