We utilized single-molecule tethered particle motion (TPM) tracking, optimized for studying the behavior of short (0.922 μm) dsDNA molecules under shear flow conditions, in the proximity of a wall (surface). These experiments track the individual trajectories through a gold nanobead (40 nm in radius), attached to the loose end of the DNA molecules. Under such circumstances, local interactions with the wall become more pronounced, manifested through hydrodynamic interactions. To elucidate the mechanical mechanism that affects the statistics of the molecular trajectories of the tethered molecules, we estimate the resting diffusion coefficient of our system. Using this value and our measured data, we calculate the orthogonal distance of the extended DNA molecules from the surface. This calculation considers the hydrodynamic drag effect that emerges from the proximity of the molecule to the surface, using the Faxén correction factors. Our finding enables the construction of a scenario according to which the tension along the chain builds up with the applied shear force, driving the loose end of the DNA molecule away from the wall. With the extension from the wall, the characteristic times of the system decrease by three orders of magnitude, while the drag coefficients decay to a plateau value that indicates that the molecule still experiences hydrodynamic effects due to its proximity to the wall.
|Number of pages||8|
|State||Published - 28 Mar 2018|
Bibliographical noteFunding Information:
We thank Moshe Gottlieb for valuable discussions, and Yossi Abulafia for imprinting gold crosses onto slides. We are also grateful to Dr Brian J. Beliveau for critically reading the manuscript. This work was supported by grants to R. B. and E. C. from the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation (Grant No. 152/11). This work was also supported in part by Israel Centers of Research Excellence (ICORE) grant 1291/17 and S. Grosskopf grant for ‘Generalized dynamic measurements in live cells’. A. V. was supported by the Ministry of Science, Technology, and Space grant 3-13733.
© 2018 The Royal Society of Chemistry.