The role of near-wall drag effects in the dynamics of tethered DNA under shear flow

Guy Nir, Einat Chetrit, Anat Vivante, Yuval Garini, Ronen Berkovich

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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.

Original languageEnglish
Pages (from-to)2219-2226
Number of pages8
JournalSoft Matter
Issue number12
StatePublished - 28 Mar 2018

Bibliographical note

Publisher Copyright:
© 2018 The Royal Society of Chemistry.


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.

FundersFunder number
Ministry of Science, Technology, and Space3-13733
Israel Science Foundation152/11
Israeli Centers for Research Excellence1291/17
Planning and Budgeting Committee of the Council for Higher Education of Israel


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