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

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The role of near-wall drag effects in the dynamics of tethered DNA under shear flow†
Soft Matter ( IF 2.9 ) Pub Date : 2018-02-05 00:00:00 , DOI: 10.1039/c7sm01328k
Guy Nir _{1,

2,

3,

4,

5} , Einat Chetrit _{6,

7,

8} , Anat Vivante _{4,

5,

8} , Yuval Garini _{4,

5,

8} , Ronen Berkovich _{6,

7,

7,

8,

9}

Affiliation

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.

中文翻译：

剪力作用下近壁阻力效应在束缚DNA动力学中的作用†

我们利用单分子束缚粒子运动（TPM）跟踪，优化用于研究短的（0.922μm）dsDNA分子在剪切流条件下在壁（表面）附近的行为。这些实验通过附着在DNA分子松散末端的金纳米珠（半径40 nm）跟踪单个轨迹。在这种情况下，与墙的局部相互作用变得更加明显，这通过流体动力相互作用得以体现。为了阐明影响束缚分子分子轨迹统计的机械机制，我们估算了系统的静息扩散系数。使用该值和我们的测量数据，我们可以计算延伸的DNA分子与表面的正交距离。该计算使用Faxén校正因子考虑了从分子与表面附近出现的流体动力学阻力效应。我们的发现使得能够构建一种方案，根据该方案，沿着链条的张力随着施加的剪切力而建立，从而驱动DNA分子的松散端远离壁。随着壁的延伸，系统的特征时间减少了三个数量级，而阻力系数下降到平稳值，这表明该分子由于靠近壁而仍受到流体动力作用。驱使DNA分子的松散末端脱离壁。随着壁的延伸，系统的特征时间减少了三个数量级，而阻力系数下降到平稳值，这表明该分子由于靠近壁而仍受到流体动力作用。驱使DNA分子的松散末端脱离壁。随着壁的延伸，系统的特征时间减少了三个数量级，而阻力系数下降到平稳值，这表明该分子由于靠近壁而仍受到流体动力作用。

更新日期：2018-02-05

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