Near–wall internal diffusion coefficients of a tethered dsDNA molecule under shear flow


  Guy Nir [1,2]  ,  Einat Chetrite [3]  ,  Anat Vivante [1]  ,  Yuval Garini [1]  ,  Ronen Berkovich [3]  
[1] Bar Ilan University, Ramat Gan 52900, Israel
[2] Harvard Medical School, Boston, MA 02115, USA
[3] Ben-Gurion University of the Negev, Beer Sheva 84105, Israel

Polymer-surface interactions govern the dialogue of a polymer and its surrounding, hence their manifestation is reflected in many fields, such as DNA interactions with the nucleus envelope, cell adhesion through its surface receptors and extracellular glycoproteins, and the formation of biofilms with the attachment of free-floating microorganisms to a surface. Although polymer-surface interactions are prevalent and acute across many disciplines, their extent in space and time, and quantification, in terms of, force acting on a polymer in the vicinity of a surface, remains elusive, partially due to challenges in decoupling the intrinsic diffusion of a polymer from surrounding affects, such as, surface proximity. Here we measured the internal diffusion of single dsDNA molecules and bead constructs using a microfluidic apparatus to probe near–wall effects. In this setup, the DNA molecule is tethered to the bottom of the microfluidic chamber while being subjected to shear flow. The proximity of the tethered spherical body under flow parallel to a wall results in an increased drag force, and reduction of velocity. Here we introduce a model that incorporates near–wall hydrodynamic effects (Faxén corrections) with the polymer nonlinear elasticity. Applying this model to the relaxation dynamics of the chain, we probe through the internal diffusion of the system the near–wall drag effect on the Faxén correction factor.