Internal diffusion coefficients of a tethered DNA molecule under shear flow

Spatiotemporal conformational dynamics of bio-entities
are key elements in a variety of biological processes and
phenomena, ranging from gene expression through chromosome pairing to misfolding induced diseases. The principal
mechanism defining these conformational dynamics can
be characterized in terms of internal diffusion coefficient.
Unlike conventional Brownian diffusion, internal diffusion
results from considerable alterations in the dihedral-space
conformation of the chain together with side-chain packing
of the collapsing and reptating structures. These in turn
influence the time scales in which these molecules physiologically perform. Here we measure the internal diffusion
of single dsDNA molecules, which serves as an established
polymer model, using a microfluidic apparatus. In this
setup, the DNA molecule is tethered to the bottom of the
microfluidic chamber while being subjected to shear flow.
The proximity of a spherical body under flow to a parallel
wall results in an increased drag force. Here we introduce
a model that incorporates near wall hydrodynamic effects
(Fax´en corrections) with the nonlinear elasticity of the
extended chain. Applying this model to the relaxation
dynamics of the chain, we measure its internal diffusion,
and consequent near wall diffusion.