Contraction and Tumbling Dynamics of DNA in Shear Flows under Confinement Induced by Transverse Viscoelastic Forces

The dynamics of single DNA molecules conveyed in a viscoelastic fluid flow with an opposing electrophoretic force are investigated by fluorescence microscopy. For balanced hydrodynamic and electrophoretic forces, DNA is confined near the walls with a much smaller elongation than in bulk shear flows. Furthermore, we observe that DNA extension is characterized by intermittent fluctuations, the characteristic time scale of which depends on the flow velocity. A model based on Rouse dynamics explains the contraction of the molecule by the coupling of monomer motion in the transverse and longitudinal directions to the flow induced by transverse viscoelastic forces. Using simulations, we suggest that the occurrence of intermittent fluctuations is analogous to tumbling dynamics characterized by the cyclic spooling motion of end monomers about the molecule center of mass.

[1]  John L. Lumley,et al.  Drag Reduction by Additives , 1969 .

[2]  Chih-Chen Hsieh,et al.  An experimental study of DNA rotational relaxation time in nanoslits , 2007 .

[3]  F. B. Usabiaga,et al.  Characteristic Times of Polymer Tumbling Under Shear Flow , 2011 .

[4]  R. Netz,et al.  Hydrodynamic effects in driven soft matter. , 2006, Soft matter.

[5]  Lijun Liu,et al.  Shape and Diffusion of Circular Polyelectrolytes in Salt-Free Dilute Solutions and Comparison with Linear Polyelectrolytes , 2017 .

[6]  A. Dutta,et al.  Migration of macromolecules under flow: the physical origin and engineering implications , 1994 .

[7]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[8]  M. Doi,et al.  Theory of the shape relaxation of a rouse chain , 1974 .

[9]  Audrey Boutonnet,et al.  DNA separation and enrichment using electro-hydrodynamic bidirectional flows in viscoelastic liquids. , 2016, Lab on a chip.

[10]  Michael D. Graham,et al.  Theory of shear-induced migration in dilute polymer solutions near solid boundaries , 2005 .

[11]  Hiroshi Watanabe,et al.  Viscoelastic and Dielectric Relaxation of Reptating Type-A Chains Affected by Reversible Head-to-Head Association and Dissociation , 2018, Macromolecules.

[12]  Chain extension of a confined polymer in steady shear flow. , 2012, The Journal of chemical physics.

[13]  Rodrigo E. Teixeira,et al.  Characteristic periodic motion of polymers in shear flow. , 2005, Physical review letters.

[14]  J. Victor,et al.  Conformational Manipulation of DNA in Nanochannels Using Hydrodynamics , 2013, 1409.0373.

[15]  C. Tardin,et al.  Dependence of DNA Persistence Length on Ionic Strength of Solutions with Monovalent and Divalent Salts: A Joint Theory-Experiment Study , 2015, 1504.02666.

[16]  Hubert Ranchon,et al.  Metrology of confined flows using wide field nanoparticle velocimetry , 2015, Scientific Reports.

[17]  N. Wagner,et al.  Poly(ethylene oxide) (PEO) and poly(vinyl pyrolidone) (PVP) induce different changes in the colloid stability of nanoparticles. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[18]  S. Lee,et al.  Particle migration and single-line particle focusing in microscale pipe flow of viscoelastic fluids , 2014 .

[19]  B. Ladoux,et al.  Dynamics of a tethered polymer in shear flow. , 2000, Physical review letters.

[20]  D. Long,et al.  Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: Motion and deformation. , 1996, Physical review letters.

[21]  Yunqi Li,et al.  Effects of excluded volume and hydrodynamic interaction on the deformation, orientation and motion of ring polymers in shear flow. , 2015, Soft matter.

[22]  R. Seidel,et al.  Mechanical and structural properties of YOYO-1 complexed DNA , 2010, Nucleic acids research.

[23]  Douglas E. Smith,et al.  Single-polymer dynamics in steady shear flow. , 1999, Science.

[24]  P. Gennes.  Coil-stretch transition of dilute flexible polymers under ultrahigh velocity gradients , 1974 .

[25]  M. Socol,et al.  Modeling of DNA transport in viscoelastic electro-hydrodynamic flows for enhanced size separation. , 2018, Soft matter.

[26]  U Dinnar,et al.  Tunable nonlinear viscoelastic "focusing" in a microfluidic device. , 2007, Physical review letters.

[27]  O. B. Usta,et al.  Flow-induced migration of polymers in dilute solution , 2006 .

[28]  Frédéric Ginot,et al.  BIABooster: Online DNA Concentration and Size Profiling with a Limit of Detection of 10 fg/μL and Application to High-Sensitivity Characterization of Circulating Cell-Free DNA. , 2018, Analytical chemistry.

[29]  M. Graham.  Fluid Dynamics of Dissolved Polymer Molecules in Confined Geometries , 2011 .

[30]  R. Winkler.  Semiflexible polymers in shear flow. , 2006, Physical review letters.

[31]  J. Viovy.  Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms , 2000 .

[32]  G. Fredrickson.  The theory of polymer dynamics , 1996 .

[33]  Cees Dekker,et al.  Conformation and dynamics of DNA confined in slitlike nanofluidic channels. , 2008, Physical review letters.

[34]  The gyration radius distribution of two‐dimensional polymer chains in a good solvent , 1990 .

[35]  Juan J de Pablo,et al.  DNA dynamics in a microchannel. , 2003, Physical review letters.

[36]  G. Gompper,et al.  Mesoscale simulations of polymer dynamics in microchannel flows , 2007, 0709.3822.

[37]  Victor Steinberg,et al.  Statistics of tumbling of a single polymer molecule in shear flow. , 2005, Physical review letters.

[38]  D E Smith,et al.  Single polymer dynamics in an elongational flow. , 1997, Science.

[39]  Thomas T. Perkins,et al.  Dynamical scaling of DNA diffusion coefficients , 1996 .

[40]  R. Larson,et al.  Tumbling and Deformation of Isolated Polymer Chains in Shearing Flow , 2012 .

[41]  Rodrigo E. Teixeira,et al.  Shear Thinning and Tumbling Dynamics of Single Polymers in the Flow-Gradient Plane , 2005 .