Nonlinear electrophoresis and focusing of macromolecules

Macro- versus microscopic view on the electrokinetics of a water-membrane interface

Electrophoresis is an experimental method widely used to study electrostatic properties of interfaces. Here, we question the validity of the macroscopic theory for the planar geometry by Helmholtz and Smoluchowski by considering a POPC bilayer in an aqueous solution with 500 mM NaCl, using molecular dynamics simulations. We find that POPC shows positive electrophoretic mobility due to adsorption of sodium ions at the lipid headgroups. The theory assumes that the region in which the water density undergoes a transition from the bulk value to zero (interfacial width) is small compared to the Debye screening length. This separation of length scale is not fullfilled in the present case. Hence, contrasting the theory, we observe that the surface is not sharply defined, continuum hydrodynamics is not applicable, the effective viscosity in the double layer is increased compared to the bulk, and the zeta potential is dominated by the dipole potential. Our results might have widespread implications for interpretation of electrokinetic studies in general.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules

We demonstrate a unique parameter for biomolecule separation that results from the nonlinear response of long, charged polymers to electrophoretic fields and apply it to extraction and concentration of nucleic acids from samples that perform poorly under conventional methods. Our method is based on superposition of synchronous, time-varying electrophoretic fields, which can generate net drift of charged molecules even when the time-averaged molecule displacement generated by each field individually is zero. Such drift can only occur for molecules, such as DNA, whose motive response to electrophoretic fields is nonlinear. Consequently, we are able to concentrate DNA while rejecting high concentrations of contaminants. We demonstrate one application of this method by extracting DNA from challenging samples originating in the Athabasca oil sands.

Transport and separation of charged macromolecules under nonlinear electromigration in nanochannels

In this work, we theoretically investigate the implications of nonlinear electrophoretic effects on the transport and size-based separation of charged macromolecules in nanoscale confinements. By employing a regular perturbation analysis, we address certain nontrivial features of interconnection among wall-induced transverse migrative fluxes, electrophoretic and electroosmotic transport, confinement-induced hindered diffusive effects, and hydrodynamic interactions in detail. We demonstrate that there occurs an optimal regime of influence of the nonlinear electrophoretic effects, within which high values of separation resolution may be achieved. This size-based optimal regime, however, can be effectively exploited only for nanochannel flows, as attributed to the strong electric double layer interactions prevalent within the same.

Ellipsoidal particles driven by intensity gradients through viscous fluids

We investigate the drift velocity v(drift) of ellipsoidal polarizable particles (ellipsoids and coated ellipsoids), driven through a viscous fluid by an electric or electromagnetic field intensity gradient. At low Reynolds number and in the dipole approximation v(drift) is proportional to the square of the principal axis along the direction of motion multiplied by a form factor, which is weakly depending on the shape of the particle, and by a frequency and shape dependent factor f(omega). Near frequencies where the real part of epsilon (m)f(omega) changes sign ( epsilon (m) is the relative dielectric function of the medium in which the partcle is immersed), v(drift) is sensitive to the shape of the particle. We suggest that our results can be used for the experimental separation of neutral polarizable particles with respect to size or shape.