Manipulation of Single DNA Molecules via Lateral Focusing in a PDMS/Glass Microchannel

Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

Role of hydrodynamic interactions in the migration of polyelectrolytes driven by a pressure gradient and an electric field

Experiments have shown that DNA molecules in capillary electrophoresis migrate across field lines if a pressure gradient is applied simultaneously. We suggest that this migration results from an electrically driven flow field around the polyelectrolyte, which generates additional contributions to the center-of-mass velocity if the overall polymer conformation is asymmetric. This hypothesis leads to a coarse-grained polymer model, without explicit charges, that quantitatively explains the experimentally observed migration. The simulations contradict the widely held notion that charge neutrality eliminates the effects of hydrodynamic interactions in electrically driven flows of polyelectrolytes. We predict a measurable increase in the electrophoretic velocity of a sheared polyelectrolyte that depends on chain length.

Dual-asymmetry electrokinetic flow focusing for pre-concentration and analysis of catecholamines in CE electrochemical nanochannels

In this research, a technique incorporating dual-asymmetry electrokinetic flow (DAEKF) was applied to a nanoCE electrochemical device for the pre-concentration and detection of catecholamines. The DAEKF was constructed by first generating a zeta-potential difference between the top and bottom walls, which had been pre-treated with O2 and H2O surface plasma, respectively, yielding a 2-D gradient shear flow across the channel depth. The shear flow was then exposed to a varying zeta-potential along the downstream direction by control of the field-effect in order to cause downward rotational flow in the channel. By this mechanism, almost all of the samples were effectively brought down to the electrode surface for analysis. Simulations were carried out to reveal the mechanism of concentration caused by the DAEKF, and the results reasonably describe our experiment findings. This DAEKF technique was applied to a glass/glass CE electrochemical nanochip for the analysis of catecholamines. The optimum detection limit was determined to be 1.25 and 3.3 nM of dopamine and catechol, respectively. A detection limit at the zeptomole level for dopamine can be obtained in this device, which is close to the level released by a single neuron cell in vitro.

Atypical mobilities of single native DNA molecules in microchip electrophoresis revealed by differential interference contrast microscopy

A transmitted-light optical microscope using differential interference contrast (DIC) was employed to follow the real-time dynamics of different kb-sized single native dsDNA molecules without fluorescent-dye labeling. In a PDMS/glass microchip, the electrophoretic migration velocities of large dsDNA molecules are lower than small dsDNA molecules in a running buffer of 0.25% v/v nonionic polymeric surfactant C16E6 (n-alkyl polyoxyethylene ether) in 100 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES) buffer because the C16E6 behaved as a dynamic polymer. However, the order of migration reversed in 50 mM Gly-Gly buffer. The radial positions of individual DNA molecules (i.e., center or walls of the microchip) did not change the migration order. The atypical migration order correlated well with the results in CE. The alignment of the deformable molecules due to viscous drag is likely responsible for these observations.

A rigid poly(dimethylsiloxane) sandwich electrophoresis microchip based on thin-casting method

We present a novel concept of glass/poly(dimethylsiloxane) (PDMS)/glass sandwich microchip and developed a thin-casting method for fabrication. Unlike the previously reported casting method for fabricating PDMS microchip, several drops of PDMS prepolymer were first added on the silanizing SU-8 master, then another glass plate was placed over the prepolymer as a cover plate, and formed a glass plate/PDMS prepolymer/SU-8 master sandwich mode. In order to form a thin PDMS membrane, a weight was placed on the glass plate. After the whole sandwich mode was cured at 80 degrees C for 30 min, the SU-8 master was easily peeled and the master microstructures were completely transferred to the PDMS membrane which was tightly stuck to the glass plate. The microchip was subsequently assembled by reversible sealing with the glass cover plate. We found that this PDMS sandwich microchip using the thin-casting method could withstand internal pressures of >150 kPa, more than 5 times higher than that of the PDMS hybrid microchip with reversible sealing. In addition, it shows an excellent heat-dissipating property and provides a user-friendly rigid interface just like a glass microchip, which facilitates manipulation of the microchip and fix tubing. As an application, PDMS sandwich microchips were tested in the capillary electrophoresis separation of fluorescein isothiocyanate-labeled amino acids.