Size separation of DNA molecules by pulsed electric field dielectrophoresis

Abstract

In this paper we propose an electrode design and a switching pattern of the applied DC electrode potentials for a microfluidic device to be used in size separation of DNA molecules. Estimates on the separation resolution, which are based on numerical solutions of a Newton-type equation on time-averaged quantities, are presented for an input batch sample of DNA fragments with sizes up to 220 base pairs (bp). The active area of the device (which can be microfabricated by standard photolitographic techniques) is a channel 6 µm wide, 8 µm deep and 150 µm in length, flanked by 23 plane parallel integrated electrodes, individually addressed with low DC voltages, up to ± 25 V. In the active area a time-dependent non-uniform electric field, or a travelling dielectrophoretic wave (TDW) is being produced. In order to enhance the separation resolution, the polarization DC potentials are switched with a relatively high frequency (≈ 10−7 s), which is chosen accordingly with the buffer conductivity and dielectric constants of the fluid and particles. Since the external field is of DC type, we put forward an explanatory model of the dielectric response of the DNA to the time-dependent applied field. We then numerically investigate the size-dependent response of the DNA in a low conductivity buffer (≈0.01 Ω−1 m−1) under the influence of the electric field, which is calculated by means of the method of moments. The results of the computer modelling indicate the existence of a threshold value for the size of the successfully transported molecules, which can be adjusted by varying the velocity of the dielectrophoretic wave produced by the system. The estimated error in selecting a chosen group of molecules with sizes above a specified value is about 5 bp, while the processing times are of the order of hundred of seconds.

Dielectrophoresis for the manipulation of nanobioparticles

“…However, processing times are long and they are not suitable for single molecule manipulation. EK forces have been demonstrated for enhancing mixing and improving detection efficiency [2,57,58]. The first method employed to handle DNA was gel EP followed by CE.…”

“…Important improvements in resolution and automation were achieved when microfabrication was combined with CE. Processing times could be reduced to the order of minutes by employing the microfabricated capillary array EP [57]. However, CE methods have an important drawback, since size fractionation of DNA cannot be achieved by employing CE since it involves the separation of molecules based on their different mass/charge ratios.…”

“…On the other hand, DEP is based on polarization effects, as shown in Eq. (1), the dielectrophoretic force exerted on a particle has a strong dependence on particle size; thus, DEP is an ideal EK technique for size fractionation [57]. Trapping, concentration, and stretching of DNA molecules have been achieved in microdevices employing DEP.…”

Electroporation of cells in microfluidic devices: a review

“…Since the electric field induces a dipolar charge distribution over the cell, the cell will be attracted to an electrode where the electric field converges. This effect has been used for cell manipulation [15], as well as for other applications such as separating DNA molecules [16] or other macromolecules [17].…”

Direct Numerical Simulation of Particles in Spatially Varying Electric Fields †

“…Therefore, in principle, DEP force can be used to separate particles with different dielectric properties [3]. For example, cancer cells can be separated from normal cells as they have different dielectric properties [12][13][14][15].…”