Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

Abstract

The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements

“…Under steady ionic current conditions assuming a uniform concentration, the electrical potential drop tends to concentrate in the narrower space. In such a narrow test section, which is far from the electrodes, the ionic current appears to obey Ohm's law 14,16,22 . Thus, when an ionic current is dominated by electrophoretic transport, the conductance is proportional to the cross-sectional area S and inversely proportional to the channel length L. Therefore, the ionic current I is expressed in terms of the conductivity σ and applied electrical potential V, as follows: I = σ(S/L)V. In the present study, the above conjectures was tested by measuring the potential difference in electrolyte solutions.…”

“…In a previous study, we investigated the transport of deoxyribonucleic acid (DNA) in nanochannels that have negative charges in electrolyte solutions [12][13][14] . By applying an potential difference, DNA molecules were found to be transported by electrophoresis in an electroosmotic flow.…”

“…Although it was clear that the behavior of electrically charged molecules was actually influenced by the externally applied field, quantitative evaluation of the local electric field in the channel was difficult. Some numerical studies predicted an potential difference in electrolyte solutions as a function of ion concentration [14][15][16][17] . By solving the Nernst-Planck and Poisson equations, the relationship between the electrical potential and the concentration was clarified 18,19 .…”

Thermophoretic Manipulation of Micro- and Nanoparticle Flow through a Sudden Contraction in a Microchannel with Near-Infrared Laser Irradiation

“…In the detection process, the velocities of targets through the nanopore are important because the velocity-control performance is directly related to the sensor accuracy. Various velocity-control techniques have been applied inside the nanopore [60][61][62]: tethering a protein larger than the nanopore diameter to prevent fast translocation [63,64], coating nanopore walls with counteractive charges [65,66] or polymers [67], using active feedback control with an applied voltage [68], decreasing the temperature to increase the viscosity of the solvent [69], and inplane guiding of targets via dielectrophoresis by AC electric fields at the nanopore entrance [70]. However, most of these techniques need highly sophisticated fabrication apparatuses and experimental skills.…”

Observation of Electrohydrodynamic Flow through a Pore in Ion-Exchange Membrane

“…In recent, novel technologies to manipulate electrophoretic behavior of single molecules [4]- [6], charged particles [7], and allergens [8] by applying EOFs have attracted much attention. Charged molecules, such as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in electrolyte solutions are electrically driven by external electric fields.…”