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.
Highlights
IntroductionThe high-speed reading of deoxyribonucleic acid (DNA) sequences is an important means of elucidating complete genetic sequences, and may enable the development of new medical treatments [1,2]
From the viewpoint of diffusivity and electrophoretic mobility, the present parameter set is acceptable when assessing the electrokinetic transport of single-stranded DNA (ssDNA)
We focused on ssDNA and developed a bead-spring model for use in the Langevin dynamics simulations
Summary
The high-speed reading of deoxyribonucleic acid (DNA) sequences is an important means of elucidating complete genetic sequences, and may enable the development of new medical treatments [1,2]. Sung and Park [13] and Muthukumar [14] studied the passage of single polymer molecules through the pores of a membrane during diffusion across a free energy barrier due to chemical potential differences Both groups modeled the stochastic processes associated with the transport of long polymers based on the Fokker–Planck equation and were able to predict a scaling law describing translocation time, τ, as a function of polymer length, N. A relationship among the electrokinetic transport of ssDNA, pore dimensions, and multiply-connected structures of the nanofluidic channel are clarified and a desirable design to control the translocation velocity is concluded.
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