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

International Journal of Molecular Sciences

Weixin Qian¹  Kentaro Doi¹  Satoshi Uehara¹  Kaito Morita¹ 

[1] Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan;

关键词: ssDNA;    micro/nanofluidics;    langevin dynamics simulation;    transpore dynamics;    coarse-graining;   

DOI  :  10.3390/ijms150813817

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.