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Int. J. Mol. Sci. 2014, 15(8), 13817-13832; doi:10.3390/ijms150813817
Article

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

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Received: 10 June 2014; in revised form: 15 July 2014 / Accepted: 22 July 2014 / Published: 11 August 2014
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
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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.
Keywords: ssDNA; micro/nanofluidics; langevin dynamics simulation; transpore dynamics; coarse-graining ssDNA; micro/nanofluidics; langevin dynamics simulation; transpore dynamics; coarse-graining
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Qian, W.; Doi, K.; Uehara, S.; Morita, K.; Kawano, S. Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA. Int. J. Mol. Sci. 2014, 15, 13817-13832.

AMA Style

Qian W, Doi K, Uehara S, Morita K, Kawano S. Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA. International Journal of Molecular Sciences. 2014; 15(8):13817-13832.

Chicago/Turabian Style

Qian, Weixin; Doi, Kentaro; Uehara, Satoshi; Morita, Kaito; Kawano, Satoyuki. 2014. "Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA." Int. J. Mol. Sci. 15, no. 8: 13817-13832.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert