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Research Papers: Fundamental Issues and Canonical Flows

Electrokinetic Flow Dynamics of Weakly Aggregated λDNA Confined in Nanochannels

[+] Author and Article Information
Satoshi Uehara, Hirofumi Shintaku

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

Satoyuki Kawano1

Department of Mechanical Science and Bioengineering,  Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japankawano@me.es.osaka-u.ac.jp

1

Corresponding author.

J. Fluids Eng 133(12), 121203 (Dec 23, 2011) (8 pages) doi:10.1115/1.4005343 History: Received April 13, 2011; Revised October 17, 2011; Published December 23, 2011; Online December 23, 2011

Flow dynamics in nano-scaled structures such as nanochannels and nanopores have recently become important in developing next-generation high-speed DNA sequencers. In the present paper, we report the electrokinetic flow dynamics of λDNA confined in nanochannels having heights that are smaller than the molecular radius of gyration. Nanochannels of varying heights of from 330 to 650 nm were used in the experiments in order to systematically investigate the effect of confinement. Weakly aggregated λDNA flowed in a direction opposite to an applied electric field as a result of the competition of electrophoresis and electroosmotic flows. The terminal velocity of λDNA was proportional to the strength of the electric field, and the mobility was found to decrease with the channel height. A simple theoretical model explaining the decrease in the mobility was developed taking into account the shear stress due to small clearances between λDNA and the walls of nanochannels. The validity of the model was confirmed by reasonable agreement between the theoretical and experimental results. The theoretical model and the transport properties under confinement provide basic design data for the development of next-generation DNA sequencers.

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Copyright © 2011 by American Society of Mechanical Engineers
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Figures

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Figure 1

Schematic diagram of long DNA confined in a nanochannel: (a) 3-D view and (b) cross sectional view. (c) Scanning electron microscope image of the cross section of the nanochannel.

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Figure 2

Fabrication process of nanochannels: (a) cover glass, (b) coating cover glass with resist thin film, (c) UV exposure through photomask, (d) development of exposed photoresist, (e) Si deposition, (f) lift off, (g) drilling holes on another cover glass, and (h) anodic bonding

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Figure 3

(a) Schematic diagram of electroosmotic flow and (b) mean velocities of two types of particles with different surface charges

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Figure 4

(a) Trajectory of weakly aggregated λDNA at |E| = 1.42 × 103 V/m and h = 430 nm for 4 s and (b) sequential images of flowing λDNA in a nanochannel of h = 430 nm. Displacements of flowing λDNA at various E in nanochannels with (c) h = 430 nm and (d) 330 nm.

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Figure 5

Time-dependent velocity fluctuation of λDNA and histogram of fluctuation in nanochannels of (a) h = 430 nm and (b) 330 nm

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Figure 6

Theoretical model of weakly aggregated λDNA introducing the permeation: (a) schematic diagram of the model and coordinate system in the x-z plane and (b) permeation flow through the DNA

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Figure 7

Comparison of moving velocity |uo |, which corresponds to |uEXP | = |uDNA -uEOF |, of weakly aggregated λDNA between the experimental measurement of the flow of fluorescently stained λDNA and the present theoretical model using a permeation flow

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