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DNA Electrophoresis in Colloidal Self-Assembled Arrays Open Access


Other title
Colloidal Self-Assembly
DNA Electrophoresis
Silica Particle
Type of item
Degree grantor
University of Alberta
Author or creator
Ye, Wenmin
Supervisor and department
Harrison, Jed (Chemistry)
Examining committee member and department
Lucy, Charles (Chemistry)
Ahn, Chong (Engineering and Applied Science, University of Cincinnati)
Petersen, Nils (Chemistry)
McDermott, Mark (Chemistry)
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
This thesis investigates electrophoretic separation of DNA molecules in different types of separation media formed by silica nanoparticles. Particle arrays within microfluidic chips are fabricated using evaporation induced colloidal self-assembly. Methods to adjust pore size and the order of the particle lattice were developed, in order to probe the effect of lattice structure and size on separation of DNA. A stepwise packing procedure was developed to fabricate structures with stepwise gradient in pore size. Monodisperse packed structures yield pore sizes from a few nanometers to a few hundred nanometers according to the particle size being used, but the electrophoresis can only be optimized for a certain range of DNA sizes. By packing separation zones with two different pore sizes, optimal separation can be achieved for larger and smaller DNA size range, by taking advantages from both larger and smaller pore sizes within one device. The separation accomplished in the upstream region is retained as DNA moves across the zone boundary, even when the separated DNA has the same deflection angle in the downstream region. Small DNA not separated in the larger pore size is then separated in the smaller, downstream pore size. The peak capacity is improved by employment of this stepwise pore gradient. Colloidal arrays with two different sized nanoparticles mixed in various proportions are prepared, yielding structures with different degrees of disorder. The roles of order within a separation matrix on DNA separation in both asymmetric pulsed field angular separation and capillary zone electrophoresis are studied systematically. Radial distribution functions and orientational order parameters are determined to characterize the scale of disorder. In pulsed field electrophoresis, the DNA separation resolution is quantified for each structure, showing a strong dependence on order within the structure. Ordered structures give better separation resolution than highly disordered structures. However, the variation of separation performance with order is not monotonic, showing a small, but statistically significant improvement in structures with short range order compared to those with long range order. In capillary zone electrophoresis, regression analysis is conducted for the electrophoretic mobility and the dispersion coefficient. Both parameters exhibit a weak monotonic dependence on matrix order, complementary to the effect of DNA size and pore size. Higher degree of matrix order is favored by higher mobility and lower dispersion coefficient.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Chapter 2, Conference presentation, MicroTAS 2010, Groningen, the NetherlandsChapter 3, Nazemifard N. et al., 2012.Lab on a Chip, 12: 146-152Chapter 4, Conference presentation, MicroTAS 2012, Okinawa, Japan

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