Investigation of migration behavior of rod-like dsDNA in gel with precisely controlled network structure
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Investigation of migration behavior of rod-like dsDNA in gel with precisely controlled network structure Xiang Li1, Kateryna Khairulina1, Ung-il Chung1, and Takamasa Sakai1 1 Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-31 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan ABSTRACT We investigated the migration behavior of rodlike double-stranded DNA (dsDNA) in polymer gels and polymer solutions. Tetra-PEG gel, which has a homogeneous network structure, was utilized as a model system, allowing us to systematically tune the polymer volume fraction and molecular weight of network strand. Although we examined the applicability of the existing models, all the models failed to predict the migration behavior. Thus, we proposed a new model based on the Ogston model, which well explained the experimental data of polymer solutions and gels. The polymer volume fraction determined the maximum mobility, while the network strand governed the size sieving effect. From these results, we conclude that the polymer network with lower polymer volume fraction and smaller network strand is better in terms of size separation. The homogeneous polymer network is vital for understanding of particles’ dynamics in polymer network and a promising material for high-performance size separation. INTRODUCTION For the separation of particles based on their size, polymer gels and solutions are conventionally used as separation media (gel electrophoresis). They act as stable (polymer gels) or transient (polymer solutions) networks and interact with polyelectrolytes in a complex manner, separating polyelectrolytes based on their size. This complex interaction, on the other hand, makes it challenging to fully understand the dynamics of polyelectrolytes in the presence of polymer network.1 Understanding of the dynamics of polyelectrolytes in polymer network is one of the most important goals in polymer science, and will help develop a high-performance separation media. These academic and industrial interests lead to a number of researches on gel electrophoresis. Ogston proposed theoretical prediction on this phenomenon.2 The Ogston model treats the network as an assembly of randomly distributed pores formed with long stiff fibers. When a particle finds a pore larger than itself, it is able to pass through the pore. Chrambach et al extended this model, and predicted the migration of a variety of particles in obstacles with a variety of geometries.3 The reduced mobility is calculated as,
μ e = μe0 exp(−K rφ ) K r ~ (Rg + r)g
(1)
, where μe and μe0 are the electrophoretic mobility in polymer network in free solution respectively, Kr is retardation coefficient, Rg is the gyration radius of particle, φ is polymer
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for the rodlike dsDNA in the range 20-160 bp. We investigated the effect of φ and Ns on μe, and proposed a new migration mechanism of rod-like dsDNA in polymer network. EXPERIMENT Tetra-amine-terminated polyethylene glycol (Tetra-PEG-NH2) and tetra-OSu-terminated polyethylene glycol (Tetra-PEG-OSu) we
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