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Updated: May 24, 2026

Agarose Gel Electrophoresis for the Separation of DNA Fragments
Published on: April 20, 2012
Diffusion and partitioning of cations in an agarose hydrogel
Mahmood Golmohamadi1, Thomas A Davis, Kevin J Wilkinson
1Department of Chemistry, University of Montreal, P.O. Box 6128, Succursale Centre-ville, Montréal, Québec, Canada, H3C 3J7.
Abstract:
Self- and mutual diffusion were measured in a low-melt 1.5% agarose hydrogel as a function of ionic strength (0.1-100 mM) and pH (3-7) for Cd(2+) and a charged rhodamine derivative. Self-diffusion was measured by fluorescence correlation spectroscopy, whereas mutual diffusion was evaluated using a diffusion cell. In contrast to the results observed for the diffusion cell, self-diffusion of rhodamine 6G increased from 50 to 90% of that found in water as the ionic strength increased from 0.1 to 100 mM (pH = 6). The combined observations of decreasing diffusive flux in parallel with an increasing diffusion coefficient were attributed to the gel's Donnan potential. Donnan potentials obtained voltammetrically using a Au amalgam microelectrode varied from -30 to 0 mV as the ionic strength increased from 0.1 to 100 mM (pH = 6). At the low ionic strengths, Donnan potentials of this magnitude accounted for a 13× enhancement of Cd(2+) concentrations in the hydrogel, which was consistent with measurements obtained by a nitric acid extraction of the gel (15×) and able to explain the apparent discrepancy between mutual and self-diffusion measurements. The overall diffusion of the positively charged substrates decreased as the pH was decreased from 12 to 3.
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