Diffusion of Macromolecules in Agarose Gels: Comparison of Linear and Globular Configurations  Alain Pluen, Paolo A. Netti, Rakesh K. Jain, David A. Berk  Biophysical Journal  Volume 77, Issue 1, Pages 542-552 (July 1999) DOI: 10.1016/S0006-3495(99)76911-0 Copyright © 1999 The Biophysical Society Terms and Conditions

Figure 1 Experimental hydrodynamic radius, RHexp, extracted from the diffusion coefficients measured in solution for all ellipsoidal macromolecules in 0.1M PBS at I=25°C as a function of the hydrodynamic radius published in the literature, RHlit. The solid line represents the experimental dependence. Experimental hydrodynamic radii are 10% larger than literature data. Biophysical Journal 1999 77, 542-552DOI: (10.1016/S0006-3495(99)76911-0) Copyright © 1999 The Biophysical Society Terms and Conditions

Figure 2 Diffusion coefficients of all nonflexible macromolecules studied as a function of their hydrodynamic radius, RH, obtained in 0.1M PBS (●) and in 2% agarose gels (▾) and I=25°C. A sharp decrease of the diffusion coefficients is observed above RH=30nm, suggesting higher interactions between the matrix and the macromolecules. Biophysical Journal 1999 77, 542-552DOI: (10.1016/S0006-3495(99)76911-0) Copyright © 1999 The Biophysical Society Terms and Conditions

Figure 3 DNA diffusion coefficients, DG, in 2% agarose gels (▾) and the DNA diffusion coefficients, D0, in solution (●) as a function of their basepair number, N0, in 0.1M PBS at T=25°C. The slope indicated for the diffusion coefficients in gels corresponds to the scaling exponent −0.52, which is in good agreement with Zimm's predictions. The scaling exponent −2.0 is the theoretical scaling exponent given by the theory (Eq. 8) whereas the scaling exponent −1.55 is the result of the experimental fit. The value Rg=a/2 corresponds to theoretical change of regime between the Rouse regime and the reptation regime for the DNA in the gels. Biophysical Journal 1999 77, 542-552DOI: (10.1016/S0006-3495(99)76911-0) Copyright © 1999 The Biophysical Society Terms and Conditions

Figure 4 Ratio of diffusivities in solution (0.1M PBS) and in 2% agarose gels as a function of the hydrodynamic radius of different macromolecules (proteins, dextrans, beads). We assumed ϵ=0.985 for all models. The different models used are effective medium theory/Brinkman model (Eq. 12), Ogston model (Eq. 7), Renkin model (Eq. 11), and partition model (Eq. 10). Boundary limits mentioned in the theoretical part of this paper were taken into account in this figure. Biophysical Journal 1999 77, 542-552DOI: (10.1016/S0006-3495(99)76911-0) Copyright © 1999 The Biophysical Society Terms and Conditions