THE RELATIONSHIP OF AGAROSE-GEL STRUCTURE TO THE SIEVING OF SPHERES DURING AGAROSE-GEL ELECTROPHORESIS

To understand the organization of fibers in an agarose gel, digitized electron micrographs are used here to determine the frequency distribution of interfiber distance (2P(c)) in thin sections of agarose gels. For a preparation of underivatized agarose, a 1.5% gel has a P(c) distribution that is indistinguishable from the P(c) distribution of a computer-generated, random-fiber gel; the log of the occurrence frequency (F) decreases linearly as a function of P(c). As the agarose concentration decreases below 1.5%, the semilogarithmic F versus P(c) plot becomes progressively less linear. Two straight lines represent the data; the plot is steeper at the lower P(c) values. As the percentage of agarose increases above 1.5%, the semilogarithmic F versus P(c) plot becomes steeper at the higher P(c) values. This change in the shape of semilogarithmic F versus P(c) plots is possibly explained by the existence in agarose gels of two zones, one whose P(c) distribution is more sensitive to the average agarose concentration than the other. To compare the structure of agarose gels to their sieving during electrophoresis, the root mean square value of P(c) (P(c)) is compared to the sieving-based radius of the effective pore (PE; Griess et aL (16)) for both underivatized agarose and a derivatized agarose that has a smaller PE at any given agarose percentage. For 0.8-2.0% gels of either underivatized or derivatized agarose, P(E)/P(c) is a constant within experimental error. Deviations from this constant are observed at lower gel percentages. This relationship of P(E) to P(c) constrains theoretical descriptions of the motion of spheres in fibrous networks.