Mobility models for stiff and flexible macromolecules in dilute gels

Abstract

SYNOPSISThe effective sphere approximation for modeling electrophoretic transport of macromolecules in highly porous gels (the "Ogston model") is examined, and contrasted with similar mobility models for stiff and flexible solutes. Calculation of segmental depletion near gel obstacles of various shapes demonstrates the limited applicability of the effective sphere approach. For highly flexible chains, both theory and experiment reveal a nonunique mapping between mobility and molecular size when the molecular radius is comparable to that of gel fibers. Turning to mobility behavior in more concentrated gels, neither flexible or stiff macromolecules behave as spheres; for the particular case of flexible chains, the presence of entropic barriers in concentrated gels can be understood in terms of a simple random planes model for the gel structure.

Concave ferguson plots of DNA fragments and convex ferguson plots of bacteriophages: Evaluation of molecular and fiber properties, using desktop computers

“…The equivalent sphere [l] of nonspherical particles is defined as one having access to the same percentage of spacings (available fractional volume) for a particular set of experimental conditions as the nonspherical particle. A possible explanation for the reduction in particle radius could be the independently observed stretching of the DNA molecule in inverse relation to the pore size of the gel ( The concept of an equivalent sphere for nonspherical particles was recently discussed [38]. The authors of this paper conclude that there is n o simple relationship between particle size, shape and the radius of an equivalent sphere and the latter concept, therefore, is dismissed.…”

Electrophoresis in Polymer Solutions: Mechanisms of Molecular Sieving

“…4,6,7 It has been described in terms of exclusion due to a surface-overlap phenomenon (19) and requires therefore the postulate of particular idealized geometric shapes of the obstacle. Historically, the mathematical model of Ogston 5 has been the one applied to gel electrophoresis.…”

Single Chain Entanglement: A Monte Carlo Simulation of Dilute Solution Capillary Electrophoresis

“…15 In a rigid gel, when the chain/pore size ratio is small, Ogston-type sieving appears to explain molecular weight dependent chain transport, 16,17 although the underpinnings of the original sieving theory by Ogston and others have been seriously questioned. 18,19 At the opposite extreme, when the chain/pore ratio is large, the reptation model describes transport with reasonable success, [20][21][22][23][24] especially with the model modified to account for field-induced chain orientation. [25][26][27] Finally for the intermediate case, when the relevant size ratio lies near unity, the entropic barriers model [28][29][30][31] suggests that a coupling of chain flexibility to medium inhomogeneity defines a regime of entropically activated transport.…”

“…In a rigid gel matrix, the motions of a homologous series of probe chains can be roughly correlated with the ratio of average chain size to average pore size. Some investigators have justified similar descriptions for probe motion in entangled solutions by viewing these sluggish but fluidlike matrix materials as “virtual gels.” In a rigid gel, when the chain/pore size ratio is small, Ogston-type sieving appears to explain molecular weight dependent chain transport, , although the underpinnings of the original sieving theory by Ogston and others have been seriously questioned. , At the opposite extreme, when the chain/pore ratio is large, the reptation model describes transport with reasonable success, − especially with the model modified to account for field-induced chain orientation. − Finally for the intermediate case, when the relevant size ratio lies near unity, the entropic barriers model − suggests that a coupling of chain flexibility to medium inhomogeneity defines a regime of entropically activated transport. Unlike either sieving or reptation depictions, entropic barriers transport explicitly accounts for the spatial variation of configurational entropy for the confined probe chain.…”