Review modeling the free solution and gel electrophoresis of biopolymers: The bead array‐effective medium model

Abstract

Free solution and gel electrophoresis is an extremely useful tool in the separation of biopolymers. The complex nature of biopolymers, coupled with the usefulness of electrophoretic methods, has stimulated the development of theoretical modeling over the last 30 years. In this work, these developments are first reviewed with emphasis on Boundary Element and bead methodologies that enable the investigator to design realistic models of biopolymers. In the present work, the bead methodology is generalized to include the presence of a gel through the Effective Medium model. The biopolymer is represented as a bead array. A peptide, for example, made up of N amino acids is modeled as 2N beads. Duplex DNA is modeled as a discrete wormlike chain consisting of touching beads. The technical details of the method are placed in three Appendices. To illustrate the accuracy and effectiveness of the approach, two applications are considered. Model studies on both the free solution mobility of 73 peptides ranging in size from 2 to 42 amino acids, and the mobility of short duplex DNA in dilute agarose gels are discussed.

Modeling the electrophoresis of highly charged peptides: Application to oligolysines

“…(1), I is the ionic strength, F is the Faraday constant, the sum over α extends over all mobile ions present in the BGE, z α is the valence of ion α, m α = c α0 /(2 I ), where c α0 is the ambient concentration of ion α, e is the fundamental charge, κ is the Debye–Hückel screening parameter, ε 0 is the permittivity of free space, ε r is the relative permittivity of the solvent, k B is the Boltzmann constant, T is the absolute temperature, and φ is the reduced (dimensionless) electrostatic potential. In evaluating the “force balance” of a bead away in an effective medium, EM, characterized by gel screening parameter, λ, the Brinkmann equation can be written as 30, 31: …”

Role and Applications of Electrostatic Effects on Nucleic Acid Conformational Transitions and Binding Processes

“…4A demonstrates the length independence of μ for long NAs. Experimental and theoretical studies of polyion electrophoresis phenomena have been reviewed extensively (Allison et al, 2007;Hoagland et al, 1999;Slater et al, 2009;Slater et al, 2002;Viovy, 2000). …”

Electrofiltration of Biopolymers

“…In general, biopolymers are difficult to filtrate but at the same time they usually are positively or negatively charged as a result of the presence of amino-, sulphate-and carboxyl groups, which opens up vast new possibilities for the purification of biotechnological products [1].…”