The Length Dependence of Translational Diffusion, Free Solution Electrophoretic Mobility, and Electrophoretic Tether Force of Rigid Rod-Like Model Duplex DNA

Abstract

In this work, boundary element modeling is used to study the transport of highly charged rod-like model polyions of various length under a variety of different aqueous salt conditions. Transport properties considered include free solution electrophoretic mobility, translational diffusion, and the components of the "tether force" tensor. The model parameters are chosen to coincide with transport measurements of duplex DNA carried out under six different salt/temperature conditions. The focus of the analysis is on the length dependence of the free solution electrophoretic mobility. In a solution containing 0.04 M Tris-acetate buffer at 25 degrees C, calculated mobilities using straight rod models show a stronger dependence on fragment length than that observed experimentally. By carrying out model studies on curved rod models, it is concluded that the "leveling off" of mobility with fragment length is due, in part at least, to the finite curvature of DNA. Experimental mobilities of long duplex DNA in monovalent alkali salts are reasonably well explained once account is taken of long-range bending and the simplifying assumptions of the model studies.

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

“…A rigorous continuum hydrodynamic-electrodynamic model describing μ found that the effective charge per base pair decreases with increasing dsDNA length (Allison et al, 2001), indicating that significantly fewer counterions were accumulated per DNA charge for short DNA oligomers than for polymeric DNA. Treating DNA as straight hemispherically capped cylinders predicted electrophoretic mobilities for DNA 60 bp within < 9% of experimental values but overestimated μ for larger fragments (Fig.…”

Weak solutions for the electrophoretic motion of charged particles

“…3 (a body force) is assumed (see Remark 2.1) and the proof of the existence theorem as Theorem 3.1 is based on the solution of an approximated system (obtained by regularization techniques). The existence of the approximated solutions is obtained by the Schauder fi xedpoint theorem (see [5]), via a solution of an appropriate inhomogeneous (linear) Stokes equation.…”

“…This phenomena is known as electrophoresis and is important in many technical applications (a vast literature is available: see for example [29], [24], [27], [2], [1], [3], [13], [30], [14]). We are considering a particle (a charged polymer, for example) immersed in an ionized solution (a viscous incompressible fluid).…”

Using electrophoretic mobility and bead modeling to characterize the charge and secondary structure of peptides

“…Without much additional difficulty, this can be generalized to an "effective ellipsoid" approach [20] and applied to globular proteins [34,35]. In order to deal in a more realistic way with the irregular topography and charge distribution of a peptide or protein at the atomic or at least primary structure level, boundary element (BE) [34,36] and "bead model" [37 -39] approaches are available. The latter "bead model" approach is particularly useful when multiple conformations need to be sampled as is the case of particular peptides under a variety of solvent -buffer-pH conditions.…”