Modeling the free solution electrophoretic mobility of short DNA fragments

The electrophoretic mobility and the zeta potential (ζ) of fluorescently labeled colloidal silica rods, with an aspect ratio of 3.8 and 6.1, were determined with microelectrophoresis measurements using confocal microscopy. In the case where the colloidal particles all move at the same speed parallel to the direction of the electric field, we record a xyz-stack over the whole depth of the capillary. This method is faster and more robust compared to taking xyt-series at different depths inside the capillary to obtain the parabolic flow profile, as was done in previous work from our group. In some cases, rodlike particles do not move all at the same speed in the electric field, but exhibit a velocity that depends on the angle between the long axis of the rod and the electric field. We measured the orientation-dependent velocity of individual silica rods during electrophoresis as a function of κa, where κ–1 is the double layer thickness and a is the radius of the rod associated with the diameter. Thus, we determined the anisotropic electrophoretic mobility of the silica rods with different sized double layers. The size of the double layer was tuned by suspending silica rods in different solvents at different electrolyte concentrations. We compared these results with theoretical predictions. We show that even at already relatively high κa when the Smoluchowski limiting law is assumed to be valid (κa > 10), an orientation dependent velocity was measured. Furthermore, we observed that at decreasing values of κa the anisotropy in the electrophoretic mobility of the rods increases. However, in low polar solvents with κa < 1, this trend was reversed: the anisotropy in the electrophoretic mobility of the rods decreased. We argue that this decrease is due to end effects, which was already predicted theoretically. When end effects are not taken into account, this will lead to strong underestimation of the experimentally determined zeta potential.

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“…We argue that is due to the fact that end effects start to play a role, which was already predicted theoretically. 29 …”

Section: Introductionmentioning

confidence: 99%

Microelectrophoresis of Silica Rods Using Confocal Microscopy

et al. 2017

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“…This tool should be able to shed light on subtle changes in transport properties that accompany conformational changes in solution due to transitions induced by temperature or salt conditions in the case of macroions, binding of substrates to enzymes, structural mutations, change of the size of the solvent, and many other effects that are buried under the typical computational errors of other widely used methods. Further extensions of the method to include the specific effects of charges and electrolytes can also be made, along the lines suggested by Allison 34…”

Section: Discussionmentioning

confidence: 99%

“…This problem has been mentioned previously by Brune and Kim50 when dealing with implementations of the BE method. Allison's implementations,31–35 on the other hand, have not attempted a precise description of the shape of a macromolecule. Allison uses an algorithm51 which requires that all atoms or groups of atoms be represented by equal sized spheres, and thus yields only a coarse description of the molecular surface, but with very nice triangle shapes.…”

Section: Implementation Of the Be Method: Best And Coalescementioning

confidence: 99%

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A precise boundary element method for macromolecular transport properties

Aragón

2004

J Comput Chem

111

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A very precise boundary element numerical solution of the exact formulation of the hydrodynamic resistance problem with stick boundary conditions is presented. BEST, the Fortran 77 program developed for this purpose, computes the full transport tensors in the center of resistance or the center of diffusion for an arbitrarily shaped rigid body, including rotation-translation coupling. The input for this program is a triangulation of the solvent-defined surface of the molecule of interest, given by Connolly's MSROLL or other suitable triangulator. The triangulation is prepared for BEST by COALESCE, a program that allows user control over the quality and number of triangles to describe the surface. High numerical precision is assured by effectively exact integration of the Oseen tensor over triangular surface elements, and by scaling the hydrodynamic computation to the precise surface area of the molecule. Efficiency of computation is achieved by the use of public domain LAPACK routines that call BLAS Level 3 hardware-optimized subroutines available for most processors. A protein computation can be done in less than 10 min of CPU time in a modern Pentium IV processor. The present work includes a complete analysis of the sources of error in the numerical work and techniques to eliminate these errors. The operation of BEST is illustrated with applications to ellipsoids of revolution, and Lysozyme, a small protein. The typical numerical accuracy achieved is 0.05% compared to analytical theory. The numerical precision for a protein is better than 1%, much better than experimental errors in these quantities, and more than 10 times better than traditional bead-based methods.

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“…Parameters used in our model is obtained from [108], where l 0 = 1.5 nm and Y = 120 K B T /nm [83]. For short dsDNA segment (20 bp), WLC model can be simplified as the straight, rigid cylinder model with reasonable adequacy [3,62]. WLC models are used for simulation consistency.…”

Section: Parametersmentioning

confidence: 99%

A Framework for Modeling DNA Based Molecular Systems

2006

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Abstract. In this paper, we propose a framework for a discrete event simulator for simulating the DNA based nano-robotical systems. We describe a physical model that captures the conformational changes of the solute molecules. We also present methods to simulate various chemical reactions due to the molecular collisions, including hybridization, dehybridization and strand displacement. The feasibility of such a framework is demonstrated by some preliminary results.

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Modeling the free solution electrophoretic mobility of short DNA fragments

Cited by 25 publications

References 9 publications

Microelectrophoresis of Silica Rods Using Confocal Microscopy

Microelectrophoresis of Silica Rods Using Confocal Microscopy

A precise boundary element method for macromolecular transport properties

A Framework for Modeling DNA Based Molecular Systems

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