Optimizing End-Labeled Free-Solution Electrophoresis by Increasing the Hydrodynamic Friction of the Drag Tag

Abstract

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of endlabeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles.It is specifically shown that the label's drag coefficient is determined by its hydrodynamic † Kai Grass et al.Optimizing ELFSE size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types.The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.

Theory of end‐labeled free‐solution electrophoresis: Is the end effect important?

“…For the latter, theories and computer simulations of electrophoresis of composite objects are necessary. Besides generic theories not making specific assumptions about the drag-tag [3] and the simplest case of a flexible diblock copolymer in a weak field [15][16][17][18], the problems considered theoretically so far include globular [15,19] and branched [18,20] drag-tags, separation and stretching of a drag-tag-DNA composite in a strong field [21][22][23][24], and dragtags attached to both ends of the DNA [25]. Besides ELFSE, such studies can also be useful for understanding other situations of practical interest involving objects consisting of two or more parts with different electrophoretic properties, for instance, different variants of affinity electrophoresis [26][27][28][29][30].…”

Mesoscale structures at complex fluid–fluid interfaces: a novel lattice Boltzmann/molecular dynamics coupling

“…In contrast to the Ladd scheme, in this approach the particles can be penetrated by the uid, but since they are off-lattice, a large variety of solutes can be easily modeled, allowing representation of structural details which are smaller than the lattice spacing, and a faster dynamics than the LB one. This approach has been successfully employed to describe polymer dynamics in conned geometries, 77 polyelectrolyte electrophoresis, [78][79][80][81] colloidal electrophoresis, [82][83][84] sedimentation, 85 microswimmer dynamics, 86 biopolymers and DNA translocation, 87,88 DNA trapping, 89 thermophoresis 90 and electroosmosis. 91 Coupling off-lattice particles with one of the multicomponent LB methods would allow addressing an even larger class of problems.…”

A highly efficient and versatile microchip capillary electrophoresis method for DNA separation using gold nanoparticle as a tag

“…Recently, an approach called “end‐labeled free‐solution electrophoresis (ELFSE)” has attracted much attention 27–30. In this approach, size‐dependent separation could be achieved without sieving medium by labeling DNA strands with uniform, neutral drag inducing body or tag.…”