Adaptation of pulsed-field gel electrophoresis for the improved fractionation of spheres

Noise-enhanced gel electrophoresis

Macromolecules confined within a nanoporous matrix experience entropic trapping when their dimensions approach the average pore size, leading to emergence of anomalous transport behavior that can be beneficial in separation applications. But the ability to exploit these effects in practical settings (e.g., electrophoretic separation of DNA) has been hindered by additional dispersion introduced as a consequence of the uncorrelated process by which the embedded macromolecules discretely hop from pore to pore. Here, we show how both the source and solution to these difficulties are intimately linked to the inherent dynamics of the underlying activated transport mechanism. By modulating the applied electric field at a frequency tuned to the characteristic activation timescale, a resonance condition can be established that synergistically combines accelerated mobility and reduced diffusion. This resonance effect can be precisely manipulated by adjusting the magnitude and period of the driving electric field, enabling enhanced separation performance and bi-directional transport of different-sized species to be achieved. Notably, these phenomena are readily accessible in ordinary hydrogels (as opposed to idealized nanomachined topologies) suggesting broad potential to apply them in a host of useful settings.

Application of the concept of an electrophoretic ratchet

Fractionation via a gel electrophoretic ratchet has previously succeeded for comparatively large (radius R > or = 95 nm) spheres (Serwer, P, Griess, G.A., Anal. Chim. Acta 1998, 372, 299-306). The electrical oscillations are the following electrical field pulses: high field --> low field --> high field, etc. The field is inverted after each pulse; the time-integral of the field can be zero. Response to the ratchet is caused by steric trapping in the high field-direction, but not in the low field-direction. Trapping and, therefore, response to the ratchet decrease as R decreases. The smaller spheres do not respond to the ratchet. In the present study, spheres with R values smaller than 95 nm are made, for the first time, to respond to a similar gel electrophoretic ratchet. To achieve this objective, the heterogeneity of pore size is increased for the gel used. The heterogeneity of pore size is increased by (i) forming the gel with degraded hydroxyethyl agarose, and (ii) gelling at comparatively high temperature. If a particle still does not respond to the ratchet (because the particle is too small), this particle has a net migration in the high field-direction, when the above-described pulsed field is biased in the high field-direction. If a particle does respond to the improved ratchet, the particle has a net migration in the low field-direction. Here, the R of ratchet-responding spheres is reduced to 30-50 nm. These ratchet-responding spheres include both intact bacteriophage particles (R = 30 nm) and latex spheres. The smaller ratchet-responding spheres have an electrophoretic mobility that decreases in magnitude as the electrical field increases in magnitude. A ratchet-based procedure is developed here to achieve continuous preparative gel electrophoresis.