Recent developments in DNA electrophoretic separations

Abstract

DNA electrophoresis is now a fairly mature technology. Nevertheless, as we approach the 21st century, new ideas are frequently suggested that could lead to a revolution for DNA sequencing and mapping. Here, we review some of the novel concepts that have been studied since ca. 1990. Our review focuses on new separation mechanisms, new sieving matrices and recent conceptual advances.

Modeling the dynamics of DNA electrophoresis on a flat surface

“…When a DNA molecule is migrating under the influence of an applied electric field, the collisions with the environment results in the separation of DNA by length inside the topologically restrictive matrix. While these methods have been successfully used to separate DNA fragments that differ by a single base, their read length is quite limited [6] (e.g., the efficiency of gel electrophoresis deteriorates seriously for DNA molecules longer than 40 000 base pairs (40 kbp)). A possible new approach to performing electrophoresis lies in a factor that has been overlooked as a possible separation mechanism -the effect of surface interactions.…”

Multiplexed DNA sizing by capillary electrophoresis using entangled polymer solutions and diode array detection

“…The reptation regime is applicable to larger DNA fragments at intermediate and high electric field strength. Even larger DNA molecules orient themselves in the direction of the electric field leading to the biased reptation model (BRM) [9,10]. The BRM is applied to describe a DNA migration strongly biasing the random walk in the forward direction so that DNA is stretched to a rod-like conformation.…”

“…According to the combination of such parameters and the DNA size, the DNA fragments migrate through the sieving media under several mechanisms [4,[8][9][10]. In brief, the major ones are the Ogston regime, the reptation mechanism, and the biased reptation model.…”

DNA Electrophoresis on Two-dimensional Arrays of SiO2 Beads

“…Separation of DNA therefore requires the use of some type of sieving matrix. Current electrophoretic methods assume that only environments with topological constrictions such as crosslinks in a gel [1,3] or entanglements in a polymer melt or solution [2] are suitable as matrices for separation of DNA by length. Since the gel structure can be very complex, recently Meistermann and Tinland [4] and Craighead [5] have proposed new methods for DNA separation that rely on rigid silica matrices with well defined porosity or micropatterned constraints.…”