DNA migration mechanism analyses for applications in capillary and microchip electrophoresis

In 2009, electrophoretically driven DNA separations in slab gels and capillaries have the sepia tones of an old-fashioned technology in the eyes of many, even while they remain ubiquitously used, fill a unique niche, and arguably have yet to reach their full potential. For comic relief, what is old becomes new again: agarose slab gel separations are used to prepare DNA samples for next-gen sequencing platforms (e.g. the Illumina and 454 machines) - dsDNA molecules within a certain size range are cut out of a gel and recovered for subsequent massively parallel pyrosequencing. In this review, we give a Barron lab perspective on how our comprehension of DNA migration mechanisms in electrophoresis has evolved, since the first reports of DNA separations by CE (similar to 1989) until now, 20 years later. Fused-silica capillaries and borosilicate glass and plastic microchips quietly offer increasing capacities for fast (and even ultra-fast), efficient DNA separations. While the channel-by-channel scaling of both old and new electrophoresis platforms provides key flexibility, it requires each unique DNA sample to be prepared in its own micro or nanovolume. This Achilles' heel of electrophoresis technologies left an opening through which pooled sample, next-gen DNA sequencing technologies rushed. We shall see, over time, whether sharpening understanding of transitions in DNA migration modes in crosslinked gels, nanogel solutions, and uncrosslinked polymer solutions will allow electrophoretic DNA analysis technologies to flower again. Microchannel electrophoresis, after a quiet period of metamorphosis, may emerge sleeker and more powerful, to claim its own important niche applications.