To answer this question, we evaluated the more relevant methods for assessing DNA length:
Variations of PFGE apply current to DNA samples in gel in different ways to alter the direction of the electric field as DNA migrates.
While some methods of PFGE can resolve fragments over 1 mb long, a single run can require several pieces of equipment, take 8 hours or more to complete, and require as much as 200 ng of input sample. Compared to capillary electrophoresis, these methods consume more budget, time, and space.
With CE, fluorescently labeled DNA is passed through a thin capillary containing a gel matrix that has an electric field applied to it.
CE systems such as the TapeStation and Fragment Analyzer from Agilent Technologies require less input sample and have relatively small footprints, faster run times, minimal hardware, and provide a visual representation of the quality of the sample analyzed as well as a quantitative score.
To assess the DNA length from our Ionic™ Purification System, we decided to use a CE system, the Agilent Fragment Analyzer and the HS Large Fragment 50 kb Kit.
A smear analysis of DNA extracted and purified on the Ionic system from samples of 1,000 cells from 3 cell lines shows that ~50% of Ionic system extracts are greater than 40 kb in length. That was over 2-fold higher than what we were able to achieve with a commercially available column-based purification kit.