Preparative Capillary Zone Electrophoresis

Capillary zone electrophoresis (CZE) is a powerful tool for efficient separation of biological molecules. CZE instruments often employ absorbance, laser-induced fluorescence, or mass spectrometry for on-line detection and analysis. However, CZE as a preparative tool is limited in each of these configurations. Instead, we employ a highly efficient automated fraction collector that interfaces CZE with a collection plate for seamless transition to downstream analyses. This preparative system deposits nanoliter fractions from the capillary, with a controlled volume of sheath liquid, in the form of a droplet. Droplets were isolated within individual wells of a microtiter plate or deposited onto a flat surface. We applied this technology to isolate oligonucleotides bound to a target protein for the efficient generation of aptamers using a single selection round. In another application, a microbiome was separated into reduced complexity fractions; electrophoretic fractionation was executed into a prepared plate for in-well cell lysis and DNA extraction. Both applications required mining deep sequence data and both were benefited by preparative CZE in comparison to traditional methods.