J. Chromatography B., 779(2), (2002), 163-171 Electrophoresis using Ultra-High Voltages Maribel Vazquez1, Gareth McKinley2, Luba Mitnik3, Samantha Desmarais3, Paul Matsudaira3, Daniel Ehrlich3 1) New York Center for Biomedical Engineering, Department of Mechanical Engineering, The City College of the City University of New York, 140th and Convent Ave T- 250, New York, NY 10031, USA 2) Department of Mechanical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Ave, 3- 250, Cambridge, MA 02139, USA 3) Whitehead Institute for Biomedical Research, 9 Cambridge Center, WI- 339, Cambridge, MA 02142,USA Abstract Optimization of electrophoretic techniques is becoming an increasingly important area of research as microdevices are now routinely adapted for numerous biology and engineering applications. The present work seeks to optimize electrophoresis within microdevices by utilizing ultra-high voltages to increase sample concentration prior to separation. By imaging fluorescently-tagged DNA samples, the effects of both conventional and atypical voltage protocols on DNA migration and separation are readily observed. Experiments illustrate that short periods of high voltage during electrophoretic injection do not destroy the quality of DNA separations, and in fact can enhance sample concentration five-fold. This study presents data that illustrate increases in average resolution, and resolution of longer fragments, obtained from electrophoretic injections utilizing voltages between 85 and 850 V/cm.