Journal of Chromatography B, 779 (2002) 163–171 www.elsevier.com / locate / chromb Electrophoresis using ultra-high voltages a, b c c * Maribel Vazquez , Gareth McKinley , Luba Mitnik , Samantha Desmarais , c c Paul Matsudaira , Daniel Ehrlich a 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 b Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., 3-250, Cambridge, MA 02139, USA c Whitehead Institute for Biomedical Research,9 Cambridge Center, WI-339, Cambridge, MA 02142, USA Received 25 February 2002; received in revised form 13 May 2002; accepted 15 May 2002 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.  2002 Elsevier Science B.V. All rights reserved. Keywords: Optimization; Ultra-high voltages electrophoresis; DNA 1. Introduction in electrophoretic applications because they dissipate heat effectively, enabling separation voltages of up The many adaptations of microdevices for numer- to 30 kV to produce rapid, efficient separations. In ous biology and engineering applications have made addition, microdevices provide a unique opportunity optimization of electrophoretic techniques a high for direct visualization, which facilitates our under- priority. Electrophoretic separations of biomolecules standing of the dynamics underlying the electro- are now routinely performed within microdevices phoretic process [4,5]. The present work seeks to due largely to the parallel analysis [1] and process optimize electrophoresis within microdevices by re- integration [2] facilitated by microfabrication [1–3]. examining the protocols used during conventional Microfabricated channels are particularly successful separations. Specifically, this work focuses on sam- ple stacking (or sample concentration effects) present during electrophoretic injection. Here, we utilize *Corresponding author. Tel.: 11-212-650-5209; fax: 11-212- ultra-high voltages to increase sample stacking (sam- 650-6727. E-mail address: vazquez@ccny.cuny.edu (M. Vazquez). ple concentration) prior to separation. The physical 1570-0232 / 02 / $ – see front matter  2002 Elsevier Science B.V. All rights reserved. PII: S1570-0232(02)00349-5