The invention is directed to a high throughput nucleic acid separation method using an improved uncrosslinked polymer separation matrix for increasing read length and separation speed, while maintaining accuracy, for, e.g., nucleic acid sequencing. The separation matrix of the invention includes a denaturant comprising dimethyl sulfoxide (DMSO). Preferably, the separation matrix may further comprise urea. Preferred matrix polymers include linear polyacrylamide, poly(ethylene oxide), hydroxyethyl cellulose, poly(dimethylacrylamide) and poly(vinylpyrrolidone).
 Part of the work leading to this invention was carried out with United States Government support provided under a grant from the Department of Energy, Human Genome Project Grant No. DE-FG02-90ER-60985. Therefore, the U.S. Government has certain rights in this invention.