Electrophoresis of long DNA molecules in linear polyacrylamide solutions

Electrophoresis of long DNA (T4 DNA; 166 kb, S. pombe chromosomal DNA; 3-6 Mb) in linear polyacrylamide solutions was investigated by fluorescence microscopy and capillary electrophoresis. In the past studies on electrophoresis of long DNA in a polymer solution, it was reported that DNA migrates in 'U-shape conformation'. We found that at higher polymer concentrations, the shape of the migrating DNA changes from U shape to linear shape ('I-shape conformation'). In the migration mode with the I-shape conformation, the DNA moves with almost constant velocity and constant shape. However, the migration velocity does depend on the DNA size, and it is possible to separate DNAs under this I-shape motion. Actually, Mb-sized DNAs are well separated within 5 min in the region for the I-shape motion by means of capillary electrophoresis with a DC field. Considering that it takes 20 h to separate Mb-sized DNAs by standard pulsed-field gel electrophoresis (PFGE), this results will be useful for the separation of giant DNAs. (C) 1998 Elsevier Science B.V. All rights reserved.