Using sodium chloride step gradients to fractionate DNA fragments

A method is described for the separation of DNA fragments by ultracentrifugation through a sodium chloride step gradient. The gradients are quickly and easily prepared and require a five- to six-hour centrifugation. Fractionated samples of DNA may be directly examined by agarose gel electrophoresis, then further analyzed by Southern transfer and hybridization. A simple ethanol precipitation followed by several ethanol washes yields fragments that ligate efficiently to vector DNA. The method has been applied to separate chromosomal DNA restriction fragments as well as bacteriophage lambda arms from insert DNA.