Large-scale isolation of covalently closed circular DNA using gel filtration chromatography

The isolation of covalently closed circular (ccc) DNA free of contamination by RNA and other forms of DNA is fundamental to molecular biology. A variety of methods have been explored but CsCl density-gradient centrifugation remains the method most widely used for preparative scale resolution. The process is expensive, time-consuming, requires the use of large amounts of the carcinogen ethidium bromide, and is subject to considerable variation in yield and purity. To avoid these problems, we have devised a procedure for the preparation of cell lysates which results in consistently good yields of biologically active ccc DNA minimally contaminated with chromosomal DNA fragments and RNA. Lysates are deproteinized, precipitated with CaCl2 to remove rRNA, concentrated by ethanol precipitation, and applied to a Sephacryl S-1000 column which resolves chromosomal fragments, open circular plasmid DNA, and residual RNA from the ccc DNA. We have found that substituting the gel filtration column for CsCl density-gradient centrifugation results in substantially better purification as well as reducing processing time, cost, and degree of difficulty. The time required from harvest of cells to final recovery of DNA is about 16 h. We have used the method to isolate plasmids from 4.4 to 12 kb and, with slight modifications, recombinant M13 replicative form DNAs.