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Published March 1, 1977 | public
Journal Article Open

Mapping of closed circular DNAs by cleavage with restriction endonucleases and calibration by agarose gel electrophoresis


The cleavage of DNA by restriction endonucleases can be limited by the addition of ethidium bromide. When closed circular DNA is used as a substrate, DNA with one-site cleavages of one or both strands can be made by adding appropriate amounts of dye. The singly cleaved DNA is a complete set of full-length permuted linear molecules. Fractionation of the products of a digestion of the permuted linears with a single-hitting restriction endonuclease by gel electrophoresis yields a series of bands that can be used to determine relative molecular weights of the DNA fragments in the gel without the introduction of standards. It is possible to determine the relative molecular weight of a fragment to within ± 2.5%. These molecular weights immediately allow the determination of the HindIII and Hpa I maps of simian virus 40. The HindIII map of bacteriophage PM2 was determined by this method with one ambiguity that was resolved by using traditional techniques.

Additional Information

© 1977 by the National Academy of Sciences. Communicated by Norman Davidson, November 22, 1976. This research was done under the leadership of Prof. Jerome Vinograd. Without his contributions, direction, and inspiration this paper would not exist. While this manuscript was in its early stages of preparation his unfortunate death occurred. We thank Dr. J. Franklin for his advice about the mathematical aspects of this paper and M. Klymkowsky for his technical assistance. We thank Dr. N. Davidson for all of the help he gave us. This work was supported in part by National Institutes of Health Grants CA08014 and GM15327. This is Contribution no. 5417 from the Division of Chemistry and Chemical Engineering.


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