Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1977 Mar;74(3):851–855. doi: 10.1073/pnas.74.3.851

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

R C Parker, R M Watson, J Vinograd
PMCID: PMC430501  PMID: 191836

Abstract

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.

Full text

PDF
851

Images in this article

852Image
on p.852

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Botchan M., Topp W., Sambrook J. The arrangement of simian virus 40 sequences in the DNA of transformed cells. Cell. 1976 Oct;9(2):269–287. doi: 10.1016/0092-8674(76)90118-5. [DOI] [PubMed] [Google Scholar]
  2. Brack C., Eberle H., Bickle T. A., Yuan R. A map of the sites on bacteriophage PM2 DNA for the restriction endonucleases HindIII and HpaII. J Mol Biol. 1976 Jun 14;104(1):305–309. doi: 10.1016/0022-2836(76)90016-4. [DOI] [PubMed] [Google Scholar]
  3. Danna K., Nathans D. Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci U S A. 1971 Dec;68(12):2913–2917. doi: 10.1073/pnas.68.12.2913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Espejo R. T., Canelo E. S. Properties of bacteriophage PM2: a lipid-containing bacterial virus. Virology. 1968 Apr;34(4):738–747. doi: 10.1016/0042-6822(68)90094-9. [DOI] [PubMed] [Google Scholar]
  5. Helling R. B., Goodman H. M., Boyer H. W. Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. J Virol. 1974 Nov;14(5):1235–1244. doi: 10.1128/jvi.14.5.1235-1244.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lai C. J., Nathans D. Deletion mutants of simian virus 40 generated by enzymatic excision of DNA segments from the viral genome. J Mol Biol. 1974 Oct 15;89(1):179–193. doi: 10.1016/0022-2836(74)90169-7. [DOI] [PubMed] [Google Scholar]
  7. Lee A. S., Sinsheimer R. L. A cleavage map of bacteriophage phiX174 genome. Proc Natl Acad Sci U S A. 1974 Jul;71(7):2882–2886. doi: 10.1073/pnas.71.7.2882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  9. Nathans D., Smith H. O. Restriction endonucleases in the analysis and restructuring of dna molecules. Annu Rev Biochem. 1975;44:273–293. doi: 10.1146/annurev.bi.44.070175.001421. [DOI] [PubMed] [Google Scholar]
  10. Neal M. W., Florini J. R. A rapid method for desalting small volumes of solution. Anal Biochem. 1973 Sep;55(1):328–330. doi: 10.1016/0003-2697(73)90325-4. [DOI] [PubMed] [Google Scholar]
  11. Nosikov V. V., Braga E. A., Karlishev A. V., Zhuze A. L., Polyanovsky O. L. Protection of particular cleavage sites of restriction endonucleases by distamycin A and actinomycin D. Nucleic Acids Res. 1976 Sep;3(9):2293–2301. doi: 10.1093/nar/3.9.2293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Pulleyblank D. E., Shure M., Tang D., Vinograd J., Vosberg H. P. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4280–4284. doi: 10.1073/pnas.72.11.4280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Rush M. G., Eason R., Vinograd J. Identification and properties of complex forms of SV40 DNA isolated from SV40-infected African Green monkey (BSC-1) cells. Biochim Biophys Acta. 1971 Feb 11;228(3):585–594. doi: 10.1016/0005-2787(71)90723-4. [DOI] [PubMed] [Google Scholar]
  14. Sharp P. A., Sugden B., Sambrook J. Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose--ethidium bromide electrophoresis. Biochemistry. 1973 Jul 31;12(16):3055–3063. doi: 10.1021/bi00740a018. [DOI] [PubMed] [Google Scholar]
  15. Subramanian K. N., Pan J., Zain S., Weissman S. M. The mapping and ordering of fragments of SV40 DNA produced by restriction endonucleases. Nucleic Acids Res. 1974 Jun;1(6):727–752. doi: 10.1093/nar/1.6.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
  17. Vinograd J., Lebowitz J., Radloff R., Watson R., Laipis P. The twisted circular form of polyoma viral DNA. Proc Natl Acad Sci U S A. 1965 May;53(5):1104–1111. doi: 10.1073/pnas.53.5.1104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wellauer P. K., Reeder R. H., Carroll D., Brown D. D., Deutch A., Higashinakagawa T., Dawid I. B. Amplified ribosomal DNA from Xenopus laevis has heterogeneous spacer lengths. Proc Natl Acad Sci U S A. 1974 Jul;71(7):2823–2827. doi: 10.1073/pnas.71.7.2823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Zeiger R. S., Salomon R., Dingman C. W., Peacock A. C. Role of base composition in the electrophoresis of microbial and crab DNA in polyacrylamide gels. Nat New Biol. 1972 Jul 19;238(81):65–69. doi: 10.1038/newbio238065a0. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES