Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Dec 20;11(24):8691–8701. doi: 10.1093/nar/11.24.8691

Mechanistic study of E. coli DNA topoisomerase I: cleavage of oligonucleotides.

Y C Tse-Dinh, B G McCarron, R Arentzen, V Chowdhry
PMCID: PMC326617  PMID: 6324095

Abstract

E. coli DNA topoisomerase I catalyzes DNA topoisomerization by transiently breaking and rejoining single DNA strands (1). When an enzyme-DNA incubation mixture is treated with alkaline or detergent, DNA strand cleavage occurs, and the enzyme becomes covalently linked to the 5'-phosphoryl end of the cleaved DNA (2). Using oligonucleotides of defined length and sequence composition, this cleavage reaction is utilized to study the mechanism of E. coli DNA topoisomerase I. dA7 is the shortest oligonucleotide tested that can be cleaved by the enzyme. dT8 is the shortest oligo(dT) that can be cleaved. The site of cleavage in both cases is four nucleotides from the 3' end of the oligonucleotide. No cleavage can be observed for oligo(dC) and oligo(dG) of length up to eleven bases long. dC15 and dC16 are cleaved at one tenth or less the efficiency of oligo(dA) and oligo(dT) of comparable length.

Full text

PDF
8691

Images in this article

8695Image
on p.8695
8695Image
on p.8695
8696Image
on p.8696
8699Image
on p.8699

Selected References

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

  1. Been M. D., Champoux J. J. Breakage of single-stranded DNA by rat liver nicking-closing enzyme with the formation of a DNA-enzyme complex. Nucleic Acids Res. 1980 Dec 20;8(24):6129–6142. doi: 10.1093/nar/8.24.6129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Been M. D., Champoux J. J. DNA breakage and closure by rat liver type 1 topoisomerase: separation of the half-reactions by using a single-stranded DNA substrate. Proc Natl Acad Sci U S A. 1981 May;78(5):2883–2887. doi: 10.1073/pnas.78.5.2883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Champoux J. J. DNA is linked to the rat liver DNA nicking-closing enzyme by a phosphodiester bond to tyrosine. J Biol Chem. 1981 May 25;256(10):4805–4809. [PubMed] [Google Scholar]
  4. Champoux J. J. Mechanism of the reaction catalyzed by the DNA untwisting enzyme: attachment of the enzyme to 3'-terminus of the nicked DNA. J Mol Biol. 1978 Jan 25;118(3):441–446. doi: 10.1016/0022-2836(78)90238-3. [DOI] [PubMed] [Google Scholar]
  5. Champoux J. J. Strand breakage by the DNA untwisting enzyme results in covalent attachment of the enzyme to DNA. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3800–3804. doi: 10.1073/pnas.74.9.3800. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Depew R. E., Liu L. F., Wang J. C. Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein. J Biol Chem. 1978 Jan 25;253(2):511–518. [PubMed] [Google Scholar]
  7. Edwards K. A., Halligan B. D., Davis J. L., Nivera N. L., Liu L. F. Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA. Nucleic Acids Res. 1982 Apr 24;10(8):2565–2576. doi: 10.1093/nar/10.8.2565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gellert M. DNA topoisomerases. Annu Rev Biochem. 1981;50:879–910. doi: 10.1146/annurev.bi.50.070181.004311. [DOI] [PubMed] [Google Scholar]
  9. Gellert M., Fisher L. M., Ohmori H., O'Dea M. H., Mizuuchi K. DNA gyrase: site-specific interactions and transient double-strand breakage of DNA. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):391–398. doi: 10.1101/sqb.1981.045.01.053. [DOI] [PubMed] [Google Scholar]
  10. Gellert M., Mizuuchi K., O'Dea M. H., Itoh T., Tomizawa J. I. Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4772–4776. doi: 10.1073/pnas.74.11.4772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Halligan B. D., Davis J. L., Edwards K. A., Liu L. F. Intra- and intermolecular strand transfer by HeLa DNA topoisomerase I. J Biol Chem. 1982 Apr 10;257(7):3995–4000. [PubMed] [Google Scholar]
  12. Kirkegaard K., Wang J. C. Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences. Cell. 1981 Mar;23(3):721–729. doi: 10.1016/0092-8674(81)90435-9. [DOI] [PubMed] [Google Scholar]
  13. Liu L. F., Wang J. C. Interaction between DNA and Escherichia coli DNA topoisomerase I. Formation of complexes between the protein and superhelical and nonsuperhelical duplex DNAs. J Biol Chem. 1979 Nov 10;254(21):11082–11088. [PubMed] [Google Scholar]
  14. Morrison A., Higgins N. P., Cozzarelli N. R. Interaction between DNA gyrase and its cleavage site on DNA. J Biol Chem. 1980 Mar 10;255(5):2211–2219. [PubMed] [Google Scholar]
  15. Prell B., Vosberg H. P. Analysis of covalent complexes formed between calf thymus DNA topoisomerase and single-stranded DNA. Eur J Biochem. 1980 Jul;108(2):389–398. doi: 10.1111/j.1432-1033.1980.tb04734.x. [DOI] [PubMed] [Google Scholar]
  16. Sugino A., Peebles C. L., Kreuzer K. N., Cozzarelli N. R. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4767–4771. doi: 10.1073/pnas.74.11.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Tse Y. C., Kirkegaard K., Wang J. C. Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. J Biol Chem. 1980 Jun 25;255(12):5560–5565. [PubMed] [Google Scholar]
  18. Wang J. C. Interaction between DNA and an Escherichia coli protein omega. J Mol Biol. 1971 Feb 14;55(3):523–533. doi: 10.1016/0022-2836(71)90334-2. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES