Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1981 Nov 25;9(22):6115–6127. doi: 10.1093/nar/9.22.6115

The effect of several nucleic acid binding drugs on the cleavage of d(GGAATTCC) and pBR 322 by the Eco RI restriction endonuclease.

M Goppelt, J Langowski, A Pingoud, W Haupt, C Urbanke, H Mayer, G Maass
PMCID: PMC327588  PMID: 6273824

Abstract

The endonucleolytic action of the EcoRI restriction enzyme on the double-stranded oligonucleotide d(GGAATTCC) and the supercoiled plasmid DNA pBR 233 is inhibited by actinomycin D, ethidium bromide, proflavin, distamycin A and netropsin. Half-maximal inhibition is observed at around 100 microM concentrations for the intercalating drugs, and around 0.1 to 1 microM concentrations for netropsin and distamycin A. The inhibitory activity of these drugs can be correlated with their affinity to the oligonucleotide and the plasmid DNA. Since at high concentrations of the drugs a complete inhibition is observed, it is concluded that the effect of the drugs on the stereochemistry of the EcoRI site is such that recognition is excluded.

Full text

PDF
6115

Images in this article

6121Image
on p.6121

Selected References

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

  1. Bauer W., Vinograd J. Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. J Mol Biol. 1970 Feb 14;47(3):419–435. doi: 10.1016/0022-2836(70)90312-8. [DOI] [PubMed] [Google Scholar]
  2. Berman H. M., Young P. R. The interaction of intercalating drugs with nucleic acids. Annu Rev Biophys Bioeng. 1981;10:87–114. doi: 10.1146/annurev.bb.10.060181.000511. [DOI] [PubMed] [Google Scholar]
  3. Bresloff J. L., Crothers D. M. Equilibrium studies of ethidium--polynucleotide interactions. Biochemistry. 1981 Jun 9;20(12):3547–3553. doi: 10.1021/bi00515a038. [DOI] [PubMed] [Google Scholar]
  4. Dattagupta N., Hogan M., Crothers D. M. Interaction of netropsin and distamycin with deoxyribonucleic acid: electric dichroism study. Biochemistry. 1980 Dec 23;19(26):5998–6005. doi: 10.1021/bi00567a009. [DOI] [PubMed] [Google Scholar]
  5. Goppelt M., Pingoud A., Maass G., Mayer H., Köster H., Frank R. The interaction of the EcoRI restriction endonuclease with its substrate. A physico-chemical study employing natural and synthetic oligonucleotides and polynucleotides. Eur J Biochem. 1980 Feb;104(1):101–107. doi: 10.1111/j.1432-1033.1980.tb04405.x. [DOI] [PubMed] [Google Scholar]
  6. Langowski J., Pingoud A., Goppelt M., Maass G. Inhibition of Eco RI action by polynucleotides. A characterization of the non-specific binding of the enzyme to DNA. Nucleic Acids Res. 1980 Oct 24;8(20):4727–4736. doi: 10.1093/nar/8.20.4727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Langowski J., Urbanke C., Pingoud A., Maass G. Transient cleavage kinetics of the Eco RI restriction endonuclease measured in a pulsed quench-flow apparatus: enzyme concentration-dependent activity change. Nucleic Acids Res. 1981 Jul 24;9(14):3483–3490. doi: 10.1093/nar/9.14.3483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Luck G., Zimmer C., Reinert K. E., Arcamone F. Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides. Nucleic Acids Res. 1977 Aug;4(8):2655–2670. doi: 10.1093/nar/4.8.2655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Modrich P. Structures and mechanisms of DNA restriction and modification enzymes. Q Rev Biophys. 1979 Aug;12(3):315–369. doi: 10.1017/s0033583500005461. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Paoletti C., LePecq J. B., Lehman I. R. The use of ethidium bromide-circular DNA complexes for the fluorometric analysis of breakage and joining of DNA. J Mol Biol. 1971 Jan 14;55(1):75–100. doi: 10.1016/0022-2836(71)90282-8. [DOI] [PubMed] [Google Scholar]
  12. Peters F., Pingoud A. Numerical analysis of binding studies: a direct procedure avoiding the pitfalls of a Scatchard analysis of equilibrium data for unknown binding models. Int J Biomed Comput. 1979 Sep;10(5):401–415. doi: 10.1016/0020-7101(79)90054-0. [DOI] [PubMed] [Google Scholar]
  13. Roberts R. J. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res. 1980 Jan 11;8(1):r63–r80. doi: 10.1093/nar/8.1.197-d. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Waring M. J. Complex formation between ethidium bromide and nucleic acids. J Mol Biol. 1965 Aug;13(1):269–282. doi: 10.1016/s0022-2836(65)80096-1. [DOI] [PubMed] [Google Scholar]
  15. Zimmer C. Effects of the antibiotics netropsin and distamycin A on the structure and function of nucleic acids. Prog Nucleic Acid Res Mol Biol. 1975;15(0):285–318. doi: 10.1016/s0079-6603(08)60122-1. [DOI] [PubMed] [Google Scholar]

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

RESOURCES