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. 1980 Oct 24;8(20):4727–4736. doi: 10.1093/nar/8.20.4727

Inhibition of Eco RI action by polynucleotides. A characterization of the non-specific binding of the enzyme to DNA.

J Langowski, A Pingoud, M Goppelt, G Maass
PMCID: PMC324382  PMID: 6255431

Abstract

The cleavage of the plasmid pBR322 by the restriction endonuclease Eco RI has been studied in the presence of various polynucleotides and the double stranded octanucleotide d-(GGAATTCC) in order to clarify whether there is a preferential interaction of Eco RI with DNA sequences other than -GAATTC-. The steady state kinetic analysis shows that all polynucleotides investigated with the possible exception of poly-dG.poly-dC inhibit the cleavage competitively with Ki values in the range of 10(-4) to 10(-5) [M nucleotides]. The Ki of d-(GGAATTCC) is 1.5.10(-6) [M nucleotides], indicating that the specific binding is approx. 2 orders of magnitude stronger than non-specific binding.

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Selected References

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

  1. Böhme H. J., Kopperschläger G., Schulz J., Hofmann E. Affinity chromatography of phosphofructokinase using Cibacron blue F3G-A. J Chromatogr. 1972 Jun 28;69(1):209–214. doi: 10.1016/s0021-9673(00)83103-9. [DOI] [PubMed] [Google Scholar]
  2. Campbell A. M. The effects of deoxyribonucleic acid secondary structure on tertiary structure. Biochem J. 1976 Dec 1;159(3):615–620. doi: 10.1042/bj1590615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Clewell D. B., Helinski D. R. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an opern circular DNA form. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1159–1166. doi: 10.1073/pnas.62.4.1159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Forsblom S., Rigler R., Ehrenberg M., Philipson L. Kinetic studies on the cleavage of adenovirus DNA by restriction endonuclease Eco RI. Nucleic Acids Res. 1976 Dec;3(12):3255–3269. doi: 10.1093/nar/3.12.3255. [DOI] [PMC free article] [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. Jovin T. M. Recognition mechanisms of DNA-specific enzymes. Annu Rev Biochem. 1976;45:889–920. doi: 10.1146/annurev.bi.45.070176.004325. [DOI] [PubMed] [Google Scholar]
  7. Klug A., Jack A., Viswamitra M. A., Kennard O., Shakked Z., Steitz T. A. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J Mol Biol. 1979 Jul 15;131(4):669–680. doi: 10.1016/0022-2836(79)90196-7. [DOI] [PubMed] [Google Scholar]
  8. Litman R. M. A deoxyribonucleic acid polymerase from Micrococcus luteus (Micrococcus lysodeikticus) isolated on deoxyribonucleic acid-cellulose. J Biol Chem. 1968 Dec 10;243(23):6222–6233. [PubMed] [Google Scholar]
  9. Marck C., Thiele D. Poly(dG).poly(dC) at neutral and alkaline pH: the formation of triple stranded poly(dG).poly(dG).poly(dC). Nucleic Acids Res. 1978 Mar;5(3):1017–1028. doi: 10.1093/nar/5.3.1017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Modrich P., Zabel D. EcoRI endonuclease. Physical and catalytic properties of the homogenous enzyme. J Biol Chem. 1976 Oct 10;251(19):5866–5874. [PubMed] [Google Scholar]
  11. Richter P. H., Eigen M. Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes. Biophys Chem. 1974 Oct;2(3):255–263. doi: 10.1016/0301-4622(74)80050-5. [DOI] [PubMed] [Google Scholar]
  12. Roberts R. J. Restriction endonucleases. CRC Crit Rev Biochem. 1976 Nov;4(2):123–164. doi: 10.3109/10409237609105456. [DOI] [PubMed] [Google Scholar]
  13. Vollenweider H. J., Koller T., Parello J., Sogo J. M. Superstructure of linear duplex DNA. Proc Natl Acad Sci U S A. 1976 Nov;73(11):4125–4129. doi: 10.1073/pnas.73.11.4125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. von Hippel P. H., Revzin A., Gross C. A., Wang A. C. Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects. Proc Natl Acad Sci U S A. 1974 Dec;71(12):4808–4812. doi: 10.1073/pnas.71.12.4808. [DOI] [PMC free article] [PubMed] [Google Scholar]

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