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. 1987 Mar 11;15(5):2221–2234. doi: 10.1093/nar/15.5.2221

DNA sequence preferences for an intercalating porphyrin compound revealed by footprinting.

K Ford, K R Fox, S Neidle, M J Waring
PMCID: PMC340629  PMID: 3562226

Abstract

The DNA sequence preferences of the compound meso-tetra-(4-N-methyl(pyridyl) porphyrin and its nickel complex have been investigated by means of footprinting experiments on several DNA fragments, using DNAase I and micrococcal nuclease as footprinting agents. A complex pattern of both AT and GC-protected sites was found. Ligand-induced long-range conformational changes were inferred in several instances to be related to the observed large-scale blockages of enzymatic cutting.

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Selected References

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  1. Banville D. L., Marzilli L. G., Strickland J. A., Wilson W. D. Comparison of the effects of cationic porphyrins on DNA properties: influence of GC content of native and synthetic polymers. Biopolymers. 1986 Oct;25(10):1837–1858. doi: 10.1002/bip.360251003. [DOI] [PubMed] [Google Scholar]
  2. Banville D. L., Marzilli L. G., Wilson W. D. 31P NMR and viscometric studies of the interaction of meso-tetra(4-N-methylpyridyl) porphine and its Ni(II) and Zn(II) derivatives with DNA. Biochem Biophys Res Commun. 1983 May 31;113(1):148–154. doi: 10.1016/0006-291x(83)90444-8. [DOI] [PubMed] [Google Scholar]
  3. Carvlin M. J., Mark E., Fiel R., Howard J. C. Intercalative and nonintercalative binding of large cationic porphyrin ligands to polynucleotides. Nucleic Acids Res. 1983 Sep 10;11(17):6141–6154. doi: 10.1093/nar/11.17.6141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Collier D. A., Neidle S., Brown J. R. Molecular models for the interaction of the anti-tumour drug nogalamycin with DNA. Biochem Pharmacol. 1984 Sep 15;33(18):2877–2880. doi: 10.1016/0006-2952(84)90210-7. [DOI] [PubMed] [Google Scholar]
  5. Dingwall C., Lomonossoff G. P., Laskey R. A. High sequence specificity of micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2659–2673. doi: 10.1093/nar/9.12.2659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Drew H. R., Travers A. A. DNA structural variations in the E. coli tyrT promoter. Cell. 1984 Jun;37(2):491–502. doi: 10.1016/0092-8674(84)90379-9. [DOI] [PubMed] [Google Scholar]
  7. Fiel R. J., Howard J. C., Mark E. H., Datta Gupta N. Interaction of DNA with a porphyrin ligand: evidence for intercalation. Nucleic Acids Res. 1979 Jul 11;6(9):3093–3118. doi: 10.1093/nar/6.9.3093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fiel R. J., Munson B. R. Binding of meso-tetra (4-N-methylpyridyl) porphine to DNA. Nucleic Acids Res. 1980 Jun 25;8(12):2835–2842. doi: 10.1093/nar/8.12.2835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fox K. R., Waring M. J. DNA structural variations produced by actinomycin and distamycin as revealed by DNAase I footprinting. Nucleic Acids Res. 1984 Dec 21;12(24):9271–9285. doi: 10.1093/nar/12.24.9271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fox K. R., Waring M. J. Nucleotide sequence binding preferences of nogalamycin investigated by DNase I footprinting. Biochemistry. 1986 Jul 29;25(15):4349–4356. doi: 10.1021/bi00363a026. [DOI] [PubMed] [Google Scholar]
  11. Hörz W., Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2643–2658. doi: 10.1093/nar/9.12.2643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kelly J. M., Murphy M. J., McConnell D. J., OhUigin C. A comparative study of the interaction of 5,10,15,20-tetrakis (N-methylpyridinium-4-yl)porphyrin and its zinc complex with DNA using fluorescence spectroscopy and topoisomerisation. Nucleic Acids Res. 1985 Jan 11;13(1):167–184. doi: 10.1093/nar/13.1.167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Low C. M., Drew H. R., Waring M. J. Sequence-specific binding of echinomycin to DNA: evidence for conformational changes affecting flanking sequences. Nucleic Acids Res. 1984 Jun 25;12(12):4865–4879. doi: 10.1093/nar/12.12.4865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Pasternack R. F., Garrity P., Ehrlich B., Davis C. B., Gibbs E. J., Orloff G., Giartosio A., Turano C. The influence of ionic strength on the binding of a water soluble porphyrin to nucleic acids. Nucleic Acids Res. 1986 Jul 25;14(14):5919–5931. doi: 10.1093/nar/14.14.5919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pasternack R. F., Gibbs E. J., Villafranca J. J. Interactions of porphyrins with nucleic acids. Biochemistry. 1983 May 10;22(10):2406–2414. doi: 10.1021/bi00279a016. [DOI] [PubMed] [Google Scholar]
  16. Pasternack R. F., Gibbs E. J., Villafranca J. J. Interactions of porphyrins with nucleic acids. Biochemistry. 1983 Nov 8;22(23):5409–5417. doi: 10.1021/bi00292a024. [DOI] [PubMed] [Google Scholar]
  17. Pasternack R. F., Sidney D., Hunt P. A., Snowden E. A., Gibbs E. J. Interactions of water soluble porphyrins with Z-poly(dG-dC). Nucleic Acids Res. 1986 May 12;14(9):3927–3943. doi: 10.1093/nar/14.9.3927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ward B., Skorobogaty A., Dabrowiak J. C. DNA cleavage specificity of a group of cationic metalloporphyrins. Biochemistry. 1986 Nov 4;25(22):6875–6883. doi: 10.1021/bi00370a021. [DOI] [PubMed] [Google Scholar]

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