• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Jun 1983; 80(11): 3213–3217.
PMCID: PMC394010

Cleavage of chromatin with methidiumpropyl-EDTA . iron(II).


Methidiumpropyl-EDTA . iron(II) [MPE . Fe (II)] cleaves double-helical DNA with considerably lower sequence specificity than micrococcal nuclease. Moreover, digestions with MPE . Fe(II) can be performed in the presence of certain metal chelators, which will minimize the action of many endogenous nucleases. Because of these properties MPE . Fe(II) would appear to be a superior tool for probing chromatin structure. We have compared the patterns generated from the 1.688 g/cm3 complex satellite, 5S ribosomal RNA, and histone gene sequences of Drosophila melanogaster chromatin and protein-free DNA by MPE . Fe(II) and micrococcal nuclease cleavage. MPE . Fe(II) at low concentrations recognizes the nucleosome array, efficiently introducing a regular series of single-stranded (and some double-stranded) cleavages in chromatin DNA. Subsequent S1 nuclease digestion of the purified DNA produces a typical extended oligonucleosome pattern, with a repeating unit of ca. 190 base pairs. Under suitable conditions, relatively little other nicking is observed. Unlike micrococcal nuclease, which has a noticeable sequence preference in introducing cleavages, MPE . Fe(II) cleaves protein-free tandemly repetitive satellite and 5S DNA sequences in a near-random fashion. The spacing of cleavage sites in chromatin, however, bears a direct relationship to the length of the respective sequence repeats. In the case of the histone gene sequences a faint, but detectable, MPE . Fe(II) cleavage pattern is observed on DNA, in some regions similar to and in some regions different from the strong chromatin-specified pattern. The results indicate that MPE . Fe(II) will be very useful in the analysis of chromatin structure.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.9M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Felsenfeld G. Chromatin. Nature. 1978 Jan 12;271(5641):115–122. [PubMed]
  • McGhee JD, Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. [PubMed]
  • Mirzabekov AD. Nucleosomes structure and its dynamic transitions. Q Rev Biophys. 1980 May;13(2):255–295. [PubMed]
  • Kornberg R. The location of nucleosomes in chromatin: specific or statistical. Nature. 1981 Aug 13;292(5824):579–580. [PubMed]
  • Zachau HG, Igo-Kemenes T. Face to phase with nucleosomes. Cell. 1981 Jun;24(3):597–598. [PubMed]
  • Cartwright IL, Abmayr SM, Fleischmann G, Lowenhaupt K, Elgin SC, Keene MA, Howard GC. Chromatin structure and gene activity: the role of nonhistone chromosomal proteins. CRC Crit Rev Biochem. 1982;13(1):1–86. [PubMed]
  • Igo-Kemenes T, Hörz W, Zachau HG. Chromatin. Annu Rev Biochem. 1982;51:89–121. [PubMed]
  • Hörz W, Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2643–2658. [PMC free article] [PubMed]
  • Dingwall C, Lomonossoff GP, Laskey RA. High sequence specificity of micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2659–2673. [PMC free article] [PubMed]
  • Keene MA, Elgin SC. Micrococcal nuclease as a probe of DNA sequence organization and chromatin structure. Cell. 1981 Nov;27(1 Pt 2):57–64. [PubMed]
  • Bryan PN, Hofstetter H, Birnstiel ML. Nucleosome arrangement on tRNA genes of Xenopus laevis. Cell. 1981 Dec;27(3 Pt 2):459–466. [PubMed]
  • Bloom KS, Carbon J. Yeast centromere DNA is in a unique and highly ordered structure in chromosomes and small circular minichromosomes. Cell. 1982 Jun;29(2):305–317. [PubMed]
  • Cartwright IL, Elgin SC. Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex. Nucleic Acids Res. 1982 Oct 11;10(19):5835–5852. [PMC free article] [PubMed]
  • Van Dyke MW, Hertzberg RP, Dervan PB. Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). Proc Natl Acad Sci U S A. 1982 Sep;79(18):5470–5474. [PMC free article] [PubMed]
  • Wu C, Bingham PM, Livak KJ, Holmgren R, Elgin SC. The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell. 1979 Apr;16(4):797–806. [PubMed]
  • Carlson M, Brutlag D. Cloning and characterization of a complex satellite DNA from Drosophila melanogaster. Cell. 1977 Jun;11(2):371–381. [PubMed]
  • Artavanis-Tsakonas S, Schedl P, Tschudi C, Pirrotta V, Steward R, Gehring WJ. The 5S genes of Drosophila melanogaster. Cell. 1977 Dec;12(4):1057–1067. [PubMed]
  • Lifton RP, Goldberg ML, Karp RW, Hogness DS. The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1047–1051. [PubMed]
  • Nedospasov SA, Georgiev GP. Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem Biophys Res Commun. 1980 Jan 29;92(2):532–539. [PubMed]
  • Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980 Aug 28;286(5776):854–860. [PubMed]
  • Samal B, Worcel A, Louis C, Schedl P. Chromatin structure of the histone genes of D. melanogaster. Cell. 1981 Feb;23(2):401–409. [PubMed]
  • Wieshahn GP, Hyde JE, Hearst JE. The photoaddition of trimethylpsoralen to Drosophila melanogaster nuclei: a probe for chromatin substructure. Biochemistry. 1977 Mar 8;16(5):925–932. [PubMed]
  • Cech T, Pardue ML. Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure. Cell. 1977 Jul;11(3):631–640. [PubMed]
  • Hsieh T, Brutlag D. Sequence and sequence variation within the 1.688 g/cm3 satellite DNA of Drosophila melanogaster. J Mol Biol. 1979 Dec 5;135(2):465–481. [PubMed]

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


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...