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Nucleic Acids Res. Oct 11, 1982; 10(19): 5835–5852.
PMCID: PMC320934

Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex.

Abstract

Limited treatment of Drosophila nuclei with the 1,10-phenanthroline-cuprous complex leads to rapid production of nucleosomal ladders indistinguishable from those obtained by micrococcal nuclease digestion. An investigation of the preferential sites of cleavage of protein-free DNA at locus 67B1 surprisingly indicated that both reagents recognized very similar features. Thus, a virtually identical pattern of preferential cleavages was generated over a 12 kb fragment encoding four transcripts at this locus. The distribution of cleavage sites was highly non-random, with major sites falling in the spacers between the genes. Both reagents cleaved certain chromatin-specific sites near the 5' ends of the genes. However, an analysis of preferential cleavages at the sequence level did not reveal the same close correspondence. We suggest that both reagents can recognize some localized secondary structural features of the DNA and that the particular distribution of sequences present at this locus results in a distinctive pattern of cleavage sites that delineates gene and spacer segments.

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Selected References

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  • Hewish DR, Burgoyne LA. Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem Biophys Res Commun. 1973 May 15;52(2):504–510. [PubMed]
  • Noll M. Subunit structure of chromatin. Nature. 1974 Sep 20;251(5472):249–251. [PubMed]
  • 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]
  • Elgin SC. DNAase I-hypersensitive sites of chromatin. Cell. 1981 Dec;27(3 Pt 2):413–415. [PubMed]
  • Ponder BA, Crawford LV. The arrangement of nucleosomes in nucleoprotein complexes from polyoma virus and SV40. Cell. 1977 May;11(1):35–49. [PubMed]
  • Musich PR, Maio JJ, Brown FL. Subunit structure of chromatin and the organization of eukaryotic highly repetitive DNA: indications of a phase relation between restriction sites and chromatin subunits in African green monkey and calf nuclei. J Mol Biol. 1977 Dec 15;117(3):657–677. [PubMed]
  • Fittler F, Zachau HG. Subunit structure of alpha-satellite DNA containing chromatin from African green monkey cells. Nucleic Acids Res. 1979 Sep 11;7(1):1–13. [PMC free article] [PubMed]
  • Singer DS. Arrangement of a highly repeated DNA sequence in the genome and chromatin of the African green monkey. J Biol Chem. 1979 Jun 25;254(12):5506–5514. [PubMed]
  • Musich PR, Brown FL, Maio JJ. Nucleosome phasing and micrococcal nuclease cleavage of African green monkey component alpha DNA. Proc Natl Acad Sci U S A. 1982 Jan;79(1):118–122. [PMC free article] [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]
  • VONHIPPEL PH, FELSENFELD G. MICROCOCCAL NUCLEASE AS A PROBE OF DNA CONFORMATION. Biochemistry. 1964 Jan;3:27–39. [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]
  • 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]
  • Corces V, Holmgren R, Freund R, Morimoto R, Meselson M. Four heat shock proteins of Drosophila melanogaster coded within a 12-kilobase region in chromosome subdivision 67B. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5390–5393. [PMC free article] [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]
  • Clewell DB, Helinski DR. 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. [PMC free article] [PubMed]
  • Clewell DB. Nature of Col E 1 plasmid replication in Escherichia coli in the presence of the chloramphenicol. J Bacteriol. 1972 May;110(2):667–676. [PMC free article] [PubMed]
  • Livak KJ, Freund R, Schweber M, Wensink PC, Meselson M. Sequence organization and transcription at two heat shock loci in Drosophila. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5613–5617. [PMC free article] [PubMed]
  • Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. [PubMed]
  • Smith DR, Calvo JM. Nucleotide sequence of the E coli gene coding for dihydrofolate reductase. Nucleic Acids Res. 1980 May 24;8(10):2255–2274. [PMC free article] [PubMed]
  • Tschudi C, Pirrotta V. Sequence and heterogeneity in the 5S RNA gene cluster of Drosophila melanogaster. Nucleic Acids Res. 1980 Feb 11;8(3):441–451. [PMC free article] [PubMed]
  • Que BG, Downey KM, So AG. Degradation of deoxyribonucleic acid by a 1,10-phenanthroline-copper complex: the role of hydroxyl radicals. Biochemistry. 1980 Dec 23;19(26):5987–5991. [PubMed]
  • Marshall LE, Graham DR, Reich KA, Sigman DS. Cleavage of deoxyribonucleic acid by the 1,10-phenanthroline-cuprous complex. Hydrogen peroxide requirement and primary and secondary structure specificity. Biochemistry. 1981 Jan 20;20(2):244–250. [PubMed]
  • Sirotkin K, Davidson N. Developmentally regulated transcription from Drosophila melanogaster chromosomal site 67B. Dev Biol. 1982 Jan;89(1):196–210. [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]
  • Keene MA, Corces V, Lowenhaupt K, Elgin SC. DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. Proc Natl Acad Sci U S A. 1981 Jan;78(1):143–146. [PMC free article] [PubMed]
  • Wu C, Wong YC, Elgin SC. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell. 1979 Apr;16(4):807–814. [PubMed]
  • Kornberg R. The location of nucleosomes in chromatin: specific or statistical. Nature. 1981 Aug 13;292(5824):579–580. [PubMed]
  • McGhee JD, Wood WI, Dolan M, Engel JD, Felsenfeld G. A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell. 1981 Nov;27(1 Pt 2):45–55. [PubMed]
  • Kunkel GR, Martinson HG. Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981 Dec 21;9(24):6869–6888. [PMC free article] [PubMed]
  • Nickol J, Behe M, Felsenfeld G. Effect of the B--Z transition in poly(dG-m5dC) . poly(dG-m5dC) on nucleosome formation. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1771–1775. [PMC free article] [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]
  • Zachau HG, Igo-Kemenes T. Face to phase with nucleosomes. Cell. 1981 Jun;24(3):597–598. [PubMed]
  • Igo-Kemenes T, Hörz W, Zachau HG. Chromatin. Annu Rev Biochem. 1982;51:89–121. [PubMed]
  • HUFF JW, SASTRY KS, GORDON MP, WACKER WE. THE ACTION OF METAL IONS ON TOBACCO MOSAIC VIRUS RIBONUCLEIC ACID. Biochemistry. 1964 Apr;3:501–506. [PubMed]
  • Rhaese HJ, Freese E. Chemical analysis of DNA alterations. I. Base liberation and backbone breakage of DNA and oligodeoxyadenylic acid induced by hydrogen peroxide and hydroxylamine. Biochim Biophys Acta. 1968 Feb 26;155(2):476–490. [PubMed]
  • Massie HR, Samis HV, Baird MB. The kinetics of degradation of DNA and RNA by H 2 O 2 . Biochim Biophys Acta. 1972 Jul 31;272(4):539–548. [PubMed]
  • Lesko SA, Lorentzen RJ, Ts'o PO. Role of superoxide in deoxyribonucleic acid strand scission. Biochemistry. 1980 Jun 24;19(13):3023–3028. [PubMed]
  • Burger RM, Peisach J, Horwitz SB. Mechanism of bleomycin action: in vitro studies. Life Sci. 1981 Feb 16;28(7):715–727. [PubMed]
  • Hanson CV, Shen CK, Hearst JE. Cross-linking of DNA in situ as a probe for chromatin structure. Science. 1976 Jul 2;193(4247):62–64. [PubMed]
  • Cech T, Potter D, Pardue ML. Electron microscopy of DNA cross-linked with trimethylpsoralen: a probe for chromatin structure. Biochemistry. 1977 Nov 29;16(24):5313–5321. [PubMed]
  • Cech TR, Karrer KM. Chromatin structure of the ribosomal RNA genes of Tetrahymena thermophila as analyzed by trimethylpsoralen crosslinking in vivo. J Mol Biol. 1980 Feb 5;136(4):395–416. [PubMed]
  • Judelson HS, Vogt VM. Accessibility of ribosomal genes to trimethyl psoralen in nuclei of Physarum polycephalum. Mol Cell Biol. 1982 Mar;2(3):211–220. [PMC free article] [PubMed]
  • Jain SC, Bhandary KK, Sobell HM. Visualization of drug--nucleic acid interactions at atomic resolution. VI. Structure of two drug--dinucleoside monophosphate crystalline complexes, ellipticine--5-iodocytidylyy (3'-5') guanosine and 3,5,6,8-tetramethyl-N-methyl phenanthrolinium--5-iodocytidylyl (3'-5') guanosine. J Mol Biol. 1979 Dec 25;135(4):813–840. [PubMed]
  • Moreau J, Marcaud L, Maschat F, Kejzlarova-Lepesant J, Lepesant JA, Scherrer K. A + T-rich linkers define functional domains in eukaryotic DNA. Nature. 1982 Jan 21;295(5846):260–262. [PubMed]
  • Müller W, Crothers DM. Interactions of heteroaromatic compounds with nucleic acids. 1. The influence of heteroatoms and polarizability on the base specificity of intercalating ligands. Eur J Biochem. 1975 May;54(1):267–277. [PubMed]
  • Müller W, Bünemann H, Dattagupta N. Interactions of heteroaromatic compounds with nucleic acids. 2. Influence of substituents on the base and sequence specificity of intercalating ligands. Eur J Biochem. 1975 May;54(1):279–291. [PubMed]
  • Howe-Grant M, Lippard SJ. Binding of platinum(II) intercalation reagents to deoxyribnonucleic acid. Dependence on base-pair composition, nature of the intercalator, and ionic strength. Biochemistry. 1979 Dec 25;18(26):5762–5769. [PubMed]
  • Feigon J, Leupin W, Denny WA, Kearns DR. Binding of ethidium derivatives to natural DNA: a 300 MHz 1H NMR study. Nucleic Acids Res. 1982 Jan 22;10(2):749–762. [PMC free article] [PubMed]
  • Krugh TR, Reinhardt CG. Evidence for sequence preferences in the intercalative binding of ethidium bromide to dinucleoside monophosphates. J Mol Biol. 1975 Sep 15;97(2):133–162. [PubMed]
  • Armstrong K, Bauer WR. Preferential site-dependent cleavage by restriction endonuclease PstI. Nucleic Acids Res. 1982 Feb 11;10(3):993–1007. [PMC free article] [PubMed]
  • Hofer B, Ruhe G, Koch A, Köster H. Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf I. Nucleic Acids Res. 1982 May 11;10(9):2763–2773. [PMC free article] [PubMed]
  • Nordheim A, Pardue ML, Lafer EM, Möller A, Stollar BD, Rich A. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 1981 Dec 3;294(5840):417–422. [PubMed]
  • Peck LJ, Wang JC. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. [PubMed]
  • Rhodes D, Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981 Jul 23;292(5821):378–380. [PubMed]
  • Dickerson RE, Drew HR. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. [PubMed]
  • Dickerson RE, Drew HR. Kinematic model for B-DNA. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7318–7322. [PMC free article] [PubMed]
  • Lomonossoff GP, Butler PJ, Klug A. Sequence-dependent variation in the conformation of DNA. J Mol Biol. 1981 Jul 15;149(4):745–760. [PubMed]
  • Karataev GI, Permogorov VI, Vologodskii AV, Frank-Kamenetskii MD. Denaturation maps of DNA: experimental and theoretical maps of phiX174 DNA. Nucleic Acids Res. 1978 Jul;5(7):2493–2500. [PMC free article] [PubMed]
  • Chan HW, Dodgson JB, Wells RD. Influence of DNA structure on the lactose operator-repressor interaction. Biochemistry. 1977 May 31;16(11):2356–2366. [PubMed]
  • Brack C, Bickle TA, Yuan R. The relation of single-stranded regions in bacteriophage PM2 supercoiled DNA to the early melting sequences. J Mol Biol. 1975 Aug 25;96(4):693–702. [PubMed]
  • Sobell HM, Lozansky ED, Lessen M. Structural and energetic considerations of wave propagation in DNA. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):11–19. [PubMed]

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