Home LiteratureArticle Details
PMID: 3822813 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Footprinting at low temperatures: evidence that ethidium and other simple intercalators can discriminate between different nucleotide sequences.

Nucleic acids research ·Vol. 15 ·No. 2 ·1987-01-26 ·Pages 491-507

Fox KR, Waring MJ

Abstract

Footprinting experiments employing DNAase I have been performed at 4 degrees C. At this temperature several simple intercalating ligands, including both ethidium and proflavine, can be seen to induce marked changes in the pattern of cleavage. From an analysis of the changes in patterns of digestion by DNAase I we deduce that ethidium binds best to regions of mixed nucleotide sequence, especially those containing alternating purines and pyrimidines. Binding seems to be weakest to poly dA sequences which consequently appear as regions of relatively enhanced cleavage. Attempts to reproduce these changes using DNAase II as a footprinting tool were unsuccessful.

MeSH Terms
Base Composition Base Sequence DNA Deoxyribonuclease I/metabolism Endodeoxyribonucleases/metabolism Ethidium Intercalating Agents Substrate Specificity
Chemicals
Intercalating Agents DNA Endodeoxyribonucleases Deoxyribonuclease I deoxyribonuclease II Ethidium
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Fox K R
Waring M J
References (23)
23 references, click to expand
  1. Complex formation between ethidium bromide and nucleic acids.
    J Mol Biol. 1965 Aug;13(1):269-82 PMID: 5859041
  2. Theoretical analysis of the footprinting experiment.
    J Biomol Struct Dyn. 1985 Feb;2(5):967-79 PMID: 2855783
  3. Studies of the binding of actinomycin and related compounds to DNA.
    J Mol Biol. 1968 Jul 28;35(2):251-90 PMID: 4107107
  4. The unwinding of circular deoxyribonucleic acid by phenanthridinium drugs: structure-activity relations for the intercalation reaction.
    Mol Pharmacol. 1974 May;10(3):544-61 PMID: 4859556
  5. Evidence for sequence preferences in the intercalative binding of ethidium bromide to dinucleoside monophosphates.
    J Mol Biol. 1975 Sep 15;97(2):133-62 PMID: 1177318
  6. The interaction of ethidium with synthetic double-stranded polynucleotides at low ionic strength.
    Nucleic Acids Res. 1978 Jan;5(1):161-71 PMID: 643605
  7. A comparative study of ethidium bromide complexes with dinucleotides and DNA: direct evidence for intercalation and nucleic acid sequence preferences.
    Biochemistry. 1978 Nov 14;17(23):4845-54 PMID: 718859
  8. Equilibrium studies of ethidium--polynucleotide interactions.
    Biochemistry. 1981 Jun 9;20(12):3547-53 PMID: 7260057
  9. Interaction of the antitumor drug 4'-(9-acridinylamino)methanesulfon-m-anisidide and related acridines with nucleic acids.
    Mol Pharmacol. 1981 Sep;20(2):404-14 PMID: 6170872
  10. 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):5470-4 PMID: 6291045
  11. On the cooperative and noncooperative binding of ethidium to DNA.
    Nucleic Acids Res. 1982 Dec 20;10(24):8211-23 PMID: 7162990
  12. Sequence specificity of actinomycin D and Netropsin binding to pBR322 DNA analyzed by protection from DNase I.
    Proc Natl Acad Sci U S A. 1983 Jun;80(11):3260-4 PMID: 6304702
  13. Methidiumpropyl-EDTA.Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA.
    Nucleic Acids Res. 1983 Aug 25;11(16):5555-67 PMID: 6225070
  14. DNA structural variations in the E. coli tyrT promoter.
    Cell. 1984 Jun;37(2):491-502 PMID: 6327070
  15. Sequence-specific binding of echinomycin to DNA: evidence for conformational changes affecting flanking sequences.
    Nucleic Acids Res. 1984 Jun 25;12(12):4865-79 PMID: 6204275
  16. Structural specificities of five commonly used DNA nucleases.
    J Mol Biol. 1984 Jul 15;176(4):535-57 PMID: 6086935
  17. Echinomycin binding sites on DNA.
    Science. 1984 Sep 14;225(4667):1122-7 PMID: 6089341
  18. DNA structural variations produced by actinomycin and distamycin as revealed by DNAase I footprinting.
    Nucleic Acids Res. 1984 Dec 21;12(24):9271-85 PMID: 6393053
  19. Substituent effects on the binding of ethidium and its derivatives to natural DNA.
    Biophys Chem. 1985 Oct;22(4):299-305 PMID: 4063454
  20. Investigations into the sequence-selective binding of mithramycin and related ligands to DNA.
    Nucleic Acids Res. 1985 Dec 20;13(24):8695-714 PMID: 2934687
  21. DNA sequence preferences for the anti-cancer drug mitoxanthrone and related anthraquinones revealed by DNase I footprinting.
    FEBS Lett. 1986 Jul 7;202(2):289-94 PMID: 3720951
  22. Nucleotide sequence binding preferences of nogalamycin investigated by DNase I footprinting.
    Biochemistry. 1986 Jul 29;25(15):4349-56 PMID: 3019386
  23. A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization.
    J Mol Biol. 1967 Jul 14;27(1):87-106 PMID: 6033613
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/15.2.491
Published
1987-01-26
Pages
491-507
Language
English
Region
England
NLM ID
0411011
PMCID
PMC340448
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/15.2.491 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2