Search tips
Search criteria 


Logo of narLink to Publisher's site
Nucleic Acids Res. 1978 September; 5(9): 3157–3170.
PMCID: PMC342238

DNAse footprinting: a simple method for the detection of protein-DNA binding specificity.


A method for studying the sequence-specific binding of proteins to DBA is described. The technique is a simple conjoining of the Maxam-Gilbert DNA-sequencing method and the technique of DNAase-protected fragment isolation. Fragments of a 5' end-labelled, double-stranded DNA segment, partially degraded by DNAase in the presence and absence of the binding protein, are visualized by electrophoresis and autoradiography alongside the base-specific reaction products of the Maxam-Gilbert sequencing method. It is then possible to see the protective "footprint" of the binding protein on the DNA sequence. The binding of lac repressor to lac operator is visualized by "footprinting" as an example. Equillibrium estimates indicate that 10-fold sequence-specificity (differential binding constant) could be studied easily using this technique.

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 (1.7M), 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

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Brown KD, Bennett GN, Lee F, Schweingruber ME, Yanofsky C. RNA polymerase interaction at the promoter--operator region of the tryptophan operon of Escherichia coli and Salmonella typhimurium. J Mol Biol. 1978 May 15;121(2):153–177. [PubMed]
  • Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc Natl Acad Sci U S A. 1975 Mar;72(3):784–788. [PubMed]
  • Mirzabekov AD, Melnikova AF. Localization of chromatin proteins within DNA grooves by methylation of chromatin with dimethyl sulphate. Mol Biol Rep. 1974 Sep;1(7):379–384. [PubMed]
  • Walz A, Pirrotta V. Sequence of the PR promoter of phage lambda. Nature. 1975 Mar 13;254(5496):118–121. [PubMed]
  • Maniatis T, Ptashne M. Structure of the lambda operators. Nature. 1973 Nov 16;246(5429):133–136. [PubMed]
  • Gilbert W. The lac repressor and the lac operator. Ciba Found Symp. 1972;7:245–259. [PubMed]
  • Johnson A, Meyer BJ, Ptashne M. Mechanism of action of the cro protein of bacteriophage lambda. Proc Natl Acad Sci U S A. 1978 Apr;75(4):1783–1787. [PubMed]
  • Bernardi A, Gaillard C, Bernardi G. The specificity of five DNAases as studied by the analysis of 5'-terminal doublets. Eur J Biochem. 1975 Apr 1;52(3):451–457. [PubMed]
  • Bernardi G, Ehrlich SD, Thiery JP. The specificity of deoxyribonucleases and their use in nucleotide sequence studies. Nat New Biol. 1973 Nov 14;246(150):36–40. [PubMed]
  • Matsuda M, Ogoshi H. Specificity of DNase I. Estimation of nucleosides present at the 5'-phosphate terminus of a limit digest of DNA by DNase I. J Biochem. 1966 Mar;59(3):230–235. [PubMed]
  • Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. [PubMed]
  • Gilbert W, Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3581–3584. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press