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MeSH Review

DNA Footprinting

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Disease relevance of DNA Footprinting

  • Gel band mobility shift and DNA footprint experiments were used to demonstrate that the CYS3 protein, expressed in Escherichia coli, binds to three distinct sites in the 5' upstream DNA of cys-14, the structural gene for sulfate permease II [1].

High impact information on DNA Footprinting


Biological context of DNA Footprinting


Associations of DNA Footprinting with chemical compounds


Gene context of DNA Footprinting

  • Fractionation of yeast extracts on heparin-agarose revealed the presence of a DNA footprinting activity that interacted specifically with the 5'-upstream region of TEF1 and TEF2 genes coding for the protein synthesis elongation factor EF-1 alpha, and of the ribosomal protein gene RP51A [16].
  • Protein-DNA binding studies using electrophoretic mobility shift and DNA footprinting assays showed that both Sp1 and Sp3 proteins bound this region of the VEGF promoter [17].
  • The results of DNA footprinting analysis show that FadR binds downstream of the uspA promoter in the noncoding region [18].
  • The MLPE site primarily binds USF1/USF2 and ERalpha, and gel mobility shift and DNA footprinting assays show that the AhR complex decreases binding of these transcription factors to the MLPE [19].
  • In vivo DNA footprinting shows a specific loss of occupancy at the IFN response factor element site in Caki-2 cells, whereas Caki-1 cells show full promoter occupancy [20].

Analytical, diagnostic and therapeutic context of DNA Footprinting

  • The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in explicit solvent [21].


  1. cys-3, the positive-acting sulfur regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. Fu, Y.H., Marzluf, G.A. J. Biol. Chem. (1990) [Pubmed]
  2. A pre-B cell nuclear protein that specifically interacts with the immunoglobulin V-J recombination sequences. Aguilera, R.J., Akira, S., Okazaki, K., Sakano, H. Cell (1987) [Pubmed]
  3. DNA footprinting with hydroxyl radical. Tullius, T.D. Nature (1988) [Pubmed]
  4. Regulation in vitro of metallothionein gene binding factors. Seguin, C., Hamer, D.H. Science (1987) [Pubmed]
  5. Amino-terminal sequences of sigmaN (sigma54) inhibit RNA polymerase isomerization. Cannon, W., Gallegos, M.T., Casaz, P., Buck, M. Genes Dev. (1999) [Pubmed]
  6. Induction of proto-oncogene fos transcription through the adenylate cyclase pathway: characterization of a cAMP-responsive element. Sassone-Corsi, P., Visvader, J., Ferland, L., Mellon, P.L., Verma, I.M. Genes Dev. (1988) [Pubmed]
  7. Identification of a novel cis-element required for the constitutive activity and osmotic response of the rat aldose reductase promoter. Iwata, T., Minucci, S., McGowan, M., Carper, D. J. Biol. Chem. (1997) [Pubmed]
  8. Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting. Tsung, K., Brissette, R.E., Inouye, M. J. Biol. Chem. (1989) [Pubmed]
  9. Nonbiased identification of DNA sequences that bind thyroid hormone receptor alpha 1 with high affinity. Katz, R.W., Koenig, R.J. J. Biol. Chem. (1993) [Pubmed]
  10. DNA binding specificity and function of retinoid X receptor alpha. Subauste, J.S., Katz, R.W., Koenig, R.J. J. Biol. Chem. (1994) [Pubmed]
  11. Binding of specific DNA base-pair mismatches by N-methylpurine-DNA glycosylase and its implication in initial damage recognition. Biswas, T., Clos, L.J., SantaLucia, J., Mitra, S., Roy, R. J. Mol. Biol. (2002) [Pubmed]
  12. Inducible in vivo DNA footprints define sequences necessary for UV light activation of the parsley chalcone synthase gene. Schulze-Lefert, P., Dangl, J.L., Becker-André, M., Hahlbrock, K., Schulz, W. EMBO J. (1989) [Pubmed]
  13. Induction of hTERT expression and telomerase activity by estrogens in human ovary epithelium cells. Misiti, S., Nanni, S., Fontemaggi, G., Cong, Y.S., Wen, J., Hirte, H.W., Piaggio, G., Sacchi, A., Pontecorvi, A., Bacchetti, S., Farsetti, A. Mol. Cell. Biol. (2000) [Pubmed]
  14. The Bacillus stearothermophilus mannitol regulator, MtlR, of the phosphotransferase system. A DNA-binding protein, regulated by HPr and iicbmtl-dependent phosphorylation. Henstra, S.A., Tuinhof, M., Duurkens, R.H., Robillard, G.T. J. Biol. Chem. (1999) [Pubmed]
  15. Function of the zinc finger in Escherichia coli Fpg protein. Tchou, J., Michaels, M.L., Miller, J.H., Grollman, A.P. J. Biol. Chem. (1993) [Pubmed]
  16. A general upstream binding factor for genes of the yeast translational apparatus. Huet, J., Cottrelle, P., Cool, M., Vignais, M.L., Thiele, D., Marck, C., Buhler, J.M., Sentenac, A., Fromageot, P. EMBO J. (1985) [Pubmed]
  17. Inhibition of vascular endothelial growth factor expression in HEC1A endometrial cancer cells through interactions of estrogen receptor alpha and Sp3 proteins. Stoner, M., Wang, F., Wormke, M., Nguyen, T., Samudio, I., Vyhlidal, C., Marme, D., Finkenzeller, G., Safe, S. J. Biol. Chem. (2000) [Pubmed]
  18. Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes. Farewell, A., Diez, A.A., DiRusso, C.C., Nyström, T. J. Bacteriol. (1996) [Pubmed]
  19. Transcriptional activation of cathepsin D gene expression by 17beta-estradiol: mechanism of aryl hydrocarbon receptor-mediated inhibition. Wang, F., Samudio, I., Safe, S. Mol. Cell. Endocrinol. (2001) [Pubmed]
  20. Loss of interferon-gamma inducibility of TAP1 and LMP2 in a renal cell carcinoma cell line. Dovhey, S.E., Ghosh, N.S., Wright, K.L. Cancer Res. (2000) [Pubmed]
  21. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition. Bailly, C., Chessari, G., Carrasco, C., Joubert, A., Mann, J., Wilson, W.D., Neidle, S. Nucleic Acids Res. (2003) [Pubmed]
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