Oligonucleotide Synthesis pp 319-342

Part of the Methods in Molecular Biology book series (MIMB, volume 288)

DNase I Footprinting of Small Molecule Binding Sites on DNA

  • Christian Bailly
  • Jérôme Kluza
  • Christopher Martin
  • Thomas Ellis
  • Michael J. Waring

Abstract

Nuclease footprinting techniques were initially developed to investigate protein-deoxyribonucleic acid (DNA) interactions but these tools of molecular biology have also become instrumental for probing sequence-selective binding of small molecules to DNA. Here, the method is described and technical details are given for performing deoxyribonuclease (DNase) I footprinting with DNA-binding drugs. An example is presented where DNase I is used (as well as DNase II and micrococcal nuclease) to probe the patterns of sequence-selective recognition of DNA by the anticancer antibiotic actinomycin D. DNase I is a convenient endonuclease for detecting and locating the position of actinomycin-binding sites within GC-rich sequences.

Key Words

Nuclease DNase I footprinting DNA-binding drugs DNase I DNase II micrococcal nuclease anticancer antibiotic actinomycin D endonuclease electrophoresis polyacrylamide gels echinomycin cooperativity drug-DNA recognition reverse transcriptase DNA polymerase I diaminopurine, inosine electroelution dimethylsulfate densitometric analysis capillary electrophoresis sequence selectivity DNA recognition 

References

  1. 1.
    Galas, D. J. and Schmitz, A. (1978) DNase footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157–3170.PubMedCrossRefGoogle Scholar
  2. 2.
    Brenowitz, M., Senear, D. F., Shea, M. A., and Ackers, G. K. (1986) Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol. 130, 132–181.PubMedCrossRefGoogle Scholar
  3. 3.
    Dabrowiak, J. C., Stankus, A. A., and Goodisman, J. (1992) Sequence-specificity of drug-DNA interactions. In Nucleic Acid Targeted Drug Design (Propst, C. L., Perun, T. J., eds.), Dekker, New York, pp. 93–149.Google Scholar
  4. 4.
    Dhavan, G. M., Mollah, A. K. M. M., and Brenowitz, M. (2002) Equilibrium and kinetic quantitative DNase I footprinting. In Advances in DNA Sequence-Specific Agents, vol. 4, (Jones, G. B., ed.), Elsevier, New York, pp. 139–155.CrossRefGoogle Scholar
  5. 5.
    Nielsen, P. E. (1990) Chemical and photochemical probing of DNA complexes. J. Mol. Recognit 3, 1–25.PubMedCrossRefGoogle Scholar
  6. 6.
    Bailly, C. and Waring, M. J. (1995) Comparison of different footprinting methodologies for detecting binding sites for a small ligand on DNA. J. Biomol. Struct. Dyn. 12, 869–898.PubMedGoogle Scholar
  7. 7.
    Travers, A. A., Lamond, A. I., Mace, H. A. F., and Berman, M. L. (1983) RNA polymerase interactions with the upstream region of E. coli tyrT promoter. Cell 35, 265–273.PubMedCrossRefGoogle Scholar
  8. 8.
    Low, C. M. L., Olsen, R. K., and Waring, M. J. (1984) Sequence preferences in the binding to DNA of triostin A and TANDEM as reported by DNase I footprinting. FEBS Lett. 176, 414–420.PubMedCrossRefGoogle Scholar
  9. 9.
    Low, C. M. L., Drew, H. R., and Waring, M. J. (1984) Sequence-specific binding of echinomycin to DNA: evidence for conformational changes affecting flanking sequences. Nucleic Acids Res. 12, 4865–4877.PubMedCrossRefGoogle Scholar
  10. 10.
    Fox, K. R. and Waring, M. J. (1986) Nucleotide sequence binding preference of nogalamycin investigated by DNase I footprinting. Biochemistry 25, 4349–4356.PubMedCrossRefGoogle Scholar
  11. 11.
    Fox, K. R. and Waring, M. J. (1987) Footprinting at low temperature: evidence that ethidium and other simple intercalators can discriminate between different nucleotide sequences. Nucleic Acids Res. 15, 491–507.PubMedCrossRefGoogle Scholar
  12. 12.
    Fox, K. R. and Waring, M. J. (1987) The use of micrococcal nuclease as a probe for drug-binding sites on DNA. Biochim. Biophys. Acta 909, 145–155.PubMedGoogle Scholar
  13. 13.
    Chaires, J. B., Fox, K. R., Herrera, J. E., Britt, M., and Waring, M. J. (1987) Site and sequence specificity of the daunomycin-DNA interaction. Biochemistry 26, 8227–8236.PubMedCrossRefGoogle Scholar
  14. 14.
    Portugal, J. and Waring M. J. (1987) Comparison of binding sites in DNA for berenil, netropsin and distamycin: a footprinting study. Eur. J. Biochem. 167, 281–289.PubMedCrossRefGoogle Scholar
  15. 15.
    Portugal, J. and Waring, M. J. (1987) Assignment of DNA binding sites for 4′,6-diamidine-2-phenylindole and bisbenzimide (Hoechst 33258): a comparative footprinting study. Biochim. Biophys. Acta 949, 158–168.Google Scholar
  16. 16.
    Bailly, C., Ohuigin, C., Rivalle, C., Bisagni, E., Hénichart, J. P., and Waring, M. J. (1990) Sequence-selective binding of an ellipticine derivative to DNA. Nucleic Acids Res. 18, 6283–6291.PubMedCrossRefGoogle Scholar
  17. 17.
    Bailly, C., Denny, W. A., Mellor, L., Wakelin, L. P. G., and Waring, M. J. (1992) Sequence-specificity of the binding of 9-aminoacridine-and amsacrine-4-carboxamides to DNA studied by DNase I footprinting. Biochemistry 31, 3514–3524.PubMedCrossRefGoogle Scholar
  18. 18.
    Bailly, C., Donkor, I. O., Gentle, D., Thornalley, M., and Waring, M. J. (1994) Sequence-selective binding of cis and trans-butamidine analogues of the anti-Pneumocystis carinii drug pentamidine. Mol. Pharmacol. 46, 313–322.PubMedGoogle Scholar
  19. 19.
    Bailly, C., Perrine, D., Lancelot, J. C., Saturnino, C., Robba, M., and Waring, M. J. (1997) Sequence-selective binding to DNA of bis(amidinophenoxy)-alkanes related to propamidine and pentamidine. Biochem. J. 323, 23–31.PubMedGoogle Scholar
  20. 20.
    Bailly, C. and Waring, M. J. (1993) Preferential intercalation at AT sequences in DNA by lucanthone, hycanthone, and indazole analogs: a footprinting study. Biochemistry 32, 5985–5993.PubMedCrossRefGoogle Scholar
  21. 21.
    Bailly, C., Hamy, F., and Waring, M. J. (1995) Cooperativity in the binding of echinomycin to DNA fragments containing closely spaced CpG sites. Biochemistry 35, 1150–1161.CrossRefGoogle Scholar
  22. 22.
    Lavesa, M. and Fox, K. R. (2001) Preferred binding sites for [N-MeCys(3), N-MeCys(7)]TANDEM determined using a universal footprinting substrate. Anal. Biochem. 293, 246–250.PubMedCrossRefGoogle Scholar
  23. 23.
    Joubert, A., Sun, X.-W., Johansson, E., Bailly, C., Mann, J., and Neidle, S. (2003) Sequence selective targeting of long stretches of the DNA minor groove by a novel dimeric bis-benzimidazole. Biochemistry 42, 5984–5992.PubMedCrossRefGoogle Scholar
  24. 24.
    Bailly, C. and Waring, M. J. (2001) Use of DNA molecules substituted with unnatural nucleotides to probe specific drug-DNA interactions. Methods Enzymol. 340, 485–502.PubMedCrossRefGoogle Scholar
  25. 25.
    Bailly, C., Payet, D., Travers, A. A., and Waring, M. J. (1996) PCR-based development of DNA substrates containing modified bases: an efficient system for investigating the role of the exocyclic groups in chemical and structural recognition by minor groove binding drugs and proteins. Proc. Natl. Acad. Sci. USA 93, 13,623–13,628.PubMedCrossRefGoogle Scholar
  26. 26.
    Buttinelli, M., Minnock, A., Panetta, G., Waring, M. J., and Travers, A. A. (1998) The exocyclic groups of DNA modulate the affinity and positioning of the histone octamer. Proc. Natl. Acad. Sci. USA 95, 8544–8549.PubMedCrossRefGoogle Scholar
  27. 27.
    Crow, S. D. G., Bailly, C., Garbay-Jaureguiberry, C., Roques, B., Ramsay Shaw, B., and Waring, M. J. (2002) DNA sequence recognition by the antitumor drug ditercalinium. Biochemistry 41, 8672–8682.PubMedCrossRefGoogle Scholar
  28. 28.
    Trauger, J. W. and Dervan, P. B. (2001) Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes. Methods Enzymol. 340, 450–466.PubMedCrossRefGoogle Scholar
  29. 29.
    Müller, W. and Crothers, D. M. (1968) Studies of the binding of actinomycin and related compounds to DNA. J. Mol. Biol. 35, 251–290.PubMedCrossRefGoogle Scholar
  30. 30.
    Waring, M. J. (1970) Variation of the supercoils in closed circular DNA by binding of antibiotics and drugs. Evidence for molecular models involving intercalation. J. Mol. Biol. 54, 247–279.PubMedCrossRefGoogle Scholar
  31. 31.
    Takusagawa, F., Dabrow, M., Neidle, S., and Berman, H. M. (1982) The structure of a pseudo intercalated complex between actinomycin and the DNA binding sequence d(GpC). Nature 296, 466–469.PubMedCrossRefGoogle Scholar
  32. 32.
    Zhou, N., James, T. L., and Shafer, R. H. (1989) Binding of actinomycin D to [d(ATCGAT)]2: NMR evidence of multiple complexes. Biochemistry 28, 5231–5239.PubMedCrossRefGoogle Scholar
  33. 33.
    Kamitori, S. and Takusagawa, F. (1994) Multiple binding modes of anticancer drug actinomycin D: X-ray, molecular modeling, and spectroscopic studies of d(GAAGCTTC)2-actinomycin D complexes and its host DNA. J. Am. Chem. Soc. 116, 4154–4165.CrossRefGoogle Scholar
  34. 34.
    Gallego, J., Ortiz, A. R., de Pascual-Teresa, B., and Gago, F. (1997) Structure-affinity relationships for the binding of actinomycin D to DNA. J. Comput. Aided Mol. Des. 11, 114–128.PubMedCrossRefGoogle Scholar
  35. 35.
    Sha, F. and Chen, F.-M. (2000) Actinomycin D binds strongly to d(CGAGACG) and d(CGTCGTCG). Biophys. J. 79, 2095–2104.PubMedCrossRefGoogle Scholar
  36. 36.
    Robinson, H., Gao, Y.-G., Yang, X., Sanishvili, R., Joachimiak, A., and Wang, A. H.-J. (2001) Crystallographic analysis of a novel complex of acinomycin D bound to the DNA decamer CGATCGATCG. Biochemistry 40, 5587–5592.PubMedCrossRefGoogle Scholar
  37. 37.
    Lane, M. J., Dabrowiak, J. C., and Vournakis, J. N. (1983) Sequence specificity of actinomycin D and netropsin binding to pBR322 DNA analyzed by protection from DNase I. Proc. Natl. Acad. Sci. USA 80, 3260–3264.PubMedCrossRefGoogle Scholar
  38. 38.
    Fox, K. R. and Waring, M. J. (1984) DNA structural variations produced by actinomycin and distamycin as revealed by DNAase I footprinting. Nucleic Acids Res. 12, 9271–9285.PubMedCrossRefGoogle Scholar
  39. 39.
    Goodisman, J., Rehfuss, R., Ward, B., and Dabrowiak, J. C. (1992) Site-specific binding constants for actinomycin D on DNA determined from footprinting studies. Biochemistry 31, 1046–1058.PubMedCrossRefGoogle Scholar
  40. 40.
    Fletcher, M. and Fox, K. R. (1996) Dissociation kinetics of actinomycin D from individual GpC sites in DNA. Eur. J. Biochem. 237, 164–170.PubMedCrossRefGoogle Scholar
  41. 41.
    Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
  42. 42.
    Drew, H. R. (1984) Structural specificities of five commonly used DNA nucleases. J. Mol. Biol. 176, 535–557.PubMedCrossRefGoogle Scholar
  43. 43.
    Fox, K. R. (1997) DNase I footprinting. In Drug-DNA Interaction Protocols: Methods in Molecular Biology, vol. 90 (Fox, K. R., ed.), Humana Press, Totowa, NJ, pp. 1–22.CrossRefGoogle Scholar
  44. 44.
    Fox, K. R. and Waring, M. J. (2001) High-resolution footprinting studies of drug-DNA complexes using chemical and enzymic probes. Methods Enzymol. 340, 412–430.PubMedCrossRefGoogle Scholar
  45. 45.
    Fletcher, M. and Fox, K. R. (1993) Visualising the kinetics of dissociation of actinomycin from individual sites in mixed sequence DNA by DNase I footprinting. Nucleic Acids Res. 21, 1339–1344.PubMedCrossRefGoogle Scholar
  46. 46.
    Fletcher, M., Olsen, R. K., and Fox, K. R. (1995) Dissociation of the AT-specific bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM from TpA sites in DNA. Biochem. J. 306, 15–19.PubMedGoogle Scholar
  47. 47.
    Bailly, C., Ridge, G., Graves, D. E., and Waring, M. J. (1994) Use of a photoactive derivative of actinomycin D to investigate shuffling between binding sites on DNA. Biochemistry 33, 8736–8745.PubMedCrossRefGoogle Scholar
  48. 48.
    Fox, K. R. and Waring, M. J. (1986) Footprinting reveals that nogalamycin and actinomycin shuffle between DNA binding sites. Nucleic Acids Res. 14, 2001–2014.PubMedCrossRefGoogle Scholar
  49. 49.
    Shafer, G. E., Price, M. A., and Tullius, T. D. (1989) Use of hydroxyl radical and gel electrophoresis to study DNA structure. Electrophoresis 10, 397–404.PubMedCrossRefGoogle Scholar
  50. 50.
    Price, M. A. and Tullius, T. D. (1992) Using hydroxyl radical to probe DNA structure. Methods Enzymol. 212, 194–219.PubMedCrossRefGoogle Scholar
  51. 51.
    Chow, C. S. and Barton, J. K. (1992) Transition metal complexes as probes of nucleic acids. Methods Enzymol. 212, 219–242.PubMedCrossRefGoogle Scholar
  52. 52.
    Routier, S., Vezin, H., Lamour, E., Bernier, J. L., Catteau, J. P., and Bailly, C. (1999) DNA cleavage by hydroxy-salen-iron complexes. Nucleic Acids Res. 27, 4160–4166.PubMedCrossRefGoogle Scholar
  53. 53.
    McPike, M. P., Goodisman, J., and Dabrowiak, J. C. (2001) Drug-RNA footprinting. Methods Enzymol. 340, 431–449.PubMedCrossRefGoogle Scholar
  54. 54.
    Yindeeyoungyeon, W. and Schell, M. A. (2000) Footprinting with an automated capillary DNA sequencer. Biotechniques 29, 1034–1036.PubMedGoogle Scholar
  55. 55.
    Wilson, D. O., Johnson, P., and McCord, B. R. (2001) Nonradiochemical DNase I footprinting by capillary electrophoresis. Electrophoresis 22, 1979–1986.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2005

Authors and Affiliations

  • Christian Bailly
    • 1
  • Jérôme Kluza
    • 2
  • Christopher Martin
    • 3
  • Thomas Ellis
    • 3
  • Michael J. Waring
    • 3
  1. 1.INSERM U-524Institut de Recherches sur le Cancer de LilleLilleFrance
  2. 2.INSERM U-524Génétique Moléculaire et Approches Thérapeutiques de éopathies MalignesLilleFrance
  3. 3.Department of PharmacologyUniversity of CambridgeCambridgeUK

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