Abstract
Footprinting analysis has been used to identify the binding sites of drugs and other ligands bound to DNA molecules (see Chapter 1) (1–3). It is particularly useful for equilibrium binding drugs or ligands that leave no record of their residence position on DNA In the footprinting procedure, the ligand-DNA complex is exposed to an agent or probe that can cleave DNA, and the oligonucleotide products from the cleavage reaction are separated using, for example, electrophoresis in a polyacrylamide gel. If the ligand, when bound, inhibits cleavage by the probe, the oligonucleotides that terminate at the ligand binding site will be underrepresented among the products analyzed using the sequencing gel. This appears as omissions or “footprints” in the spots on the sequencing autoradiogram
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
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. and Perun T. J., eds.), Marcel Dekker New York, pp 93–149.
Shubsda M., Kishlkawa H., Goodisman J., and Dabrowtak J. C. (1994) Quantitative footprinting analysis J Mol Recogn 7, 133–139
Dabrowiak J. C. and Goodisman J. (1989) Quantitative footprinting analysis of drug-DNA interactions in Chemistry and Physzcs of DNA-Ligand Interactions (Kallenbach N. P., ed), Adenine Guilderland, NY, pp 143–174
Rehfuss R., Goodisman J., and Dabrowlak J. C. (1990) Quantitative footprinting analysis of the actinomycin D-DNA interaction, inMolecular Basis of Specificity in Nucleic Acid-Drug Interactions (Pullman B and Jortner J., eds.), Kluwer Academic Netherlands, pp 157–166
Ward B., Rehfuss R., Goodisman J., and Dabrowiak J. C. (1988) Rate enhancements in the DNase I footprinting experiment. Nucleic Acids Res 16,1359–1369
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
Sambrook J., Fritsch E. F., and Maniatis T. (1989) Molecular Cloning, A Laboratory Manual, 2nd ed, Cold Spring Harbor Laboratory Cold Spring Harbor, NY
Ward B. and Dabrowiak J. C. (1988) Stability of DNase I in footprinting expenments Nucleic Acids Res 16,8724
Gale E. F., Cundliffe E., Reynolds P. E., Richmond M. H., and Waring M. J. (1981) The molecular basis of antibiotic action Wiley, London
Suck D., Lahm A., and Oefner C. (1988) Structure refined to 2Å of a nicked DNA octanucleotide complex with DNase I Nature 332, 465–468.
Goodisman J. and Dabrowiak J. C. (1992) Structural changes and enhancements in DNase I footprinting experiments. Biochemistry 31, 1058–1064.
Chen F-M. (1992) Binding specificities of actinomycin D to non-self-complementary XGCY-tetranucleotide sequences. Biochemistry 31, 6223–6228
Winkle S. A. and Krugh T. R. (1981) Equilibrium binding of carcinogen and antitumor antiblotics to DNA site selectivity, cooperativity, allosterism Nucleic Acids Res. 9,375–3186.
Snyder J. G., Hartman N. G., D’eEstantoit B. L., Kennard O., Remeta D. P., and Bresiauer K. J. (1989), Binding of actinomycin D to DNA evidence for a non-classical high-affinity binding mode that does not require GpC sites Proc Natl Acad. Sci USA 86, 3968–3972
Kamitori S. and Takusagawa F. (1992) Crystal structure of the 2.1 complex between d(GAAGCTTC) and the anticancer drug actmomycin D J Mol Biol 225, 445–456.
Ward B. (1996) Type IIS restriction enzyme footprinting I. Measurement of a triple helix dissociation constant with Eco571 at 25°C Nucleic Acids Res 24,2435–2440
Best G. C. and Dervan P. B. (1995) Energetics of formation of sixteen triple helical complexes which vary at a single position within a pyrimidine motif J Am Chem Soc 117,1187–1193
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1997 Humana Press Inc., Totowa NJ
About this protocol
Cite this protocol
Dabrowiak, J.C., Goodisman, J., Ward, B. (1997). Quantitative DNA Footprinting. In: Fox, K.R. (eds) Drug-DNA Interaction Protocols. Methods in Molecular Biology™, vol 90. Humana Press, Totowa, NJ. https://doi.org/10.1385/0-89603-447-X:23
Download citation
DOI: https://doi.org/10.1385/0-89603-447-X:23
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-447-1
Online ISBN: 978-1-59259-574-7
eBook Packages: Springer Protocols